Short title: CPuORF33 represses AtHB1 translation Corresponding … · 2017. 9. 27. · 80 two-hybrid and in vitro pull-down assays (Capella et al., 2014). ... 90 when rdr6-12 mutant

1

1

Short title: CPuORF33 represses AtHB1 translation 1 §Corresponding author: Raquel Lía Chan. Instituto de Agrobiotecnología del Litoral 2

CONICET-UNL, Centro Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nac. Nº 3

168 km. 0, Paraje El Pozo. 3000 Santa Fe – Argentina 4

E-mail: [email protected] 5

Tel/Fax: 54-342-4511370 extension: 5018 6

7

Title: A uORF represses the transcription factor AtHB1 in aerial tissues to avoid a deleterious 8

phenotype 9

10

Pamela A. Ribone#, Matías Capella#, Agustín L. Arce, Raquel L. Chan§ 11

12

Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral, CONICET, Centro 13

Científico Tecnológico CONICET Santa Fe, Colectora Ruta Nacional Nº 168 km. 0, Paraje El 14

Pozo, (3000) Santa Fe, Argentina. 15 16 #These authors equally contributed to this work 17

18

One sentence summary: An upstream ORF encoded in an homeodomain-leucine zipper I gene 19

and regulated by a chloroplast signal causes ribosome stalling in aerial tissues that had been 20

exposed to light. 21

22

23

24

Responsible author for distribution of materials: Raquel Chan 25

26 Authors’ contributions 27

Conceived and designed the experiments: PAR, MC, ALA and RLC. Performed the experiments: 28

PAR and MC. Analyzed the data: PAR, MC, ALA and RLC. Performed the computational 29

analysis: ALA. Conceived and wrote the paper: RLC 30

31

Plant Physiology Preview. Published on September 27, 2017, as DOI:10.1104/pp.17.01060

Copyright 2017 by the American Society of Plant Biologists

https://plantphysiol.orgDownloaded on March 5, 2021. - Published by Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.

https://plantphysiol.org

2

2

Funding information: 32

This work was supported by Agencia Nacional de Promoción Científica y Tecnológica (PICT 33

2012 0955 and PICT 2014 3300). PAR and ALA are postdoctoral CONICET Fellows, MC is a 34

former CONICET Ph. D. Fellow and RLC is a career member of the same institution. 35

36



3

3

Abstract 37

AtHB1 is an Arabidopsis homeodomain-leucine zipper transcription factor that participates in 38

hypocotyl elongation under short day conditions. Here we show that its expression is post-39

transcriptionally regulated by an upstream open reading frame (uORF) located in its 5’ UTR. 40

This uORF encodes a highly conserved peptide (CPuORF), present in varied monocot and dicot 41

species. The Arabidopsis uORF and its maize homolog repressed the translation of the main 42

ORF in cis, independent of the sequence of the latter. Published ribosome footprinting results 43

and the analysis of a frame shifted uORF, in which the repression capability was lost, indicated 44

that the uORF causes ribosome stalling. The regulation exerted by the CPuORF was tissue-45

specific and did not act in the absence of light. Moreover, a photosynthetic signal is needed for 46

the CPuORF action since plants with uncoupled chloroplasts did not show uORF-dependent 47

repression. Plants transformed with the native AtHB1 promoter driving AtHB1 expression did not 48

show differential phenotypes, whereas those transformed with a construct in which the uORF 49

was mutated exhibited serrated leaves, compact rosettes, and most significantly, short non-50

dehiscent anthers and siliques containing fewer or no seeds. We thus propose that the 51

uncontrolled expression of AtHB1 is deleterious for the plant and hence, finely repressed by a 52

translational mechanism. 53



4

54

Introduction 55

Plants, as sessile organisms, have evolved complex traits to cope with the surrounding environment 56

and show high resilience to external perturbations that are somehow buffered by the regulatory 57

interaction of developmental networks. Transcription factors (TFs) play key roles in such networks 58

by acting as mediators between the perception of environmental factors and the cellular responses. 59

Six percent of plant genes encode TFs, which are classified in different families and subfamilies 60

(reviewed by Ribichich et al., 2014). This classification is mainly based on their DNA-binding 61

domain structures. Among these families, the homeodomain-leucine zipper (HD-Zip) TF family has 62

been assigned roles in the response to biotic and abiotic stresses, as well as in developmental 63

processes (Capella et al., 2015a; Ribone et al., 2015a). The family has been divided into four 64

subfamilies, denoted I to IV, based on structural and functional features. Members of subfamily I 65

were identified in several plant species and related to different stress responses, but also with 66

processes such as leaf senescence and morphology (Vlad et al., 2014), stem elongation, hypocotyl 67

elongation, venation patterning and pollen hydration (Wang et al., 2003; Manavella et al., 2006; Ré 68

et al., 2014; Capella et al., 2015b; Ribone et al., 2015b; Moreno Piovano et al., 2017). Besides the 69

HD-Zip domain, HD-Zip I TFs contain conserved motifs in their carboxy- and amino-termini (Arce 70

et al., 2011). In vitro and in vivo experiments in different plant species showed that the HD-Zip I 71

carboxy termini have key functional roles (Hofer et al., 2009; Arce et al., 2011; Sakuma et al., 2013). 72

A motif similar to the AHA (Aromatic and large Hydrophobic residues in an Acidic context) 73

transactivation motif was identified at the end of the carboxy-termini and was functionally 74

characterized for Arabidopsis AtHB1, AtHB7, AtHB12 and AtHB13 members (Capella et al., 2014). 75

Most Arabidopsis HD-Zip I proteins were resolved as pairs in phylogenetic trees. Some of these 76

pairs exhibited cross regulation and overlapping functions in certain conditions (Ré et al., 2014; 77

Ribone et al., 2015b). This was not the case for AtHB1 which belongs to clade III and does not have 78

a paralog (Arce et al., 2011). This HD-Zip I TF was shown to interact with AtTBP2 both in yeast 79

two-hybrid and in vitro pull-down assays (Capella et al., 2014). The expression of this gene was 80

repressed in NaCl-treated plants and in plants subjected to low temperatures, but was induced by 81

darkness (Henriksson et al., 2005). In tobacco plants grown in absolute darkness, AtHB1 82

overexpression caused constitutive photomorphogenesis (Aoyama et al., 1995). More recently, it was 83

demonstrated that AtHB1 expression is significant in hypocotyls and roots and this expression is 84

regulated by PIF1 (Phytochrome-Interacting Factor 1) to promote hypocotyl elongation under a 85

short day regime (Capella et al., 2015b). The analysis of athb1 and pif1 mutants, as well as their 86

double mutants, indicated that PIF1 and AtHB1 regulate genes involved in cell wall synthesis. 87



5

Notably, AtHB1 overexpressor lines never exhibited expression levels higher than x5 the endogenous 88

levels, suggesting a post-transcriptional regulatory mechanism. Such a mechanism was evidenced 89

when rdr6-12 mutant plants, which have non-functional small RNA silencing machinery, were 90

transformed with the same constructs as wild type Col-0 plants. Those rdr6-12/AtHB1 plants 91

exhibited high transcript levels and differential phenotypes (Romani et al., 2016), indicating that a 92

silencing mechanism is taking place when AtHB1 is an overexpressed transgene. 93

It is well known that the 5’UTR of mRNAs can contain different regulatory elements such as loops, 94

protein binding sites, intern segments for ribosome entry and uORFs (upstream Open Reading 95

Frames; Somers et al., 2013). These uORFs are located upstream from the main ORF (mORF) and, 96

following Kozak’s model for translation initiation, their first AUG codon starting from the CAP, is 97

recognized by the ribosome to commence translation. Hence, when a uORF exists, its AUG is the 98

initiation codon triggering a less efficient mORF translation in most cases (Kozak, 1987; Kozak, 99

2002). 100

In eukaryotic organisms, about 20-50 % of the transcripts have uORFs. However, those that encode 101

conserved peptides occur in less than 1 % of transcripts. In these cases, the uORF is called CPuORF 102

(Conserved Peptide uORF; Jorgensen and Dorantes-Acosta, 2012). The analysis of Arabidopsis and 103

rice transcriptomes allowed the identification of 26 different CPuORFs (Hayden and Jorgensen, 104

2007), most of which are present in regulatory genes. Though the function of the CPuORFs is not yet 105

well studied, a few reports have indicated that these sequences modulate the translational efficiency 106

of the downstream main ORF in combination with small signal molecules (Rahmani et al., 2009; 107

Ivanov et al., 2010; Alatorre-Cobos et al., 2012; Guerrero-Gonzalez et al., 2014; Laing et al., 2015). 108

For example, the translation of the bHLH transcription factor SUPPRESSOR OF ACAULIS5 LIKE3 109

(SACL3) is blocked by a uORF in the absence of thermospermine (Katayama et al., 2015). Genes 110

that do not encode TFs, like the Arabidopsis polyamine oxidase-2, were also shown to be regulated 111

by a uORF and, in this case, the amino acid sequence was crucial for this regulation (Guerrero-112

González et al., 2016). Similarly, a noncanonical uORF represses GDP-L-galactose phosphorylase 113

(GGP), the major control enzyme of ascorbate biosynthesis when ascorbate concentration is high 114

(Laing et al., 2015). 115

A uORF encoding a conserved peptide was previously identified in the 5’UTR of AtHB1 and called 116

CPuORF33 (At3G01472.1) (Hayden and Jorgensen, 2007). Thus, it is conceivable that AtHB1 117

expression is regulated through mRNA translation. Indeed, by using in vitro translation approaches, 118

it has recently been shown that many CPuORFs, including CPuORF33, have the ability to cause 119

ribosomal arrest (Hayashi et al., 2017). However, the physiological role of CPuORF33 and whether 120

its mechanism of action is also functional in vivo remain unresolved. 121



6

Here we show that AtHB1 translation is repressed in vivo by a mechanism involving CPuORF33. Our 122

results indicate that this element acts via a ribosome stalling mechanism, independently of the 123

sequence of the mORF downstream of the uORF. The CPuORF33 exerts its repressive effect only in 124

aerial tissues except in darkness. Moreover, the maize CPuORF33 homolog showed a conserved 125

function. Finally, we show that such a fine and sophisticated regulation is essential for the plant in 126

order to avoid aberrant and lethal phenotypes caused by the uncontrolled expression of AtHB1. 127

128

129

130

131

132

133



7

134



8

Results 135

136

AtHB1 has a conserved open reading frame in its 5’ untranslated region 137

In 2007, Hayden and Jorgensen revealed the presence of a conserved encoded peptide upstream from 138

the main coding sequence of AtHB1, located in its 5’UTR. To investigate if such a sequence/peptide 139

has a biological function, we carried out an in silico analysis of AtHB1 homologs from other plant 140

species. Using the AtHB1 protein sequence as a query against the NCBI non-redundant protein 141

sequences database, a search with BLASTP allowed the retrieval of 45 different nucleotide 142

sequences encoding AtHB1 homologs belonging to 43 plant species, including mono- and dicots 143

(Supplemental Table 1). These homologous sequences were assessed for the presence of ORFs 144

upstream of the mORF; only ORFs starting with ATG and containing at least 24 bp were considered. 145

This analysis led to the identification of 44 different uORFs, all of them belonging to the previously 146

identified group 14 (Hayden and Jorgensen, 2007). An alignment of these sequences indicated a high 147

degree of conservation and a difference in peptide length between mono- and dicots (Figure 1). In 148

monocot AtHB1 homologs, the peptide had 38 amino acids whereas in dicots the length varied 149

between 29 and 30. Accordingly, a phylogenetic tree resolved two clades (Figure 1B). Nucleotide 150

sequences were also conserved but to a lesser extent than the amino acid sequences (Supplemental 151

Figure 1). A BLAST analysis performed using either the monocot or the dicot consensus peptide did 152

not find any other plant peptide or protein with sufficiently high similarity. 153

The Kozak rule describes the optimal sequence around the initiator AUG for an efficient translation 154

(Kozak, 1986) and has been verified by different studies (Zur et al., 2013). Important positions 155

include position -3 with an A or G, and position +4 with a G, which can be summarized as 156

(A/G)XXATGG. This rule is generally fit by the sequence context of AUGs from uORFs having a 157

single initial AUG; as well as those AUGs aligned to them but belonging to uORFs having two 158

initial AUGs (Supplemental Figure 2). 159

A further analysis of AtHB1 (and its homologs) uORF sequences indicated that the length is another 160

conserved trait, though other characteristics of these sequences were also interesting. For example, 161

no overlap between the uORF and the mORF was observed in any case. Additionally, other 162

properties of the sequence traits were assessed but no remarkable features were found. Among the 163

tested properties were: the distances between the CAP and the uORF starting site and between the 164

uORF stop codon and the mORF AUG, as well as the phase of the uORF and the mORF 165

(Supplemental Figure 3). The high sequence similarity between species strongly suggested a 166

regulatory role for the CPuORF33. However, no motifs or a strong indication of secondary structure 167

were found for the encoded peptide (data not shown). 168



9

169



10

CPuORF33 represses the expression of AtHB1 170

In light of the observations described above, we presumed that the CPuORF33 could play a 171

regulatory role in the expression of AtHB1 and its homologs. To address this hypothesis, two genetic 172

constructs were generated (Figure 2A); in the first, the expression of the mORF of AtHB1 was 173

controlled by the 1415 bp upstream region from its ATG (PromAtHB1:AtHB1) and in the second, 174

two point mutations (T→C) deleting both ATGs at the beginning of CPuORF33 were introduced 175

(PromAtHB1mut:AtHB1). These constructs were used to transform Col-0 Arabidopsis thaliana 176

plants. T1 plants transformed with PromAtHB1:AtHB1 did not exhibit phenotypic differences with 177

respect to the WT control. In contrast, those transformed with PromAtHB1mut:AtHB1 presented 178

serrated leaves, short siliques with fewer or no seeds and a notable delay in bolting and entry to the 179

senescent stage. A similar phenotype was observed in plants expressing AtHB1 at high levels 180

(Romani et al., 2016). Notably, the T2 generation of PromAtHB1mut:AtHB1 plants recovered the 181

WT phenotype (Figure 2B). To understand this observation, AtHB1 transcript levels were quantified 182

in both generations (T1 and T2) resulting high in T1 and clearly low in T2, even lower than in the 183

WT, indicating that a silencing mechanism was in action (Supplemental Figure 4). For this analysis 184

15 single-copy lines were used; these lines were selected on the basis of herbicide resistance 185

segregation in the T1 generation. Notably, this silencing observed in T2 plants was independent of 186

CPuORF33, since both genotypes transformed with either PromAtHB1:AtHB1 or 187

PromAtHB1mut:AtHB1, exhibited lower transcript levels in T2 compared to T1. 188

Silencing mediated by small RNAs, and triggered by the overexpression of the transgene, has been 189

already described for the HD-Zip I encoding genes AtHB1 and AtHB12 when driven by the 190

constitutive 35S CaMV promoter (Romani et al., 2016), but this is the first time this silencing has 191

been observed using the endogenous promoter. 192

To gain further insights into the molecular mechanism explaining the phenotypes regarding the 193

CPuORF33, rdr6-12 mutant plants were transformed with the same constructs. These plants have a 194

mutation in the gene encoding the RNA-dependent RNA polymerase 6 (RDR6), which is absolutely 195

necessary to display the small RNA mediated silencing cascade. As shown in Figure 2, the 196

phenotype of the rdr6-12 plants transformed with PromAtHB1:AtHB1 was indistinguishable from 197

that of plants transformed with the empty vector, whereas those transformed with 198

PromAtHB1mut:AtHB1 exhibited serrated leaves both in T1 and T2. Quantification of transcript 199

levels in these new transgenic plants indicated high overexpression of the transgene in T1 and T2 200

(Supplemental Figure 4). These results strongly indicated that the small RNA silencing mechanism is 201

independent of the uORF. In addition, AtHB1 expression levels were similar comparing Col-0 and 202

rdr6-12 plants without further transformation (Supplemental Figure 5), indicating that the silencing 203



11

mechanism is only displayed as a result of AtHB1 overexpression. Considering that the plants 204



12

transformed with PromAtHB1mut:AtHB1 and those transformed with 35S:AtHB1 in the rdr6-12 205

background exhibited almost identical phenotypes, it can be concluded that those possessing the 206

mutated version of the uORF are overexpressing AtHB1. 207

208

CPuORF33 is capable of repressing the translation of different main ORFs 209

Considering the differential phenotypes showed by PromAtHB1mut:AtHB1 plants compared to those 210

transformed with the construct bearing the native uORF, we found it reasonable to assume that the 211

uORF is repressing AtHB1 at the translational level. Supporting this hypothesis, a recent report has 212

shown that CPuORF33 can arrest ribosomes during mRNA translation in vitro (Hayashi et al., 2017). 213

Moreover, we did not observe significant differences in AtHB1 transcript levels between plants 214

transformed with the native or mutated CPuORF33 when the average levels from independent 215

transgenic lines were calculated (Supplemental Figure 4C). Unfortunately, AtHB1 protein levels 216

were not detectable by western blots in Col-0 plants, despite using antibodies against two different 217

tags (HA or His). 218

Upon discarding CPuORF33 action at the transcriptional level, we decided to perform new genetic 219

constructs in which the expression of the GUS reporter gene was driven by the AtHB1 promoter and 220

the 5’UTR with the native or mutated uORF (PromAtHB1:GUS and PromAtHB1mut:GUS). 221

Arabidopsis Col-0 and rdr6-12 plants were transformed with these constructs and several 222

independent single-copy lines were obtained. Considering that the different insertion points for each 223

independent line could lead to different expression levels, lines transformed with each of the 224

constructs and showing similar GUS transcript levels (in 14-day-old plants) were selected and taken 225

as pairs. These paired plants were analyzed by histochemistry resulting in the detection of GUS 226

activity in the same tissues (hypocotyls, vascular tissue of the roots and leaves) for both constructs, 227

but with a strong difference in the signal intensity (Figure 3). Plants transformed with 228

PromAtHB1:GUS had a weak expression, whereas those transformed with the construct in which the 229

uORF was mutated exhibited a strong GUS color, especially in the leaf lamina (Figures 3B and 3C). 230

Consistent with the observations performed by histochemistry, the quantified GUS enzymatic 231

activity was higher in the extracts obtained from PromAtHB1mut:GUS plants than in those from 232

PromAtHB1:GUS plants (Figure 3C). These results were independent of the genotype used (Col-0 or 233

rdr6-12), indicating the action of a small RNA independent mechanism for translational repression 234

(Supplemental Figure 6). 235

236

CPuORF33 represses the translation of the main ORF by a ribosome stalling mechanism 237



13

There are several known mechanisms by which uORFs control translation. Among them, NMD 238

(Nonsense-Mediated Decay) and ribosome stalling are the most studied. We then considered which 239

mechanism was taking place in the regulation exerted by CPuORF33 on AtHB1 translation. 240

In view of the preceding findings, it was unlikely that NMD was taking place. To confirm this and 241

discard the possibility of NMD occurrence, insertional mutant plants of UPF1 and UPF3 (upf1-5 and 242

upf3-1, respectively), genes encoding key proteins for NMD, were grown under standard conditions. 243

AtHB1 transcripts were evaluated in these mutants and the levels were similar to those measured in 244

Col-0 controls (Supplemental Figure 7), indicating that CPuORF33 translational control was not 245

mediated through NMD. 246

To investigate whether CPuORF33 is capable of acting in trans at the transcriptional level, 247

endogenous AtHB1 transcript levels were assessed in rdr6-12 mutant plants transformed either with 248

PromAtHB1:AtHB1 or with PromAtHB1mut:AtHB1. To be sure that the quantified transcripts 249



14

corresponded to the endogenous AtHB1, RT-qPCR assays were performed with primers annealing in 250

the 3’UTR, which is absent in the constructs used to transform these plants. AtHB1 transcript levels 251

were similar in both genotypes, suggesting that CPuORF33 is not able to act in trans at the 252

transcriptional level (Supplemental Figure 8). 253

Once NMD and trans-action were discarded as possible mechanisms exerted by CPuORF33, 254

ribosome stalling was analyzed. Recently, ribosome footprinting analyses with Arabidopsis mRNAs 255

were performed by three different research groups (Juntawong et al., 2014; Merchante et al., 2015, 256

Hsu et al., 2016). These studies permit the identification of transcript regions protected by ribosomes 257

from nucleases action (Ingolia et al., 2009). We used these data to inspect if CPuORF33 is in fact 258

translated and whether it is generating the stalling of the ribosomes. Among these ribosome 259

footprinting experiments, those described by Juntawong et al. (2014) and Hsu et al. (2016) were the 260

most informative for the case of AtHB1. These authors used seedlings grown under long-day 261

regimes, similar experimental conditions to those used in our experiments, whereas Merchante et al. 262

(2015) used etiolated seedlings. 263

The analyses of the data are shown in Supplemental Figure 9. The results indicated that the uORF 264

had a higher occupation density compared to other 5’UTR regions and to the mORF. Weak peaks 265

upstream from the CPuORF33 were also detected and, considering the absence of AUGs in this 266

region, they indicated that uORFs starting at non-AUG codons (Laing et al., 2015) should not be 267

discarded. However, the differences in translation efficiency would suggest that their relative 268

importance with respect to CPuORF33 is much lower. 269



15

Furthermore, the CPuORF33 did not exhibit a normal distribution but presented a peak at the end of 270

the uORF, suggesting ribosome stalling. It is important to note that three different experiments 271

resulted in similar results, showing clearly different ribosome footprinting profiles when compared to 272

that of AtHB13, another TF from the same HD-Zip I family (Supplemental Figure 9). A ribosome 273

stalling process implies the interaction between the nascent peptide and the ribosome. Hence, we 274

decided to test the importance of the CPuORF33 amino acid sequence by generating an additional 275

genetic construct in which the frame of the uORF was shifted. In order to make the analysis 276

independent of the transcriptional activity of AtHB1 promoter, the native or mutated 5’UTR of 277

AtHB1 were cloned downstream of the 35S CaMV constitutive promoter driving the expression of 278

the GUS reporter gene (35S:native-uORF:GUS and 35S:FS-uORF:GUS, respectively). A schematic 279

representation of these constructs is shown in Figure 4A. In the 35S:FS-uORF:GUS construct, the 280

nucleotide sequence exhibits minimal changes, whereas the amino acid sequence is completely 281

altered. Col-0 plants were transformed using these genetic constructs and the GUS expression pattern 282



16

analyzed by histochemistry. As shown in Figure 4B, the uORF with the shifted frame was unable to 283

repress GUS expression. 284

To further test the importance of the amino acid sequence, different mutations were generated in the 285

uORF sequence. They were cloned upstream from the GFP mORF and yeast cells were transformed 286

with these constructs. Protein extracts were analyzed by western blots indicating reduced levels of 287

GFP when the native uORF was used (Supplemental Figure 10). In contrast, no repression was 288

observed when the amino acid sequence of the uORF was significantly altered (from residues 3 to 25 289

or 3 to 29). Interestingly, changes on the N-terminal of the CPuORF33 partially repressed GFP 290

levels, indicating that certain amino acids are more important than others for translational repression 291

(Supplemental Figure 10). Altogether, these results supported the ribosome stalling mechanism and 292

its dependence on the amino acid sequence encoded by the uORF. 293

294

The activity of CPuORF33 is tissue-specific 295



17

In view of the described observations, we wondered whether CPuORF33 activity depended on the 296

tissue, developmental stage or growth condition. To address this question, Col-0 plants transformed 297

with 35S:native-uORF:GUS or 35S:GUS were analyzed in detail by histochemistry (Figure 5A). 298

Cotyledons of five-day-old seedlings, fully developed leaves and inflorescences of plants 299

transformed with 35S:native-uORF:GUS, grown under a long-day photoperiod, clearly showed 300

CPuORF33 repression (Figure 5). However, leaf primordia and roots of the same plants exhibited the 301

same GUS staining as those transformed with 35S:GUS. The observations indicated that the action 302

exerted by CPuORF33 was tissue-specific. Similar results were obtained when plants transformed 303

with 35S:native-uORF:GUS were compared with plants transformed with 35S:FS-uORF:GUS (data 304

not shown). RiboSeq assays performed in roots and aerial tissue by Hsu et al. (2016) were consistent 305

with our observations (Supplemental Figure 11). 306

This phenomenon could be the result of an alternative splicing event or the presence of a secondary 307

transcription start site (TSS) that prevents the inclusion of the complete CPuORF in the mature 308

mRNA. Indeed, the inspection of publicly available TSS results from whole A. thaliana roots using 309

the PEAT (Paired-End Analysis of Transcription start sites) protocol indicated that the AtHB1 locus 310

presented a second TSS with a “weak peak” pattern between locus positions 194 and 403 311

(Peak_40644; Supplemental Figure 12A; Morton et al., 2014). This TSS would exclude from the 312

mRNA the CPuORF start codon, which is at position 163. To further investigate this hypothesis, we 313

used published RNA-Seq data to compare the mRNA profiles between shoots and roots and found no 314

strong indication of alternative splicing and disparate results for a secondary TSS (Supplemental 315

Figure 12B-E). To test the secondary TSS hypothesis in our conditions, the tissue differential 316

presence of a shorter AtHB1 transcript excluding the CPuORF start codon was tested by RT-qPCR in 317

roots and shoots using two sets of oligonucleotides (Supplemental Figure 12A). A within-tissue ratio 318

of amplification products was calculated and compared between shoots and roots; but results 319

indicated no significant differences (data not shown). In consequence, although there is some 320

evidence supporting the existence of a secondary TSS, this would not be the key mechanism 321

explaining the tissue-specificity observed for the activity of the CPuORF. 322

323

CPuORF33 repression activity is triggered by light in aerial tissues 324

As mentioned above, CPuORF33 was active in aerial tissues and inactive in roots (Figure 5). Thus, 325

an attractive hypothesis was that CPuORF action could be triggered somehow by light. In order to 326

test this, 35S:native-uORF:GUS transformed plants were grown during six days in complete 327

darkness or under the long-day photoperiod (LDP) and GUS activity was evaluated by 328

histochemistry. As shown in Figure 6A, cotyledons of seedlings grown in darkness were completely 329



18

stained, indicating a lack of uORF repression under this condition, whereas the opposite scenario was 330

obtained under LDP. Moreover, the effect of illumination was not reverted in these plants after two 331

days of darkness (Figure 6B). Similar results were obtained using 15-day-old plants placed in 332

darkness for five additional days (Supplemental Figure 13). 333

To determine whether CPuORF33 repression activity was the result of the illumination quality, 6-334

day-old seedlings transformed with 35S:native-uORF:GUS were grown under LDP exposed to blue, 335

red or white light. All these treatments resulted in similar observations, i.e. CPuORF33 actively 336

repressed GUS activity in aerial tissues (Supplemental Figure 13). Additional treatments with ABA, 337

IAA and gibberellins were also carried out on dark-grown seedlings, indicating that none of these 338

hormones were able to modify CPuORF33 repression (data not shown). Considering the hypothesis 339

of a chloroplast signal as the switch to activate CPuORF33, 35S:native-uORF:GUS seedlings grown 340

in complete darkness over six days were treated with DCMU (dichlorophenyl dimethylurea) and 341

transferred to light conditions for an additional 24 h. Notably, the repression action of CPuORF33 342

was avoided as GUS activity was clearly detected in cotyledons (Figure 6C), indicating that a signal 343

from coupled chloroplasts is responsible for initiating CPuORF33 activity. 344

345

The homologous maize CPuORF also functions as a translational repressor 346



19

Monocot plants exhibit an insertion of seven amino acids in the carboxy-termini of the CPuORF, 347



20

which makes them longer than those of dicot plants (Figure 1A). To evaluate whether this longer 348

peptide resulted in a different function, we decided to clone a monocot uORF and analyze its 349

activity. To this end, the maize 5’UTR region of the AtHB1 homolog (ZmHB115) was cloned 350

between the constitutive 35S CaMV promoter and the GUS reporter gene. Arabidopsis plants were 351

then transformed and analyzed by GUS histochemistry (Figure 7A). The results indicated that the 352

maize uORF represses GUS translation in the aerial portions of the plant, similar to the inhibition 353

seen for the Arabidopsis CPuORF33. Notably, as its Arabidopsis homolog, the maize uORF also 354

exhibited tissue-specific activity and did not function as a repressor in roots (Figure 7A). 355

Aiming to elucidate if this uORF is active in maize, data obtained from ribosome footprinting 356

analyses performed with samples of 14-day-old maize seedlings were examined (Supplemental 357

Figure 14; Lei et al., 2015). As expected, translation seemed to be stalled in the uORF region and 358

less ribosomes were detected in the mORF (Supplemental Figure 14), supporting both the proposed 359

ribosome stalling mechanism and the conservation between species of the uORF´s function. 360

361

The absence of a tightly regulated expression of AtHB1 causes severe deleterious effects 362

It was surprising to discover such a sophisticated mechanism repressing AtHB1 expression, 363

especially because we were not able to detect strong differential phenotypes in athb1 mutants and 364

certainly no lethality in Col-0 plants transformed with 35S:AtHB1 (Capella et al., 2015b). 365

To understand such phenomena, we decided to further analyze rdr6-12 plants transformed with 366

PromAtHB1mut:AtHB1 in which neither ribosome stalling nor small RNA silencing were possible. 367

As controls, we used rdr6-12 plants transformed with an empty vector or with PromAtHB1:AtHB1. 368



21

Hypocotyl length was analyzed in these plants since this developmental trait is affected by AtHB1 369

(Capella et al., 2015b). As expected, rdr6-12 plants transformed with PromAtHB1mut:AtHB1 370

showed longer hypocotyls than the other transformed plants (Figure 8A). In parallel, plants from the 371

three genotypes were grown on soil under standard conditions. PromAtHB1mut:AtHB1 plants 372

exhibited compact rosettes, a delay in bolting and more importantly, a strongly altered flower 373

morphology. Pistils were reduced, anthers were extremely short and non-dehiscent, and siliques were 374

small and had fewer or no seeds. In several lines, the analysis of a second generation was not 375

possible because T1 plants were sterile (Figure 8B). Altogether, these results could explain why such 376

a sophisticated mechanism is acting to repress overexpression of this TF, i.e. unregulated increased 377

expression of AtHB1 conducted to an infertile, delayed and aberrant phenotype. 378

379

380

381

382

383



22

384



23

Discussion 385

386

The adaptation of plants throughout evolution involved the loss and the acquisition of genome DNA 387

sequences including the conservation of key elements. Many of such conserved regulatory elements 388

must be fundamental for plant development, reproduction and/or survival. Here we demonstrated that 389

a highly conserved genetic element, the CPuORF33, is important to avoid plant sterility. 390

Although uORFs are present in a considerable number of mRNAs (Hayden et al., 2008; Nagalakshmi 391

et al., 2008; Calvo et al., 2009), it is remarkable that only a small portion of these varied genetic 392

elements has been conserved between species, and only a few members within this group were 393

assigned a function. Here we show that CPuORF33 negatively regulates AtHB1 translation during 394

plant development and this regulatory mechanism is conserved in maize. Hence, it is tempting to 395

suggest that a similar scenario occurs in other species with AtHB1 homologs. Notably, in all the 396

available DNA sequences encoding AtHB1 homologs that have known 5’UTRs, either from monocot 397

or dicot species, CPuORF33 was identified. Considering that the number of sequences continuously 398

increases, it would be interesting to repeat this analysis in the near future. 399

Besides the high conservation of the nucleotide sequence, it is important to note that the amino acid 400

sequence is even more conserved, indicating that the peptide, and not the RNA, is the active element. 401

This suggestion was also supported by the absence of overlap between CPuORF33 and the main 402

ORF. This characteristic is relevant to allow ribosome reinitiation and the translation of the mORF. 403

Overlap of the CPuORF and the mORF was described as being linked to NMD regulating the 404

abundance of many gene transcripts involved in plant development, including TFs, RNA processing 405

factors and stress response genes (Kalyna et al., 2011). 406

According to previous reports, the regulation exerted by eukaryotic uORFs on transcript levels of the 407

main ORF occurs through several different mechanisms of action, but most uORFs exert their effects 408

in a sequence-independent manner (Calvo et al., 2009). In contrast, certain uORFs control translation 409

of the mORF in a peptide sequence-dependent manner (Ito et al., 2013; von Armin et al., 2014). 410

Among the possible repression mechanisms exerted by uORFs, NMD is the one acting in the 411

regulation of AdoMetDC1, which causes polyamine-responsive ribosomal arrest, the SAC51 gene 412

encoding a bHLH transcription factor, and AtMHX, which encodes a vacuolar magnesium-413

zinc/proton exchanger (Bender and Fink, 1998; Imai et al., 2006; Combier et al., 2008; Saul et al., 414

2009; Uchiyama-Kadokura et al., 2014). On the other hand, other mechanisms displayed by uORFs 415

regulate RNA translation; among them are ribosome stalling (Rahmani et al., 2009; Alatorre-Cobos 416

et al., 2012; Wiese et al., 2004), ribosome reinitiation (Wang and Wessler, 1998), a combination of 417

both (Hanfrey et al., 2005) and others not well understood (Kwak and Lee, 2001). Among the 418



24

possible mechanisms of CPuORF33 action, we were able to show that this particular element 419

repressed AtHB1 translation in cis. 420

During translation, ribosome movement along the mRNA molecule can be stopped either by a stable 421

secondary structure in the mRNA or by the nascent translated peptide. Both cases can be observed in 422

ribosome footprinting experiments as an evident increase in the number of reads in a particular 423

region. The ribosome footprinting analyses for the 5’UTR region of AtHB1 showed a clear coverage 424

peak ~40 bp upstream of the uORF stop codon, suggesting the stalling of ribosomes in this region. 425

This peak should not be confused with the one caused by the deceleration of ribosome movement 426

during translational termination, which appears ~16 pb upstream of the stop codon (Juntawong et al., 427

2014; Hou et al., 2016). Taking into account the high conservation observed in the amino acid 428

sequences of CPuORF33 homologs, not so evident at the nucleotide level, it is tempting to speculate 429

that the ribosome stalling is caused by the nascent peptide and not by a secondary structure in the 430

mRNA. Supporting this conclusion, the repressive activity of the uORF is lost when frame shift 431

mutations were introduced, in both plants and yeast, even though there are only minor changes in the 432

RNA sequence. 433

In this work we demonstrated the importance of the peptide structure of the CPuORF33 for in vivo 434

translational repression, most likely by ribosome stalling. In this mechanism, the interaction between 435

the polypeptide being synthesized and the ribosome tunnel can regulate translation rate. The tunnel 436

allows the formation of secondary structures like α-helix or Zinc finger motifs (Nilsson et al., 2015). 437

A recent report by Ebina and coworkers (2015) identified 16 novel uORFs in which the amino acids 438

located at the carboxy-termini were crucial in determining their repressive action. In order to test the 439

functionality of the CPuORF33 carboxy terminus, its peptide sequence was changed by two point 440

mutations; one located at amino acid 24 (H→Q) and the second one deleting the stop codon, which 441

adds 30 additional amino acids (mut5’UTR). However, no differences were observed in plants 442

transformed with 35S:mut5’UTR:GUS compared to those transformed with the native 5’UTR (data 443

not shown). This indicates that CPuORF33 is more likely a class II uORF in which, according to 444

Takahashi et al. (2012), the carboxy-terminal is not relevant for its action. 445

In contrast with our results, using an in vitro system Hayashi et al. (2017) showed that CPuORF33 446

(called At3g01470 by the authors) arrests ribosomes in a peptide sequence-independent manner. A 447

plausible explanation for this discrepancy could be that the sequence-dependent ribosome arrest 448

activity needs a certain biomolecule to be absent in the in vitro system. An alternative explanation 449

could be that, as in the in vitro assay, an N-terminal GST fusion protein was used, such that the 3D 450

structure of the CPuORF33 could have been affected. 451



25

There are some reports showing that the ribosome stalling mechanism involves small molecules like 452

ascorbate, boron (as H3BO3 in solution), phosphocholine or sucrose (Rahmani et al., 2009; Alatorre-453

Cobos et al., 2012; Laing et al., 2016; Tanaka et al., 2016). Further studies will be necessary to 454

reveal whether those or other molecules are necessary for CPuORF33 action. Nonetheless, even 455

when unidentified molecules were necessary for AtHB1 repression, such molecules are normally 456

present in plant leaves and flowers since we observed the repression exerted by CPuORF33 in these 457

tissues, especially when using stably transformed plants with the 35S:native-uORF:GUS and 458

35S:FS-uORF:GUS constructs, which make the analysis independent of transcriptional regulation. 459

Moreover and in view of the tissue specific action of CPuORF33, one could speculate that such 460

molecules, that could also be proteins, are not present in roots and apical meristems. 461

Considering the differences between the roots and aerial parts of the plant, and also those between 462

darkness and light, chloroplast functionality was assessed for its capacity to regulate CPuORF33 463

using DCMU (a known photosynthesis uncoupler). This treatment was able to inhibit CPuORF 464

repressor action (Figure 6). Additionally, several molecules related to photosynthesis, including 465

sugars and hormones, were tested with negative results. Further investigation will be needed to 466

reveal which is the chloroplast signal responsible for this effect. 467

Another mechanism which might be potentially responsible for the tissue-specific action of 468

CPuORF33 was considered. A secondary transcription start site in AtHB1 was found by Morton et al. 469

(2014) and was defined as a region located downstream of the uORF start codon (Supplemental 470

Figure 12A). Transcripts starting at this region would therefore lack the full uORF, preventing the 471

stalling of ribosomes and allowing the uninhibited expression of the mORF. However, the 472

comparison of RNA transcript profiles between roots and shoots using publicly available data was 473

not conclusive and our qPCR assays comparing these tissues did not support this mechanism. In 474

consequence, the presence of a secondary TSS would not be able to explain the tissue-specificity of 475

uORF activity. Nonetheless, we cannot rule out that this TSS could be functional in bypassing the 476

repressive action of the uORF under certain conditions, as reported for other uORFs (Pumplin et al., 477

2016). 478

The second mechanism repressing AtHB1 expression described in this work is mediated by small 479

RNAs, although this might only function when it is expressed as a transgene. It is already known that 480

above a certain threshold, the expression of several transgenes like GUS, GFP or SPT (Streptomycin 481

Phosphotransferase) is silenced by such a mechanism, being threshold dependent on the gene 482

(Schubert et al., 2004; Rajeevkumar et al., 2015). Two different mechanisms acting to silence 483

transgenes have been described: the TGS (Transcriptional Gene Silencing) and the PTGS (Post-484

Transcriptional Gene Silencing). In the first one, a DNA segment encoding a certain mRNA is 485



26

methylated inhibiting transcription, whereas in the second the mRNA is degraded by siRNA after the 486

formation of the mRNA (Matzke et al., 2001). PTGS occurs during plant development and after 487

meiosis initiation, whereas TGS occurs during meiosis and is heritable (Vaucheret and Fagard, 488

2001). Since the repression of AtHB1 in transgenic plants takes place in the second generation, TGS 489

is likely the silencing mechanism. However, it is rather infrequent that such silencing was displayed 490

when the overexpression is controlled by a native promoter since this scenario has been observed 491

only with constitutive promoters like the 35S CaMV. These observations indicate that AtHB1 492

overexpression is tightly regulated to avoid expression above the threshold and that this threshold is 493

very close to endogenous transcript levels. Moreover, AtHB1 was not silenced when the construct 494

used to perform the transformation did not have the AtHB1 CDS (not shown), indicating that the 495

silencing is caused by AtHB1 transcript or protein levels but not by the promoter itself. 496

We can conclude that the CPuORF33 present in the 5’ untranslated region of the Arabidopsis 497

homeodomain-leucine zipper transcription factor AtHB1 and its homologs in at least other 43 species 498

exerts a strong tissue and condition specific regulation at the translational level by ribosome stalling 499

in order to avoid an aberrant phenotype. 500

501



27

Materials and methods 502

503

Plant material and growth conditions 504

Arabidopsis plants were grown directly on soil in a growth chamber at 22–24 °C under long-day 505

photoperiod (16 h light), at an intensity of approximately 120 µmol m-2 s-1, in 8 x 7 cm pots. Short 506

photoperiod conditions were used only to evaluate hypocotyl length as indicated in the 507

corresponding figure legend. 508

Arabidopsis thaliana ecotype Columbia (Col-0), and the mutants athb1-1 (SALK_123216C), upf3-1 509

(SALK_025175) and upf1-5 (SALK_112922), all in the Col-0 ecotype background, were obtained 510

from the Arabidopsis Biological Resource Center (ABRC, http://www.arabidopsis.org; Columbus, 511

OH, USA). The mutant seeds rdr6-12 (Peragine et al., 2004) were kindly provided by Dr. Pablo 512

Manavella from the Instituto de Agrobiotecnología del Litoral, Santa Fe, Argentina. pKGWFS7 513

PromAtHB1:GUS plants were previously described (Capella et al., 2015b). Homozygous lines were 514

selected after two complete growth cycles. 515

516

DCMU treatments 517

Seeds were surface sterilized and then plated in Petri dishes with 0.5 x Murashige and Skoog 518

medium supplemented with vitamins (MS, PhytoTechnology LaboratoriesTM). Plates were placed at 519

4 °C during 2 days and transferred to the growth chamber (22–24 °C under long-day photoperiod) 520

for the periods indicated in the corresponding figure legends. Another group of plates was transferred 521

to the same chamber but inside a dark box. For DCMU treatments, these plants were vacuum-522

infiltrated with 50 μM DCMU solution; then, the liquid reagent was discarded and plants were 523

placed under long-day photoperiod under light for additional 24 h. 524

525

Genetic constructs 526

pCambia HA-AtHB1 was previously described (Capella et al., 2015b). 527

PromAtHB1mut:GUS: This construct was carried out by PCR amplification and overlapping with 528

the oligonucleotides (Higuchi et al., 1988) listed in the Supplemental Table S2 using as probe the 529

pKGWFS7 PromAtHB1:GUS construct. The amplification PCR product was cloned in pBluescript 530

SK-. This last construct was restricted with BglII and HindIII and finally inserted in pKGWFS7 531

PromAtHB1:GUS, replacing the wild-type sequence. The correct insertion was verified by 532

sequencing. 533

PromAtHB1:AtHB1 and PromAtHB1mut:AtHB1: The native and mutated versions of AtHB1 534

promoter were amplified using specific oligonucleotides (Supplemental Table S2) and pKGWFS7 535



28

PromAtHB1:GUS and pKGWFS7 PromAtHB1mut:GUS as templates, respectively. The PCR 536

products were cloned into the SalI and XbaI sites of pMTL22, and then the obtained clones were 537

digested with BamHI and XbaI. Finally, these products were cloned into the BglII and XbaI sites of 538

pCambia HA-AtHB1, replacing the 35S cauliflower mosaic virus (CaMV). 539

35S:native-uORF:GUS: The AtHB1 5’UTR was amplified by PCR using as template the pCambia 540

PromAtHB1:AtHB1 clone and specific oligonucleotides (Supplemental Table S2). The amplification 541

product was then cloned into the XbaI and BamHI sites of pBI121. 542

35S:FS-uORF:GUS: The indicated mutations were introduced by PCR amplification and 543

overlapping with the oligonucleotides listed in the Supplemental Table S2 and using as probe the 544

pCambia PromAtHB1:At1 clone. The PCR product was cloned into the XbaI and BamHI sites of 545

pBI121. 546

35S:ZmHB115-5’UTR:GUS: The ZmHB115 5’UTR was amplified by PCR using genomic DNA as 547

template and specific oligonucleotides (Supplemental Table S2). The amplification product was then 548

cloned into the XbaI and BamHI sites of pBI121. 549

pADH::yeGFP and pADH::NLS::yeGFP: The yeast enhanced GFP (yeGFP), with or without the 550

SV40 NLS, was amplified by PCR using as template the pYM25 vector and specific oligonucleotides 551

(Supplemental Table S2). The amplification products were then cloned into the BamHI and SalI sites 552

of YCplac22 pADH. 553

pADH::uORF::yeGFP and pADH::FS-uORF::yeGFP mutant constructs: native-uORF and FS-554

uORF were amplified using specific oligonucleotides (Supplemental Table S2) and the 35S:native-555

uORF:GUS and 35S:FS-uORF:GUS clones as probes. By Gibson cloning (NEB), the PCR products 556

were clone into pADH::yeGFP, previously restricted with BamHI. Finally, the indicated mutations 557

(FS1, FS2 and FS3) were introduced by QuikChange II Site-Directed Mutagenesis (Agilent), using 558

pADH::FS-uORF::yeGFP as template. 559

560

Stable Arabidopsis plants transformation 561

Transformed Agrobacterium tumefaciens strain LBA4404 was used to obtain transgenic Arabidopsis 562

plants by the floral dip procedure (Clough and Bent, 1998). Transformed plants were selected on the 563

basis of their specific resistance in Petri dishes with 0.5 x Murashige and Skoog medium 564

supplemented with vitamins (MS, PhytoTechnology LaboratoriesTM) and the appropriate selector 565

chemical (kanamycin 50 mg/l or hygromycin 25 mg/l). The seeds were surface sterilized, plated and 566

after 2 days of incubation at 4 °C placed in a growth chamber at 22–24 °C. 567

The insertion of each transgene was checked by PCR using genomic DNA as template with specific 568

oligonucleotides listed in Supplemental Table S2. Three/four positive independent lines for each 569



29

construct were further reproduced and homozygous T3 and T4 plants were used in order to analyze 570

expression levels of the specific transgene and plants phenotypes. T1 plants were used in a specific 571

experiment as indicated in the corresponding figure legend. 572

573

RNA extraction and analysis 574

Total RNA for transcript levels evaluation by RT-qPCR was isolated from Arabidopsis leaves using 575

the Trizol® reagent (Invitrogen) according to the manufacturer’s instructions. One μg of RNA was 576

reverse-transcribed using oligo(dT)18 and M-MLV reverse transcriptase II (Promega). For alternative 577

TSS assay, a different oligonucleotide (AtHB1qPCRR) was used for reverse transcription. 578

Quantitative real-time PCR (qPCR) was performed with the Mx3000P Multiplex qPCR system 579

(Stratagene, La Jolla, CA) in a 20 μl final volume containing 2 μl SyBr green (4 x), 8 pmol of each 580

primer, 2 mM MgCl2, 10 μl of a 1/15 dilution of the RT reaction and 0.1 μl Taq Platinum 581

(Invitrogen). Fluorescence was measured at 72 °C during 40 cycles. Specific primers were designed 582

(Table S3). Quantification of mRNA levels was performed by normalization with the Actin 583

transcripts levels (ACTIN2 and ACTIN8) according to the ΔΔCt method (Pfaffl, 2001). All the 584

reactions were performed with, at least, three replicates. For a better visualization of the results, the y 585

axes of the figures containing transcripts evaluation were represented in a logarithmic scale. 586

587

Histochemical GUS staining 588

GUS staining was performed as described by Jefferson et al. (1987). Plants were immersed in GUS 589

staining buffer (1 mM 5-bromo-4-chloro-3-indolyl-glucuronic acid in 100 mM sodium phosphate pH 590

7.0, 0.1 % Triton X-100, 100 mM potassium ferrocyanide), vacuum was applied for 5 min, and then 591

plants were incubated at 37 °C for 12 h. Chlorophyll was cleared from the plant tissues by immersion 592

in 70 % ethanol. 593

594

Phenotype analyses 595

Plants were grown as described above and photographed using a Panasonic DMC-FH4 camera. 596

Flowers and siliques were detached and photographed under a stereomicroscope Nikon SMZ800. 597

Hypocotyl length measurements were carried out as described (Capella et al., 2015b). 598

599

In-silico sequence analysis 600

To retrieve nucleotide sequences, initially a BLASTP search was conducted with the full-length 601

sequence of AtHB1 transcription factor against the NCBI non-redundant protein sequence database 602

(default parameters were used, January 18, 2016; Altschul et al., 1990). Sequence redundancy was 603



30

checked using the “skipredundant” program of the EMBOSS package (Rice et al., 2000) and the 604

results were manually inspected and curated. After this filtering, full mRNA-containing hits were 605

selected for further analysis. 606

The amino acid sequence of CPuORF33 was analyzed for the prediction of secondary structure using 607

Jpred 4 (http://www.compbio.dundee.ac.uk/jpred4; Drozdetskiy et al., 2015) and for known motifs 608

using hmmscan (https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan; Finn et al., 2015) and 609

including all HMM databases (Pfam, TIGRFAM, Gene3D, Superfamily and PIRSF). 610

The uORF nucleotide and amino acid sequences were aligned with ClustalW (Larkin et al., 2007; 611

Goujon et al., 2010), using a Multiple Alignment Mode, iterated in each step, and the following 612

parameters: Gap extension: 0, Gap opening: 15, Negative matrix: Off, DNA transition weight: 0.5, 613

Delay divergent seq: 30, Protein weight matrix: Gonnet series, DNA weight matrix: IUB. Identity 614

and IUB quality was used for protein and DNA analysis respectively. 615

Maximum likehood phylogenetic tree was constructed using the ClustalW alignments, the JTT+I+G 616

model (Jones et al., 1992; Reeves, 1992; Yang, 1993) and 100 bootstrap repeats. 617

618

Ribosome footprints analysis 619

Ribosome Footprints (RF) sequence reads were obtained from Juntawong et al., 2014 (SRX345243, 620

SRX345250, SRX345242, SRX345246); Merchante et al., 2015 (SRX976546, SRX976568, 621

SRX976713, SRX976714), Lei et al., 2015 (SRX845439, SRX845455, SRX847137, SRX847138) 622

and Hsu et al., 2016 (SRX1756756, SRX1756757, SRX1756758, SRX1756759, SRX1756760, 623

SRX1756761, SRX1756762, SRX1756763, SRX1756764, SRX1756765, SRX1756766, 624

SRX1756767). Reads of non-stressed plants were used in this analysis. The coverage was computed 625

for the entire read in RNA-seq samples, and for the nucleotide 13 in each read for Ribo-seq samples. 626

Translation efficiency was calculated as the relationship between the read count in the Ribo-seq 627

sample and the read count in the total RNA sample for each ORF. 628

629

RNA profile analysis 630

The raw reads from the studies analyzed were retrieved from the Gene Expression Omnibus 631

repository. The corresponding accession numbers are: GSE68560 (Mancini et al., 2015), GSE61545 632

(Liu et al., 2016) and GSE87760 (unpublished work). Reads were first processed to remove adapters 633

and low quality bases using Trimmomatic ver. 0.36 (Bolger et al., 2014) with the suggested options: 634

“LEADING:3 TRAILING:3, SLIDINGWINDOW:4:15 MINLEN:36”; with “MAXINFO:90:0.4” 635

and removing Illumina adapter sequences using the “ILLUMINACLIP” option. The quality of reads 636



31

before and after trimming was evaluated with FastQC 637

(http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). 638

Processed reads were mapped to the A. thaliana genome (TAIR10, Lamesch et al., 2012) using 639

Tophat2 ver. 2.1.1 (Kim et al., 2013) with the default settings. Duplicate reads were removed with 640

MarkDuplicates from the picard toolkit ver. 2.7.0 (http://picarDsourceforge.net/). The results were 641

graphically inspected with IGV (Thorvaldsdottir et al., 2012), which was also used to obtain the 642

Sashimi plots. The comparison of RNA profiles was carried out with the RNAprof software ver. 643

1.2.6 (Tran Vdu et al., 2016), only for the AtHB1 locus. 644

645

Yeast cell culture, transformation and immunoblotting 646

Saccharomyces cerevisiae DF5 MATα cells were grown and transformed as described (Capella et al., 647

2014). Cells were cultured to exponential growth in synthetic minimal medium lacking Trp; one 648

OD600 was collected and total cell protein extracts were prepared by TCA precipitation. Proteins 649

were resolved on NuPAGE 12 % gels (Invitrogen), and analyzed by standard immunoblotting 650

techniques using mouse monoclonal antibodies against GFP (B-2; Santa Cruz Biotechnology) and 651

Pgk1 (22C5; Invitrogen), and HRP-Rabbit anti-mouse (Invitrogen). 652

653

Accession numbers: 654

AtHB1 (At3G01472.1); ZmHB115 (GRMZM2G021339) 655

656

List of Supplemental Material 657

Figure S1: Nucleotide sequence alignment of the coding sequences of the peptides listed in Figure 658

1B. 659

Figure S2: The context of the second ATG codon fits Kozak rule better 660

Figure S3: The length of the uORF is the most conserved feature differing only between 661

monocotyledonous and dicotyledonous plants 662

Figure S4: AtHB1 overexpression is impaired by a mechanism involving siRNA 663

Figure S5: AtHB1 expression is only impaired while AtHB1 is overexpressed 664

Figure S6: The negative regulation exerted by CPuORF33 in not dependent on small RNAs 665

Figure S7: CPuORF33 action is not mediated by NMD 666

Figure S8: Transgenic expression of CPuORF33 does not affect the expression of endogenous 667

AtHB1 668

Figure S9: Comparative ribosome footprinting profile of AtHB1 and AtHB13 transcripts 669



32

Figure S10: The CPuORF33 represses translation in a sequence-dependent manner in the 670

heterologous yeast system. 671

Figure S11: Comparative ribosome footprinting profile of AtHB1 transcripts in root vs. shoots. 672

Figure S12: AtHB1 potentially has a secondary TSS that could explain the activity of the differential 673

CPuORF in certain cases 674

Figure S13: Histochemical detection of GUS in 35S:native-uORF:GUS plants grown under different 675

light regimes. 676

Figure S14: Ribosome footprinting profile of the transcripts of the maize AtHB1 homolog ZmHB115 677

Table S1: Species used in the bioinformatic analysis and the accession number of the corresponding 678 sequence 679

Table S2: Oligonucleotides used in this work 680

681



33

Acknowledgements 682

We would like to thank Dr. Federico Ariel for critical reading of the MS. 683

684

685



34

Figure legends 686

687

Figure 1. The predicted amino acid sequence of the CPuORF33 is highly conserved 688

between species 689

A. Schematic representation of AtHB1 gene. In grey, exons; in light grey, the 5’ and 3’UTR; in 690

red, the CPuORF33; and the introns in simple lines. 691

B. Left panel: Phylogenetic tree constructed using the predicted uORF amino acid sequences of 692

44 AtHB1 homologs from different species, available in public databases. Two main clades can 693

be distinguished: dicotyledonous and monocotyledonous plants. Right panel: amino acid 694

sequence alignment. 695

C. Amino acid sequence logo of CPuORF33. Sequence logo resulted from the alignment of the 696

uORF amino acid sequences of 44 AtHB1 homologs from different species. Letters height 697

corresponds to the frequency in the alignment. 698

699

Figure 2. AtHB1 overexpressor plants bearing a uORF mutated in the putative start codons 700

present abnormal phenotypes 701

A. Schematic representation of the native AtHB1 promoter (PromAtHB1) and a mutated version 702

(PromAtHB1mut), both including their 5’UTR Two single nucleotides, located within the first 703

two codons of the uORF, were mutated (T→C) and are signaled in green. 704

B. Illustrative photographs of 30-day-old Col-0 plants transformed with PromAtHB1:AtHB1 and 705

PromAtHB1mut:AtHB1 compared to control plants transformed with an empty pCambia vector. 706

C. Illustrative photographs of 30-day-old rdr6-12 mutant plants transformed with 707

PromAtHB1:AtHB1 and PromAtHB1mut:AtHB1 compared to control plants transformed with an 708

empty pCambia. 709

Two independent transgenic lines for each genotype were analyzed. First (T1) and second (T2) 710

generations are shown in the upper and lower panel, respectively. 711

712

Figure 3. Mutations in the CPuORF33 enhance the translation of different downstream 713

main ORFs 714

A. Transcript levels of GUS in 14-day-old seedlings of Col-0 plants transformed with native 715

PromAtHB1:GUS or PromAtHB1mut:GUS. Three independent lines of each genotype are 716



35

shown, paired according to their transcript levels. Transcript levels in whole rosettes were 717

measured by RT-qPCR and the values were normalized with the smaller absolute value using the 718

ΔΔCt method. Y axis is shown in log2 scale. 719

B. GUS expression analyzed by histochemical detection of GUS enzymatic activity in 14-day-720

old plants. 721

C. GUS activity evaluated by fluorometry in whole rosette protein extracts from the same plants 722

as in A. Error bars: SD of five biological replicates. 723

T-tests were performed and p-values < 0.05 are signaled with asterisks. 724

725

Figure 4. Ribosome footprinting pattern and mutations in the uORF amino acid sequence 726

suggest ribosome stalling at the CPuORF33 727

A. Schematic representation of the constructs used in Arabidopsis transformation, showing the 728

nucleotide (above) and amino acid (below) sequence of the native and mutated uORF. FS: Frame 729

shift. Black: 35SCaMV promoter, white: AtHB1 5’UTR, Light blue: CPuORF33, Grey: GUS 730

ORF Stars: Single base modification, Arrow: Insertion introduced. 731

B. Illustrative photograph of 20-day-old leaves transformed with the indicated constructs and 732

analyzed by GUS histochemisty. 733

734

Figure 5. CPuORF33 repression action depends on the tissue and environmental condition 735

Illustrative photographs of organs/tissues of plants revealed by GUS histochemisty. A: 5-day-736

old seedling transformed with 35S:GUS grown under long day photoperiod (LDP). Bar: 2 mm; 737

B: 5-day-old seedling transformed with 35S:native-uORF:GUS grown under LDP. Bar: 2 mm; 738

C: hypocotyl detail of B. Bar: 500 µm; D: 10-day-old seedling transformed with 35S:GUS grown 739

under LDP. Bar: 2 mm; E: 10-day-old seedling transformed with 35S:native-uORF:GUS grown 740

under LDP. Bar: 2 mm; F: hypocotyl detail of E. Bar: 500 µm; G: root detail of VI. Bar: 200 741

µm; H: inflorescence of plants transformed with 35S:GUS. Bar: 5 mm; I: inflorescence of plants 742

transformed with 35S:native-uORF:GUS. Bar: 5 mM 743

Figure 6. Light-dependent CPuORF33 repression action in cotylendons is not reverted in 744

darkness but avoided by DCMU 745

Illustrative photographs of seedlings transformed with 35S:GUS or 35S:native-uORF:GUS and 746

revealed by GUS histochemistry. A: Left: 6-day-old seedling transformed with 35S:native-747



36

uORF:GUS grown under long photoperiod (LDP). Center: 6-day-old seedling transformed with 748

35S:GUS grown in darkness. Right: 6-day-old seedling transformed with 35S:native-uORF:GUS 749

grown in darkness. Bar: 2 mm; B: Left: 8-day-old 35S:native-uORF:GUS seedlings grown under 750

long photoperiod. Right: 6-day-old 35S:native-uORF:GUS seedlings grown under LDP and then 751

transferred for 2 additional days to darkness. Bar: 2 mm; C: Left: 6-day-old 35S:native-752

uORF:GUS seedlings grown in darkness and treated with ethanol during 24 h with ethanol under 753

LDP. Right: 6-day-old 35S:native-uORF:GUS seedlings grown in darkness and treated during 24 754

h with 50 µM DCMU under LDP. Bar: 2 mm 755

756

Figure 7. The uORF of maize AtHB1’ homolog functions as a translational repressor 757

A: Illustrative photographs of 14-day old plants revealed by GUS histochemisty. Left 758

photograph: Arabidopsis plants transformed with 35S:GUS grown under long photoperiod. Right 759

photographs: three independent lines of Arabidopsis plants transformed with 760

35S:maize5’UTR:GUS grown under long photoperiod. Bar: 500 µm. 761

762

Figure 8. Expression levels of AtHB1 are fine-tuned due to the detrimental effects for plant 763

reproduction and survival generated by its overexpression 764

A. Hypocotyl length of plants grown under short photoperiod for 5 days. Control plants of Col-0 765

and rdr6-12 backgrounds are shown as well as the same plants transformed with 766

PromAtHB1:AtHB1 (PromAtHB1:At1) and PromAtHB1mut:AtHB1 (PromAtHB1mut: At1). Two 767

independent lines for each genotype are shown. An ANOVA test was performed and pair-wise 768

differences were evaluated with a Tukey post hoc test; different groups were marked with letters 769

at 0.05 significance level. 770

B. Illustrative photographs of rdr6-12 plants transformed with PromAtHB1:AtHB1 and 771

PromAtHB1mut:AtHB1. I. 25-day-old rosette leaves of control and transformed plants. Four 772

independent lines are shown for each genotype. II. Front photograph of the same plants as in I 773

III Flowers of 40-day-old plants. IV. Siliques of the same plants. 774

775

776

777

778



37

Legends to Supplemental Figures 779

780

Figure S1. Nucleotide sequence alignment of the coding sequences of the peptides listed in 781

Figure 1B. 782

783

Figure S2. The context of the second ATG codon fits Kozak rule better 784

A fragment of the mRNA encoding the uORFs, as presented in Figure 1C, is displayed to 785

highlight the sequence context around the starting codon. For sequences with two initial 786

methionines the first ATG was called ATG1 and the second, ATG2. A position count matrix 787

shows the number of each nucleotide in the alignment whereas their location relative to each 788

ATG is indicated below. 789

790

Figure S3. The length of the uORF is the most conserved feature differing only between 791

monocotyledonous and dicotyledonous plants 792

A. Distribution of the distances comprised between the predicted stop codon of the uORF and the 793

start codon of the main ORF (mORF). 794

B. Distribution of the distances comprised between the predicted 5’ cap (CAP) site and the start 795

codon of the uORF 796

C. Distribution of the uORF length depending on the species 797

D. Percentage of species in which the uORF and the mORF are in frame 798

Forty-four uORF sequences from different species were used for the analysis 799

800

Figure S4. AtHB1 overexpression is impaired by a mechanism involving siRNA 801

A. AtHB1 relative transcript levels in 30-day-old Col-0 plants transformed with the indicated 802

construction. Eight single-copy independent lines of each genotype are shown. Black: T1 plants, 803

White: T2 plants. All the values were normalized with the one obtain in Col-0 plants transformed 804

with pCambia using the ΔΔCt method. 805

B. AtHB1 relative transcript levels in 30-day-old rdr6-12 plants transformed with the indicated 806

construction. Eight single-copy independent lines of each genotype are shown. Black: T1 plants, 807

White: T2 plants. All the values were normalized with the one obtain in rdr6 plants transformed 808

with pCambia using the ΔΔCt method. 809



38

C. Mean value of AtHB1 transcript levels in the T1 plants showed in A and B. Values were 810

normalized with the one obtain in Col-0 or rdr6-12 plants, respectively, transformed with 811

pCambia using the ΔΔCt method. In A., B. and C. the y axis is shown in log2 scale. A two-way 812

ANOVA test was performed and no differences were detected at a significance level of 0.05. 813

814

Figure S5. AtHB1 expression is only impaired while AtHB1 is overexpressed 815

Transcript levels of AtHB1 in 14-day-old Col-0 and rdr6-12 plants grown under normal 816

conditions. Values were normalized with the one obtain in Col-0 plants using the ΔΔCt method. 817

Y axis is shown in log 2 scale T-tests were performed and p-values < 0.05 are signaled with 818

asterisks. 819

820

Figure S6. The negative regulation exerted by CPuORF33 in not dependent on small RNAs 821

A. Transcript levels of GUS in 14-day-old seedlings of rdr6-12 plants transformed with 822

PromAtHB1:GUS or PromAtHB1mut:GUS Transcript levels in independent transgenic lines 823

were randomly evaluated and normalized with the value measured in the line exhibiting the 824

lowest GUS transcript level using the ΔΔCt method with the Actin transcripts levels (ACTIN2 825

and ACTIN8). Numbers in the x axis correspond to each independent line name. The y axis is 826

shown in log2 scale. An ANOVA test was performed and pair-wise differences were evaluated 827

with a Tukey post hoc test; different groups were marked with letters at 0.05 significance level. 828

B. GUS expression analyzed by histochemical detection of GUS enzymatic activity in 14-day-829

old plants of the same lines showed above. 830

831

Figure S7. CPuORF33 action is not mediated by NMD 832

Transcript levels of AtHB1 in 14-day-old Col-0, upf1-5 and upf3-1 plants. Values were 833

normalized with the one obtain in Col-0 plants using the ΔΔCt method. Y axis is shown in log2 834

scale. An ANOVA test was performed and pair-wise differences were evaluated with a Tukey 835

post hoc test; different groups were marked with letters at 0.05 significance level. T-tests were 836

performed and p-values < 0.05 are signaled with asterisks. 837

838

Figure S8. Transgenic expression of CPuORF33 does not affect the expression of 839

endogenous AtHB1 840



39

Transcript levels of AtHB1 in 30-day-old rdr6-12 plants transformed with PromAtHB1:AtHB1 or 841

PromAtHB1mut:AtHB1. Three independent lines of each genotype were measure. Total AtHB1 842

transcript levels were obtained using oligonucleotides annealing in the CDS region, while 843

endogenous AtHB1 levels were obtain using oligonucleotides annealing in the 3’UTR region. All 844

the values were normalized with the one obtain in rdr6-12 plants transformed with pCambia 845

using the ΔΔCt method. The y axis is shown in log 2 scale. T-tests were performed between 846

genotypes for total AtHB1 vs total AtHB1, and for endogenous AtHB1 vs endogenous AtHB1. 847

There were no differences at a significance level of 0.05 848

849

Figure S9. Comparative ribosome footprinting profile of AtHB1 and AtHB13 transcripts 850

A. RNA-seq coverage and ribosome footprints (P-site) of AtHB1 transcript in shoots from 4-day-851

old seedlings (Hsu et al., 2016). Upper panel: Coverage of RNA-seq reads. Lower panel: 852

Ribosome occupancy. Light blue: CPuORF33; Grey: mORF; white: 5’ and 3’UTR. The relative 853

frequency was calculated as the depth in relation to the sum over whole transcript. 854

B. RNA-seq coverage and ribosome footprints (P-site) of AtHB1 transcript in 7-day-old 855

seedlings (Juntawong et al, 2014). Upper panel: Coverage of RNA-seq reads.Lower panel: 856

Ribosome occupancy. 857

C. RNA-seq coverage and ribosome footprints (P-site) of AtHB1 transcript in 4-day-old 858

seedlings (Merchante et al., 2015). Upper panel: Coverage of RNA-seq reads. Lower panel: 859

Ribosome occupancy. 860

D. RNA-seq coverage and ribosome footprints (P-site) of AtHB13 transcript in 4-day-old 861

seedlings (Hsu et al, 2016). Upper panel: Coverage of RNA-seq reads. Lower panel: Ribosome 862

occupancy. Light blue: uORF; Grey: mORF; white: 5' and 3' UTR. 863

864

Figure S10. The CPuORF33 represses translation in a sequence-dependent manner in the 865

heterologous yeast system. 866

A. Schematic representation of the constructs used in Saccharomyces cerevisiae transformation, 867

showing the nucleotide (above) and amino acid (below) sequence of the native and mutated 868

uORF. Changes in the amino acid sequence with respect to the native uORF are highlighted in 869

red. FS: Frame shift, Black: ADH promoter, White: 5'UTR, Light blue: CPuORF33, Green: 870



40

yeGFP ORF, Stars: Single base modification, Arrow: Insertion introduced or nucleotide 871

removed. 872

B. Expression levels of GFP analyzed by immunobloting of yeast transformed with the indicated 873

genetic constructs. Pgk1 serves as a loading control. 874

875

Figure S11. Comparative ribosome footprinting profile of AtHB1 transcripts in root vs. 876

shoots. 877

A. RNA-seq coverage and ribosome footprints (P-site) of AtHB1 transcript in shoots (upper 878

panel) and roots (lower panel) from 4-day-old seedlings (Hsu et al, 2016). Light blue: 879

CPuORF33; Grey: mORF; white: 5’ and 3’UTR B. Relation between mORF and uORF 880

translation efficiency in 4-day-old seedlings (Hsu et al., 2016). 881

882

Figure S12. AtHB1 potentially has a secondary TSS that could explain the activity of the 883

differential CPuORF in certain cases 884

A. Representation of the AtHB1 locus. Coding regions are depicted with broad boxes and introns 885

are shown as lines with arrowheads indicating the sense of transcription. The transcription start 886

sites (TSSs) defined by Morton et al (2014) are highlighted with the names given by the authors. 887

Red arrows indicate target sites of oligonucleotides used in the RT-qPCR assay. B. Sashimi plots 888

showing the RNA coverage profile along the AtHB1 locus, used for mapping the reads, for the 889

rosette and root samples from Grillet and Schmidt (GEO accession GSE87760). C. Output graph 890

from the RNAprof (Tran et al, 2016) program contrasting the RNA coverage profiles. The region 891

that presented a significant difference between tissues (p-value 2.9e-4) is highlighted over the 892

profile. The location of the uORF and the TSS from Morton et al. (2014) have been added to the 893

graph. D. Sashimi plots obtained with sequencing data from Mancini et al. (2016) showing the 894

RNA coverage profile along the AtHB1 locus. In this case no differences in the profile was found 895

with RNAprof when comparing dark and light grown plants. E. The upper panel shows the 896

Sashimi plots obtained with sequencing data from Liu et al. (2016) showing the RNA coverage 897

profile along the AtHB1 locus. The lower panel shows the output of running RNAprof for the 898

comparison of the RNA coverage profiles. The region presenting a differential profile between 899

tissues is highlighted and annotated with coordinates, score (fold-change) and p-value 900

information on top. 901



41

902

Figure S13. Histochemical detection of GUS in 35S:native-uORF:GUS plants grown under 903

different light regimes. Panels A, B and C show 8-day-old 35S:native-uORF:GUS seedlings 904

grown in: darkness (A, bar: 2 mm), 6 days in darkness and then transferred to long day 905

photoperiod (LDP) for 2 additional days; (B, bar: 0.5 mm); and 6 days in darkness, then exposed 906

to light for 1 h and then, transferred to darkness for 2 additional days (C, bar: 2 mm). Panels D, 907

E and F show 20-day-old seedling of: 35S:GUS grown under LDP (D, bar: 2 mm); 35S:native-908

uORF:GUS grown under LDP (E, bar: 2 mm); and 35S:native-uORF:GUS grown under LDP for 909

15 days and then transferred to darkness for 5 additional days (F, bar: 2 mm). Panels G, H and I 910

show 6-day-old 35S:native-uORF:GUS seedlings grown in: white light and LDP (N, bar: 1 mm); 911

blue light (480 nm) and LDP (H, bar: 1 mm); and red light (680 nm) and LDP (I, bar: 2 mm). 912

913

Figure S14. Ribosome footprinting profile of the transcripts of the maize AtHB1 homolog 914

ZmHB115 915

RNA-seq coverage and ribosome footprintings (P-site) of ZmHB115 transcript in 14-day-old 916

seedlings (Lei et al., 2015). Upper panel: Coverage of RNA-seq reads. Lower panel: Ribosome 917

occupancy. Light blue: uORF; Grey: mORF; white: 5’ and 3’UTR. 918



42

919

920



Parsed CitationsAlatorre-Cobos F, Cruz-Ramírez A, Hayden CA, Pérez-Torres CA, Chauvin AL, Ibarra-Laclette E, Alva-Cortés E, Jorgensen RA, Herrera-Estrella L (2012) Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogeneticallyconserved upstream open reading frame 30. J Exp Bot 63:5203-5221

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local aignment search tool. J Mol Biol 215:403-410Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Aoyama T, Dong CH Wu Y, Carabelli M, Sessa G, Ruberti I, Morelli G, Chua, NH (1995) Ectopic expression of the Arabidopsistranscriptional activator Athb-1 alters leaf cell fate in tobacco. Plant Cell 7:1773-1785


Arce AL, Raineri J, Capella M, Cabello JV, Chan RL (2011) Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zipsubfamily I transcription factors; a potential source of functional diversity. BMC Plant Biol 11:42


Bender J, Fink GR (1998) A Myb homologue, ATR1, activates tryptophan gene expression in Arabidopsis. Proc Natl Acad Sci USA95:5655-5660


Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics 30:2114-2120Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Calvo SE, Pagliarini DJ, Mootha VK (2009) Upstream open reading frames cause widespread reduction of protein expression and arepolymorphic among humans. Proc Natl Acad Sci USA 106:7507-7512


Capella M, Ré DA, Arce AL, Chan RL (2014) Plant homeodomain-leucine zipper I transcription factors exhibit different functional AHAmotifs that selectively interact with TBP or/and TFIIB. Plant Cell Rep 33:955-967


Capella M, Ribone PA, Arce AL, Chan RL (2015a) Homeodomain–leucine zipper transcription factors: structural features of theseproteins, unique to plants. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects. (Eds: González, DH)Elsevier, Amsterdam, The Netherlands, 113-126


Capella M, Ribone PA, Arce AL, Chan RL (2015b) Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I)transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation. New Phytol 207:669-682


Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J16:735-743


Combier JP, de Billy F, Gamas P, Niebel A, Rivas S (2008) Trans-regulation of the expression of the transcription factor MtHAP2-1 by auORF controls root nodule development. Genes Dev 22:1549-1559

Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title https://plantphysiol.orgDownloaded on March 5, 2021. - Published by

Copyright (c) 2020 American Society of Plant Biologists. All rights reserved.

http://www.ncbi.nlm.nih.gov/pubmed?term=Alatorre%2DCobos F%2C Cruz%2DRam�rez A%2C Hayden CA%2C P�rez%2DTorres CA%2C Chauvin AL%2C Ibarra%2DLaclette E%2C Alva%2DCort�s E%2C Jorgensen RA%2C Herrera%2DEstrella L %282012%29 Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30%2E J Exp Bot 63%3A5203%2D5221&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Alatorre-Cobos F, Cruz-Ram�rez A, Hayden CA, P�rez-Torres CA, Chauvin AL, Ibarra-Laclette E, Alva-Cort�s E, Jorgensen RA, Herrera-Estrella L (2012) Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30. J Exp Bot 63:5203-5221

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Alatorre-Cobos&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Translational regulation of Arabidopsis XIPOTL1 is modulated by phosphocholine levels via the phylogenetically conserved upstream open reading frame 30&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Alatorre-Cobos&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Altschul SF%2C Gish W%2C Miller W%2C Myers EW%2C Lipman DJ %281990%29 Basic local aignment search tool%2E J Mol Biol 215%3A403%2D410&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local aignment search tool. J Mol Biol 215:403-410

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Altschul&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Basic local aignment search tool&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Basic local aignment search tool&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Altschul&as_ylo=1990&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Aoyama T%2C Dong CH Wu Y%2C Carabelli M%2C Sessa G%2C Ruberti I%2C Morelli G%2C Chua%2C NH %281995%29 Ectopic expression of the Arabidopsis transcriptional activator Athb%2D1 alters leaf cell fate in tobacco%2E Plant Cell 7%3A1773%2D1785&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Aoyama T, Dong CH Wu Y, Carabelli M, Sessa G, Ruberti I, Morelli G, Chua, NH (1995) Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco. Plant Cell 7:1773-1785

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Aoyama&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Ectopic expression of the Arabidopsis transcriptional activator Athb-1 alters leaf cell fate in tobacco&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Aoyama&as_ylo=1995&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Arce AL%2C Raineri J%2C Capella M%2C Cabello JV%2C Chan RL %282011%29 Uncharacterized conserved motifs outside the HD%2DZip domain in HD%2DZip subfamily I transcription factors%3B a potential source of functional diversity%2E BMC Plant Biol 11%3A42&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Arce AL, Raineri J, Capella M, Cabello JV, Chan RL (2011) Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity. BMC Plant Biol 11:42

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Arce&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Uncharacterized conserved motifs outside the HD-Zip domain in HD-Zip subfamily I transcription factors; a potential source of functional diversity.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Arce&as_ylo=2011&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bender J%2C Fink GR %281998%29 A Myb homologue%2C ATR1%2C activates tryptophan gene expression in Arabidopsis%2E Proc Natl Acad Sci USA 95%3A5655%2D5660&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bender J, Fink GR (1998) A Myb homologue, ATR1, activates tryptophan gene expression in Arabidopsis. Proc Natl Acad Sci USA 95:5655-5660

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bender&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bender&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Bolger AM%2C Lohse M%2C Usadel B %282014%29 Trimmomatic%3A A flexible trimmer for Illumina Sequence Data%2E Bioinformatics 30%3A2114%2D2120&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: A flexible trimmer for Illumina Sequence Data. Bioinformatics 30:2114-2120

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Bolger&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Trimmomatic: A flexible trimmer for Illumina Sequence Data&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Trimmomatic: A flexible trimmer for Illumina Sequence Data&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Bolger&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Calvo SE%2C Pagliarini DJ%2C Mootha VK %282009%29 Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans%2E Proc Natl Acad Sci USA 106%3A7507%2D7512&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Calvo SE, Pagliarini DJ, Mootha VK (2009) Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans. Proc Natl Acad Sci USA 106:7507-7512

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Calvo&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Calvo&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Capella M%2C R� DA%2C Arce AL%2C Chan RL %282014%29 Plant homeodomain%2Dleucine zipper I transcription factors exhibit different functional AHA motifs that selectively interact with TBP or%2Fand TFIIB%2E Plant Cell Rep 33%3A955%2D967&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Capella M, R� DA, Arce AL, Chan RL (2014) Plant homeodomain-leucine zipper I transcription factors exhibit different functional AHA motifs that selectively interact with TBP or/and TFIIB. Plant Cell Rep 33:955-967

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Capella&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Plant homeodomain-leucine zipper I transcription factors exhibit different functional AHA motifs that selectively interact with TBP or/and TFIIB&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Plant homeodomain-leucine zipper I transcription factors exhibit different functional AHA motifs that selectively interact with TBP or/and TFIIB&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Capella&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Capella M%2C Ribone PA%2C Arce AL%2C Chan RL %282015a%29 Homeodomain�??leucine zipper transcription factors%3A structural features of these proteins%2C unique to plants%2E In Plant Transcription Factors%3A Evolutionary%2C Structural and Functional Aspects%2E %28Eds%3A González%2C DH%29 Elsevier%2C Amsterdam%2C The Netherlands%2C 113%2D126&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Capella M, Ribone PA, Arce AL, Chan RL (2015a) Homeodomain?leucine zipper transcription factors: structural features of these proteins, unique to plants. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects. (Eds: Gonz�lez, DH) Elsevier, Amsterdam, The Netherlands, 113-126


http://scholar.google.com/scholar?as_q=Homeodomainâ�?�?leucine zipper transcription factors: structural features of these proteins, unique to plants.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Homeodomainâ�?�?leucine zipper transcription factors: structural features of these proteins, unique to plants.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Capella&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Capella M%2C Ribone PA%2C Arce AL%2C Chan RL %282015b%29 Arabidopsis thaliana HomeoBox 1 %28AtHB1%29%2C a Homedomain%2DLeucine Zipper I %28HD%2DZip I%29 transcription factor%2C is regulated by PHYTOCHROME%2DINTERACTING FACTOR 1 to promote hypocotyl elongation%2E New Phytol 207%3A669%2D682&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Capella M, Ribone PA, Arce AL, Chan RL (2015b) Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation. New Phytol 207:669-682


http://scholar.google.com/scholar?as_q=Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis thaliana HomeoBox 1 (AtHB1), a Homedomain-Leucine Zipper I (HD-Zip I) transcription factor, is regulated by PHYTOCHROME-INTERACTING FACTOR 1 to promote hypocotyl elongation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Capella&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Clough SJ%2C Bent AF %281998%29 Floral dip%3A a simplified method for Agrobacterium%2Dmediated transformation of Arabidopsis thaliana%2E Plant J 16%3A735%2D743&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16:735-743

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Clough&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Clough&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Combier JP%2C de Billy F%2C Gamas P%2C Niebel A%2C Rivas S %282008%29 Trans%2Dregulation of the expression of the transcription factor MtHAP2%2D1 by a uORF controls root nodule development%2E Genes Dev 22%3A1549%2D1559&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Combier JP, de Billy F, Gamas P, Niebel A, Rivas S (2008) Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development. Genes Dev 22:1549-1559

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Combier&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Trans-regulation of the expression of the transcription factor MtHAP2-1 by a uORF controls root nodule development&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Combier&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1


Drozdetskiy A, Cole C, Procter J, Barton GJ (2015) JPred4: a protein secondary structure prediction server. Nucleic Acids Res43:W389-394


Ebina I, Takemoto-Tsutsumi M, Watanabe S, Koyama H, Endo Y, Kimata K, Igarashi T, Murakami K, Kudo R, Ohsumi A, Noh AL,Takahashi H, Naito S, Onouchi H (2015) Identification of novel Arabidopsis thaliana upstream open reading frames that controlexpression of the main coding sequences in a peptide sequence-dependent manner. Nucleic Acids Res 43:1562-1576


Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR (2015) HMMER web server: 2015 update.Nucleic Acids Res 43:W30-38


Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res W695-699


Guerrero-González ML, Rodríguez-Kessler M, Jiménez-Bremont JF (2014) uORF, a regulatory mechanism of the Arabidopsispolyamine oxidase 2. Mol Biol Rep 41:2427-2443


Guerrero-González ML, Ortega-Amaro MA, Juárez-Montiel M, Jiménez-Bremont JF (2016) Arabidopsis polyamine oxidase-2 uORF isrequired for downstream translational regulation. Plant Physiol Biochem 108:381-390


Hanfrey C, Elliott KA, Franceschetti M, Mayer MJ, Illingworth C, Michael AJ (2005) A dual upstream open reading frame-basedautoregulatory circuit controlling polyamine-responsive translation. J Biol Chem 280:39229-39237


Hayashi N, Sasaki S, Takahashi H, Yamashita Y, Naito S, Onouchi H (2017) Identification of Arabidopsis thaliana upstream open readingframes encoding peptide sequences that cause ribosomal arrest. Nucleic Acid Res gkx528. doi: 10.1093/nar/gkx528


Hayden CA, Jorgensen RA (2007) Identification of novel conserved peptide uORF homology groups in arabidopsis and rice revealsancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biol 5:32


Hayden CA, Bosco G (2008) Comparative genomic analysis of novel conserved peptide upstream open reading frames in drosophilamelanogaster and other dipteran species. BMC Genomics 9:61


Henriksson E, Olsson ASB, Johannesson H, Johansson H, Hanson J, Engström P, Söderman E (2005) Homeodomain Leucine Zipperclass I genes in Arabidopsis expression patterns and phylogenetic relationships. Plant Physiol 139:509-518


Higuchi R, Krummel B, Saiki RK (1988) A general method of in vitro preparation and specific mutagenesis of DNA fragments: study ofprotein and DNA interactions. Nucleic Acids Res 16:7351–7367


Hofer J, Turner L, Moreau C, Ambrose M, Isaac P, Butcher S, Weller J, Dupin A, Dalmais M, Le Signor C, Bendahmane A, Ellis N (2009)Tendril-Less regulates tendril formation in pea leaves. Plant Cell 21:420-428 https://plantphysiol.orgDownloaded on March 5, 2021. - Published by


http://www.ncbi.nlm.nih.gov/pubmed?term=Drozdetskiy A%2C Cole C%2C Procter J%2C Barton GJ %282015%29 JPred4%3A a protein secondary structure prediction server%2E Nucleic Acids Res 43%3AW389%2D394&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Drozdetskiy A, Cole C, Procter J, Barton GJ (2015) JPred4: a protein secondary structure prediction server. Nucleic Acids Res 43:W389-394

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Drozdetskiy&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Drozdetskiy&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ebina I%2C Takemoto%2DTsutsumi M%2C Watanabe S%2C Koyama H%2C Endo Y%2C Kimata K%2C Igarashi T%2C Murakami K%2C Kudo R%2C Ohsumi A%2C Noh AL%2C Takahashi H%2C Naito S%2C Onouchi H %282015%29 Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence%2Ddependent manner%2E Nucleic Acids Res 43%3A1562%2D1576&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ebina I, Takemoto-Tsutsumi M, Watanabe S, Koyama H, Endo Y, Kimata K, Igarashi T, Murakami K, Kudo R, Ohsumi A, Noh AL, Takahashi H, Naito S, Onouchi H (2015) Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner. Nucleic Acids Res 43:1562-1576

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ebina&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of novel Arabidopsis thaliana upstream open reading frames that control expression of the main coding sequences in a peptide sequence-dependent manner&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ebina&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Finn RD%2C Clements J%2C Arndt W%2C Miller BL%2C Wheeler TJ%2C Schreiber F%2C Bateman A%2C Eddy SR %282015%29 HMMER web server%3A 2015 update%2E Nucleic Acids Res 43%3AW30%2D38&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR (2015) HMMER web server: 2015 update. Nucleic Acids Res 43:W30-38

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Finn&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=HMMER web server: 2015 update&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=HMMER web server: 2015 update&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Finn&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Goujon M%2C McWilliam H%2C Li W%2C Valentin F%2C Squizzato S%2C Paern J%2C Lopez R %282010%29 A new bioinformatics analysis tools framework at EMBL%2DEBI%2E Nucleic Acids Res W695%2D699&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Goujon M, McWilliam H, Li W, Valentin F, Squizzato S, Paern J, Lopez R (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res W695-699

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Goujon&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A new bioinformatics analysis tools framework at EMBL-EBI.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A new bioinformatics analysis tools framework at EMBL-EBI.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Goujon&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Guerrero%2DGonz�lez ML%2C Rodr�guez%2DKessler M%2C Jim�nez%2DBremont JF %282014%29 uORF%2C a regulatory mechanism of the Arabidopsis polyamine oxidase 2%2E Mol Biol Rep 41%3A2427%2D2443&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Guerrero-Gonz�lez ML, Rodr�guez-Kessler M, Jim�nez-Bremont JF (2014) uORF, a regulatory mechanism of the Arabidopsis polyamine oxidase 2. Mol Biol Rep 41:2427-2443

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Guerrero-González&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=uORF, a regulatory mechanism of the Arabidopsis polyamine oxidase 2&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=uORF, a regulatory mechanism of the Arabidopsis polyamine oxidase 2&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Guerrero-González&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Guerrero%2DGonz�lez ML%2C Ortega%2DAmaro MA%2C Ju�rez%2DMontiel M%2C Jim�nez%2DBremont JF %282016%29 Arabidopsis polyamine oxidase%2D2 uORF is required for downstream translational regulation%2E Plant Physiol Biochem 108%3A381%2D390&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Guerrero-Gonz�lez ML, Ortega-Amaro MA, Ju�rez-Montiel M, Jim�nez-Bremont JF (2016) Arabidopsis polyamine oxidase-2 uORF is required for downstream translational regulation. Plant Physiol Biochem 108:381-390

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Guerrero-González&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis polyamine oxidase-2 uORF is required for downstream translational regulation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis polyamine oxidase-2 uORF is required for downstream translational regulation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Guerrero-González&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hanfrey C%2C Elliott KA%2C Franceschetti M%2C Mayer MJ%2C Illingworth C%2C Michael AJ %282005%29 A dual upstream open reading frame%2Dbased autoregulatory circuit controlling polyamine%2Dresponsive translation%2E J Biol Chem 280%3A39229%2D39237&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hanfrey C, Elliott KA, Franceschetti M, Mayer MJ, Illingworth C, Michael AJ (2005) A dual upstream open reading frame-based autoregulatory circuit controlling polyamine-responsive translation. J Biol Chem 280:39229-39237

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hanfrey&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A dual upstream open reading frame-based autoregulatory circuit controlling polyamine-responsive translation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A dual upstream open reading frame-based autoregulatory circuit controlling polyamine-responsive translation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hanfrey&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hayashi N%2C Sasaki S%2C Takahashi H%2C Yamashita Y%2C Naito S%2C Onouchi H %282017%29 Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest%2E Nucleic Acid Res gkx528%2E doi%3A 10%2E1093%2Fnar%2Fgkx528&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hayashi N, Sasaki S, Takahashi H, Yamashita Y, Naito S, Onouchi H (2017) Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest. Nucleic Acid Res gkx528. doi: 10.1093/nar/gkx528

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hayashi&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of Arabidopsis thaliana upstream open reading frames encoding peptide sequences that cause ribosomal arrest.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hayashi&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hayden CA%2C Jorgensen RA %282007%29 Identification of novel conserved peptide uORF homology groups in arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor%2Dencoding genes%2E BMC Biol 5%3A32&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hayden CA, Jorgensen RA (2007) Identification of novel conserved peptide uORF homology groups in arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes. BMC Biol 5:32

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hayden&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of novel conserved peptide uORF homology groups in arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Identification of novel conserved peptide uORF homology groups in arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hayden&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hayden CA%2C Bosco G %282008%29 Comparative genomic analysis of novel conserved peptide upstream open reading frames in drosophila melanogaster and other dipteran species%2E BMC Genomics 9%3A61&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hayden CA, Bosco G (2008) Comparative genomic analysis of novel conserved peptide upstream open reading frames in drosophila melanogaster and other dipteran species. BMC Genomics 9:61

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hayden&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Comparative genomic analysis of novel conserved peptide upstream open reading frames in drosophila melanogaster and other dipteran species.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Comparative genomic analysis of novel conserved peptide upstream open reading frames in drosophila melanogaster and other dipteran species.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hayden&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Henriksson E%2C Olsson ASB%2C Johannesson H%2C Johansson H%2C Hanson J%2C Engstr�m P%2C S�derman E %282005%29 Homeodomain Leucine Zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships%2E Plant Physiol 139%3A509%2D518&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Henriksson E, Olsson ASB, Johannesson H, Johansson H, Hanson J, Engstr�m P, S�derman E (2005) Homeodomain Leucine Zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships. Plant Physiol 139:509-518

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Henriksson&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Homeodomain Leucine Zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Homeodomain Leucine Zipper class I genes in Arabidopsis expression patterns and phylogenetic relationships&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Henriksson&as_ylo=2005&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Higuchi R%2C Krummel B%2C Saiki RK %281988%29 A general method of in vitro preparation and speciﬁc mutagenesis of DNA fragments%3A study of protein and DNA interactions%2E Nucleic Acids Res 16%3A7351�??7367&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Higuchi R, Krummel B, Saiki RK (1988) A general method of in vitro preparation and speci?c mutagenesis of DNA fragments: study of protein and DNA interactions. Nucleic Acids Res 16:7351?7367

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Higuchi&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A general method of in vitro preparation and speciï¬�c mutagenesis of DNA fragments: study of protein and DNA interactions.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A general method of in vitro preparation and speciï¬�c mutagenesis of DNA fragments: study of protein and DNA interactions.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Higuchi&as_ylo=1988&as_allsubj=all&hl=en&c2coff=1



Hou CY, Lee WC, Chou HC, Chen AP, Chou SJ, Chen HM (2016) Global analysis of truncated RNA ends reveals new insights intoribosome stalling in plants. Plant Cell 28: 2398–2416


Hsu PY, Calviello L, Larry Wud H-Y, Li F-W, Rothfels CJ, Ohlerb U, Benfey PN (2016) Super-resolution ribosome profiling revealsunannotated translation events in Arabidopsis. Proc Natl Acad Sci USA 113: E7126–E7135


Imai A, Hanzawa Y, Komura M, Yamamoto KT, Komeda Y, Takahashi T (2006) The dwarf phenotype of the Arabidopsis acl5 mutant issuppressed by a mutation in an upstream ORF of a bHLH gene. Development 133:3575-3585


Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotideresolution using ribosome profiling. Science 324:218-223


Ito K, Chiba S (2013) Arrest peptides: cis -acting modulators of translation. Annu Rev Biochem 82:171-202Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Ivanov IP, Atkins JF, Michael AJ (2010) A profusion of upstream open reading frame mechanisms in polyamine-responsive translationalregulation. Nucleic Acids Res 38:353-359


Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker inhigher plants. EMBO J 6:3901-3907


Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Bioinformatics8:275-282


Jorgensen RA, Dorantes-Acosta AE (2012) Conserved peptide upstream open reading frames are associated with regulatory genes inangiosperms. Front Plant Sci 3:1-11


Juntawong P, Girke T, Bazin J, Bailey-Serres J (2014) Translational dynamics revealed by genome-wide profiling of ribosomefootprints in Arabidopsis. Proc Natl Acad Sci USA 111:E203-E212.


Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A,Brown JWS (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes inArabidopsis. Nucleic Acids Res 40:2454-2469


Katayama H, Iwamoto K, Kariya Y, Asakawa T, Kan T, Fukuda H, Ohashi-Ito K (2015) A negative feedback loop controlling bHLHcomplexes is involved in vascular cell division and differentiation in the root apical meristem. Curr Biol 25:3144–3150



http://www.ncbi.nlm.nih.gov/pubmed?term=Hofer J%2C Turner L%2C Moreau C%2C Ambrose M%2C Isaac P%2C Butcher S%2C Weller J%2C Dupin A%2C Dalmais M%2C Le Signor C%2C Bendahmane A%2C Ellis N %282009%29 Tendril%2DLess regulates tendril formation in pea leaves%2E Plant Cell 21%3A420%2D428&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hofer J, Turner L, Moreau C, Ambrose M, Isaac P, Butcher S, Weller J, Dupin A, Dalmais M, Le Signor C, Bendahmane A, Ellis N (2009) Tendril-Less regulates tendril formation in pea leaves. Plant Cell 21:420-428

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hofer&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Tendril-Less regulates tendril formation in pea leaves&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Tendril-Less regulates tendril formation in pea leaves&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hofer&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hou CY%2C Lee WC%2C Chou HC%2C Chen AP%2C Chou SJ%2C Chen HM %282016%29 Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants%2E Plant Cell 28%3A 2398�??2416&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hou CY, Lee WC, Chou HC, Chen AP, Chou SJ, Chen HM (2016) Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants. Plant Cell 28: 2398?2416

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hou&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Global analysis of truncated RNA ends reveals new insights into ribosome stalling in plants.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hou&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Hsu PY%2C Calviello L%2C Larry Wud H%2DY%2C Li F%2DW%2C Rothfels CJ%2C Ohlerb U%2C Benfey PN %282016%29 Super%2Dresolution ribosome profiling reveals unannotated translation events in Arabidopsis%2E Proc Natl Acad Sci USA 113%3A E7126�??E7135&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Hsu PY, Calviello L, Larry Wud H-Y, Li F-W, Rothfels CJ, Ohlerb U, Benfey PN (2016) Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis. Proc Natl Acad Sci USA 113: E7126?E7135

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Hsu&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Super-resolution ribosome profiling reveals unannotated translation events in Arabidopsis.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Hsu&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Imai A%2C Hanzawa Y%2C Komura M%2C Yamamoto KT%2C Komeda Y%2C Takahashi T %282006%29 The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene%2E Development 133%3A3575%2D3585&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Imai A, Hanzawa Y, Komura M, Yamamoto KT, Komeda Y, Takahashi T (2006) The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene. Development 133:3575-3585

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Imai&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The dwarf phenotype of the Arabidopsis acl5 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Imai&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ingolia NT%2C Ghaemmaghami S%2C Newman JRS%2C Weissman JS %282009%29 Genome%2Dwide analysis in vivo of translation with nucleotide resolution using ribosome profiling%2E Science 324%3A218%2D223&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218-223

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ingolia&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ingolia&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ito K%2C Chiba S %282013%29 Arrest peptides%3A cis %2Dacting modulators of translation%2E Annu Rev Biochem 82%3A171%2D202&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ito K, Chiba S (2013) Arrest peptides: cis -acting modulators of translation. Annu Rev Biochem 82:171-202

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ito&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Arrest peptides: cis -acting modulators of translation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Arrest peptides: cis -acting modulators of translation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ito&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ivanov IP%2C Atkins JF%2C Michael AJ %282010%29 A profusion of upstream open reading frame mechanisms in polyamine%2Dresponsive translational regulation%2E Nucleic Acids Res 38%3A353%2D359&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ivanov IP, Atkins JF, Michael AJ (2010) A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation. Nucleic Acids Res 38:353-359

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ivanov&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ivanov&as_ylo=2010&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jefferson RA%2C Kavanagh TA%2C Bevan MW %281987%29 GUS fusions%3A beta%2Dglucuronidase as a sensitive and versatile gene fusion marker in higher plants%2E EMBO J 6%3A3901%2D3907&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jefferson RA, Kavanagh TA, Bevan MW (1987) GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J 6:3901-3907

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jefferson&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=GUS fusions: beta-glucuronidase as a sensitive and versatile gene fusion marker in higher plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jefferson&as_ylo=1987&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jones DT%2C Taylor WR%2C Thornton JM %281992%29 The rapid generation of mutation data matrices from protein sequences%2E Bioinformatics 8%3A275%2D282&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Bioinformatics 8:275-282

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jones&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The rapid generation of mutation data matrices from protein sequences&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The rapid generation of mutation data matrices from protein sequences&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jones&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Jorgensen RA%2C Dorantes%2DAcosta AE %282012%29 Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms%2E Front Plant Sci 3%3A1%2D11&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Jorgensen RA, Dorantes-Acosta AE (2012) Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms. Front Plant Sci 3:1-11

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Jorgensen&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Conserved peptide upstream open reading frames are associated with regulatory genes in angiosperms&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Jorgensen&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Juntawong P%2C Girke T%2C Bazin J%2C Bailey%2DSerres J %282014%29 Translational dynamics revealed by genome%2Dwide profiling of ribosome footprints in Arabidopsis%2E Proc Natl Acad Sci USA 111%3AE203%2DE212%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Juntawong P, Girke T, Bazin J, Bailey-Serres J (2014) Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci USA 111:E203-E212.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Juntawong&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Translational dynamics revealed by genome-wide profiling of ribosome footprints in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Juntawong&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kalyna M%2C Simpson CG%2C Syed NH%2C Lewandowska D%2C Marquez Y%2C Kusenda B%2C Marshall J%2C Fuller J%2C Cardle L%2C McNicol J%2C Dinh HQ%2C Barta A%2C Brown JWS %282012%29 Alternative splicing and nonsense%2Dmediated decay modulate expression of important regulatory genes in Arabidopsis%2E Nucleic Acids Res 40%3A2454%2D2469&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kalyna M, Simpson CG, Syed NH, Lewandowska D, Marquez Y, Kusenda B, Marshall J, Fuller J, Cardle L, McNicol J, Dinh HQ, Barta A, Brown JWS (2012) Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis. Nucleic Acids Res 40:2454-2469

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kalyna&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kalyna&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Katayama H%2C Iwamoto K%2C Kariya Y%2C Asakawa T%2C Kan T%2C Fukuda H%2C Ohashi%2DIto K %282015%29 A negative feedback loop controlling bHLH complexes is involved in vascular cell division and differentiation in the root apical meristem%2E Curr Biol 25%3A3144�??3150&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Katayama H, Iwamoto K, Kariya Y, Asakawa T, Kan T, Fukuda H, Ohashi-Ito K (2015) A negative feedback loop controlling bHLH complexes is involved in vascular cell division and differentiation in the root apical meristem. Curr Biol 25:3144?3150

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Katayama&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A negative feedback loop controlling bHLH complexes is involved in vascular cell division and differentiation in the root apical meristem.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A negative feedback loop controlling bHLH complexes is involved in vascular cell division and differentiation in the root apical meristem.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Katayama&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1


Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presenceof insertions, deletions and gene fusions. Genome Biol 14:R36


Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryoticribosomes. Cell 44:283-292


Kozak M (1987) Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes. Mol Cell Biol 7:3438-3445Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Kozak M (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299:1-34Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Kwak SH, Lee SH (2001) The regulation of ornithine decarboxylase gene expression by sucrose and small upstream open readingframe in tomato (Lycopersicon Esculentum Mill). Plant Cell Physiol 42:314-323


Laing WA, Martínez-Sánchez M, Wright MA, Bulley SM, Brewster D, Dare AP, Rassam M, Wang D, Storey R, Macknight RC, Hellens RP(2015) An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis. Plant Cell 27:772-786


Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M,Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR):Improved gene annotation and new tools. Nucleic Acids Res 40 (Database issue): D1202-1210


Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD,Gibson TJ, Higgins DG (2007) Clustal W. and Clustal X version 2.0. Bioinformatics 23:2947-2948.


Lei L, Shi J, Chen J, Zhang M, Sun S, Xie S, Li X, Zeng B, Peng L, Hauck A, Zhao H, Song W, Fan Z, Lai, J (2015) Ribosome profilingreveals dynamic translational landscape in maize seedlings under drought stress. Plant J 84:1206-1218


Liu J, Deng S, Wang H, Ye J, Wu HW, Sun HX, Chua, NH (2016) CURLY LEAF Regulates gene sets coordinating seed size and lipidbiosynthesis. Plant Physiol 171:424-436


Manavella PA, Arce AL, Dezar CA, Bitton F, Renou JP, Crespi M, Chan, RL (2006) Cross-talk between ethylene and drought signallingpathways is mediated by the sunflower Hahb-4 transcription factor. Plant J 48:125-137


Mancini E, Sanchez SE, Romanowski A, Schlaen RG, Sanchez-Lamas M, Cerdán PD, Yanovsky MJ (2016) Acute Effects of Light onAlternative Splicing in Light-Grown Plants. Photochem Photobiol 92:126-133


Matzke MA, Matzke AJM, Pruss GJ, Vance VB (2001) RNA-based silencing strategies in plants. Curr Opin Genet Dev 11:221-227Pubmed: Author and TitleCrossRef: Author and Title https://plantphysiol.orgDownloaded on March 5, 2021. - Published by


http://www.ncbi.nlm.nih.gov/pubmed?term=Kim D%2C Pertea G%2C Trapnell C%2C Pimentel H%2C Kelley R%2C Salzberg SL %282013%29 TopHat2%3A accurate alignment of transcriptomes in the presence of insertions%2C deletions and gene fusions%2E Genome Biol 14%3AR36&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kim&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kim&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kozak M %281986%29 Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes%2E Cell 44%3A283%2D292&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kozak M (1986) Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes. Cell 44:283-292

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kozak&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Point mutations define a sequence flanking the AUG initiator codon that modulates translation by eukaryotic ribosomes&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kozak&as_ylo=1986&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kozak M %281987%29 Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes%2E Mol Cell Biol 7%3A3438%2D3445&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kozak M (1987) Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes. Mol Cell Biol 7:3438-3445


http://scholar.google.com/scholar?as_q=Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Effects of intercistronic length on the efficiency of reinitiation by eucaryotic ribosomes&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kozak&as_ylo=1987&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kozak M %282002%29 Pushing the limits of the scanning mechanism for initiation of translation%2E Gene 299%3A1%2D34&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kozak M (2002) Pushing the limits of the scanning mechanism for initiation of translation. Gene 299:1-34


http://scholar.google.com/scholar?as_q=Pushing the limits of the scanning mechanism for initiation of translation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Pushing the limits of the scanning mechanism for initiation of translation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kozak&as_ylo=2002&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Kwak SH%2C Lee SH %282001%29 The regulation of ornithine decarboxylase gene expression by sucrose and small upstream open reading frame in tomato %28Lycopersicon Esculentum Mill%29%2E Plant Cell Physiol 42%3A314%2D323&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Kwak SH, Lee SH (2001) The regulation of ornithine decarboxylase gene expression by sucrose and small upstream open reading frame in tomato (Lycopersicon Esculentum Mill). Plant Cell Physiol 42:314-323

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Kwak&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The regulation of ornithine decarboxylase gene expression by sucrose and small upstream open reading frame in tomato (Lycopersicon Esculentum Mill)&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The regulation of ornithine decarboxylase gene expression by sucrose and small upstream open reading frame in tomato (Lycopersicon Esculentum Mill)&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Kwak&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Laing WA%2C Mart�nez%2DS�nchez M%2C Wright MA%2C Bulley SM%2C Brewster D%2C Dare AP%2C Rassam M%2C Wang D%2C Storey R%2C Macknight RC%2C Hellens RP %282015%29 An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis%2E Plant Cell 27%3A772%2D786&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Laing WA, Mart�nez-S�nchez M, Wright MA, Bulley SM, Brewster D, Dare AP, Rassam M, Wang D, Storey R, Macknight RC, Hellens RP (2015) An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis. Plant Cell 27:772-786

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Laing&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Laing&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Lamesch P%2C Berardini TZ%2C Li D%2C Swarbreck D%2C Wilks C%2C Sasidharan R%2C Muller R%2C Dreher K%2C Alexander DL%2C Garcia%2DHernandez M%2C Karthikeyan AS%2C Lee CH%2C Nelson WD%2C Ploetz L%2C Singh S%2C Wensel A%2C Huala E %282012%29 The Arabidopsis Information Resource %28TAIR%29%3A Improved gene annotation and new tools%2E Nucleic Acids Res 40 %28Database issue%29%3A D1202%2D1210&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis Information Resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Res 40 (Database issue): D1202-1210

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lamesch&hl=en&c2coff=1


http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lamesch&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Larkin MA%2C Blackshields G%2C Brown NP%2C Chenna R%2C McGettigan PA%2C McWilliam H%2C Valentin F%2C Wallace IM%2C Wilm A%2C Lopez R%2C Thompson JD%2C Gibson TJ%2C Higgins DG %282007%29 Clustal W%2E and Clustal X version 2%2E0%2E Bioinformatics 23%3A2947%2D2948%2E&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W. and Clustal X version 2.0. Bioinformatics 23:2947-2948.

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Larkin&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Clustal W&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Clustal W&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Larkin&as_ylo=2007&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Lei L%2C Shi J%2C Chen J%2C Zhang M%2C Sun S%2C Xie S%2C Li X%2C Zeng B%2C Peng L%2C Hauck A%2C Zhao H%2C Song W%2C Fan Z%2C Lai%2C J %282015%29 Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress%2E Plant J 84%3A1206%2D1218&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Lei L, Shi J, Chen J, Zhang M, Sun S, Xie S, Li X, Zeng B, Peng L, Hauck A, Zhao H, Song W, Fan Z, Lai, J (2015) Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress. Plant J 84:1206-1218

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Lei&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Ribosome profiling reveals dynamic translational landscape in maize seedlings under drought stress&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Lei&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Liu J%2C Deng S%2C Wang H%2C Ye J%2C Wu HW%2C Sun HX%2C Chua%2C NH %282016%29 CURLY LEAF Regulates gene sets coordinating seed size and lipid biosynthesis%2E Plant Physiol 171%3A424%2D436&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Liu J, Deng S, Wang H, Ye J, Wu HW, Sun HX, Chua, NH (2016) CURLY LEAF Regulates gene sets coordinating seed size and lipid biosynthesis. Plant Physiol 171:424-436

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Liu&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=CURLY LEAF Regulates gene sets coordinating seed size and lipid biosynthesis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=CURLY LEAF Regulates gene sets coordinating seed size and lipid biosynthesis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Liu&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Manavella PA%2C Arce AL%2C Dezar CA%2C Bitton F%2C Renou JP%2C Crespi M%2C Chan%2C RL %282006%29 Cross%2Dtalk between ethylene and drought signalling pathways is mediated by the sunflower Hahb%2D4 transcription factor%2E Plant J 48%3A125%2D137&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Manavella PA, Arce AL, Dezar CA, Bitton F, Renou JP, Crespi M, Chan, RL (2006) Cross-talk between ethylene and drought signalling pathways is mediated by the sunflower Hahb-4 transcription factor. Plant J 48:125-137

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Manavella&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Cross-talk between ethylene and drought signalling pathways is mediated by the sunflower Hahb-4 transcription factor&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Cross-talk between ethylene and drought signalling pathways is mediated by the sunflower Hahb-4 transcription factor&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Manavella&as_ylo=2006&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Mancini E%2C Sanchez SE%2C Romanowski A%2C Schlaen RG%2C Sanchez%2DLamas M%2C Cerd�n PD%2C Yanovsky MJ %282016%29 Acute Effects of Light on Alternative Splicing in Light%2DGrown Plants%2E Photochem Photobiol 92%3A126%2D133&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Mancini E, Sanchez SE, Romanowski A, Schlaen RG, Sanchez-Lamas M, Cerd�n PD, Yanovsky MJ (2016) Acute Effects of Light on Alternative Splicing in Light-Grown Plants. Photochem Photobiol 92:126-133

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Mancini&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Acute Effects of Light on Alternative Splicing in Light-Grown Plants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Acute Effects of Light on Alternative Splicing in Light-Grown Plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Mancini&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Matzke MA%2C Matzke AJM%2C Pruss GJ%2C Vance VB %282001%29 RNA%2Dbased silencing strategies in plants%2E Curr Opin Genet Dev 11%3A221%2D227&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Matzke MA, Matzke AJM, Pruss GJ, Vance VB (2001) RNA-based silencing strategies in plants. Curr Opin Genet Dev 11:221-227


Google Scholar: Author Only Title Only Author and Title

Merchante C, Brumos J, Yun J, Hu Q, Spencer KR, Enríquez P, Binder BM, Heber S, Stepanova AN, Alonso JM (2015) Gene-Specifictranslation regulation mediated by the hormone-signaling molecule EIN2. Cell 163:684-697


Moreno Piovano GS, Moreno JE, Cabello JV, Arce AL, Otegui ME, Chan, RL (2017) A role for LAX2 in regulating xylem development andlateral-vein symmetry in the leaf. Ann Bot doi: 10.1093/aob/mcx091


Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M (2014) Paired-end analysis of transcriptionstart sites in Arabidopsis reveals plant-specific promoter signatures. Plant Cell 26:2746-2760


Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genomedefined by RNA sequencing. Science 320:1344-1349


Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R,von Heijne G (2015) Cotranslational protein folding inside the ribosome exit tunnel. Cell Rep 12:1533-1540


Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (2004) SGS3 and SGS2/SDE1/RDR6 Are Required for Juvenile Developmentand the Production of Trans-Acting siRNAs in Arabidopsis. Genes Dev 18:2368-2379


Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Pumplin N, Sarazin A, Jullien PE, Bologna NG, Oberlin S, Voinnet O (2016) DNA methylation influences the expression of DICER-LIKE4isoforms, which encode proteins of alternative localization and function. Plant Cell 28:2786-2804


Rahmani F, Hummel M, Schuurmans J, Wiese-Klinkenberg A, Smeekens S, Hanson, J (2009) Sucrose control of translation mediated byan upstream open reading frame-encoded peptide. Plant Physiol 150:1356-1367


Rajeevkumar S, Anunanthini P, Sathishkumar R (2015) Epigenetic silencing in transgenic plants. Front Plant Sci 6:693Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Re DA, Capella M, Bonaventure G, Chan, RL (2014) Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processesassociated with growth and responses to water stress. BMC Plant Biol 14:150


Reeves JH (1992) Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J Mol Evol35:17-31


Ribichich KF, Arce AL, Chan, RL (2014) Coping with drought and salinity stresses: role of transcription factors in crop improvemenT InClimate Change and Plant Abiotic Stress Tolerance (Eds.: Tuteja N y Gill SS) Wiley-VCH Verlag GmbH & CO KGaA, Weinheim, Germany,pp: 641-684


http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Matzke&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=RNA-based silencing strategies in plants&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=RNA-based silencing strategies in plants&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Matzke&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Merchante C%2C Brumos J%2C Yun J%2C Hu Q%2C Spencer KR%2C Enr�quez P%2C Binder BM%2C Heber S%2C Stepanova AN%2C Alonso JM %282015%29 Gene%2DSpecific translation regulation mediated by the hormone%2Dsignaling molecule EIN2%2E Cell 163%3A684%2D697&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Merchante C, Brumos J, Yun J, Hu Q, Spencer KR, Enr�quez P, Binder BM, Heber S, Stepanova AN, Alonso JM (2015) Gene-Specific translation regulation mediated by the hormone-signaling molecule EIN2. Cell 163:684-697

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Merchante&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Gene-Specific translation regulation mediated by the hormone-signaling molecule EIN2&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Gene-Specific translation regulation mediated by the hormone-signaling molecule EIN2&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Merchante&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Moreno Piovano GS%2C Moreno JE%2C Cabello JV%2C Arce AL%2C Otegui ME%2C Chan%2C RL %282017%29 A role for LAX2 in regulating xylem development and lateral%2Dvein symmetry in the leaf%2E Ann Bot doi%3A 10%2E1093%2Faob%2Fmcx091&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Moreno Piovano GS, Moreno JE, Cabello JV, Arce AL, Otegui ME, Chan, RL (2017) A role for LAX2 in regulating xylem development and lateral-vein symmetry in the leaf. Ann Bot doi: 10.1093/aob/mcx091

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Moreno&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A role for LAX2 in regulating xylem development and lateral-vein symmetry in the leaf.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A role for LAX2 in regulating xylem development and lateral-vein symmetry in the leaf.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Moreno&as_ylo=2017&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Morton T%2C Petricka J%2C Corcoran DL%2C Li S%2C Winter CM%2C Carda A%2C Benfey PN%2C Ohler U%2C Megraw M %282014%29 Paired%2Dend analysis of transcription start sites in Arabidopsis reveals plant%2Dspecific promoter signatures%2E Plant Cell 26%3A2746%2D2760&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Morton T, Petricka J, Corcoran DL, Li S, Winter CM, Carda A, Benfey PN, Ohler U, Megraw M (2014) Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures. Plant Cell 26:2746-2760

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Morton&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Morton&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Nagalakshmi U%2C Wang Z%2C Waern K%2C Shou C%2C Raha D%2C Gerstein M%2C Snyder M %282008%29 The transcriptional landscape of the yeast genome defined by RNA sequencing%2E Science 320%3A1344%2D1349&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344-1349

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nagalakshmi&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The transcriptional landscape of the yeast genome defined by RNA sequencing&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The transcriptional landscape of the yeast genome defined by RNA sequencing&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nagalakshmi&as_ylo=2008&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Nilsson OB%2C Hedman R%2C Marino J%2C Wickles S%2C Bischoff L%2C Johansson M%2C M�ller%2DLucks A%2C Trovato F%2C Puglisi JD%2C O%27Brien EP%2C Beckmann R%2C von Heijne G %282015%29 Cotranslational protein folding inside the ribosome exit tunnel%2E Cell Rep 12%3A1533%2D1540&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, M�ller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G (2015) Cotranslational protein folding inside the ribosome exit tunnel. Cell Rep 12:1533-1540

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Nilsson&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Cotranslational protein folding inside the ribosome exit tunnel&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Cotranslational protein folding inside the ribosome exit tunnel&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Nilsson&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Peragine A%2C Yoshikawa M%2C Wu G%2C Albrecht HL%2C Poethig RS %282004%29 SGS3 and SGS2%2FSDE1%2FRDR6 Are Required for Juvenile Development and the Production of Trans%2DActing siRNAs in Arabidopsis%2E Genes Dev 18%3A2368%2D2379&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Peragine A, Yoshikawa M, Wu G, Albrecht HL, Poethig RS (2004) SGS3 and SGS2/SDE1/RDR6 Are Required for Juvenile Development and the Production of Trans-Acting siRNAs in Arabidopsis. Genes Dev 18:2368-2379

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Peragine&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=SGS3 and SGS2/SDE1/RDR6 Are Required for Juvenile Development and the Production of Trans-Acting siRNAs in Arabidopsis&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=SGS3 and SGS2/SDE1/RDR6 Are Required for Juvenile Development and the Production of Trans-Acting siRNAs in Arabidopsis&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Peragine&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Pfaffl MW %282001%29 A new mathematical model for relative quantification in real%2Dtime RT%2DPCR%2E Nucleic Acids Res 29%3Ae45&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29:e45

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pfaffl&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A new mathematical model for relative quantification in real-time RT-PCR.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A new mathematical model for relative quantification in real-time RT-PCR.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pfaffl&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Pumplin N%2C Sarazin A%2C Jullien PE%2C Bologna NG%2C Oberlin S%2C Voinnet O %282016%29 DNA methylation influences the expression of DICER%2DLIKE4 isoforms%2C which encode proteins of alternative localization and function%2E Plant Cell 28%3A2786%2D2804&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Pumplin N, Sarazin A, Jullien PE, Bologna NG, Oberlin S, Voinnet O (2016) DNA methylation influences the expression of DICER-LIKE4 isoforms, which encode proteins of alternative localization and function. Plant Cell 28:2786-2804

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Pumplin&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=DNA methylation influences the expression of DICER-LIKE4 isoforms, which encode proteins of alternative localization and function&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=DNA methylation influences the expression of DICER-LIKE4 isoforms, which encode proteins of alternative localization and function&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Pumplin&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Rahmani F%2C Hummel M%2C Schuurmans J%2C Wiese%2DKlinkenberg A%2C Smeekens S%2C Hanson%2C J %282009%29 Sucrose control of translation mediated by an upstream open reading frame%2Dencoded peptide%2E Plant Physiol 150%3A1356%2D1367&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Rahmani F, Hummel M, Schuurmans J, Wiese-Klinkenberg A, Smeekens S, Hanson, J (2009) Sucrose control of translation mediated by an upstream open reading frame-encoded peptide. Plant Physiol 150:1356-1367

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rahmani&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Sucrose control of translation mediated by an upstream open reading frame-encoded peptide&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Sucrose control of translation mediated by an upstream open reading frame-encoded peptide&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rahmani&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Rajeevkumar S%2C Anunanthini P%2C Sathishkumar R %282015%29 Epigenetic silencing in transgenic plants%2E Front Plant Sci 6%3A693&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Rajeevkumar S, Anunanthini P, Sathishkumar R (2015) Epigenetic silencing in transgenic plants. Front Plant Sci 6:693

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rajeevkumar&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Epigenetic silencing in transgenic plants.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Epigenetic silencing in transgenic plants.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rajeevkumar&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Re DA%2C Capella M%2C Bonaventure G%2C Chan%2C RL %282014%29 Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processes associated with growth and responses to water stress%2E BMC Plant Biol 14%3A150&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Re DA, Capella M, Bonaventure G, Chan, RL (2014) Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processes associated with growth and responses to water stress. BMC Plant Biol 14:150

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Re&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processes associated with growth and responses to water stress.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Arabidopsis AtHB7 and AtHB12 evolved divergently to fine tune processes associated with growth and responses to water stress.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Re&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Reeves JH %281992%29 Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA%2E J Mol Evol 35%3A17%2D31&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Reeves JH (1992) Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA. J Mol Evol 35:17-31

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Reeves&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Heterogeneity in the substitution process of amino acid sites of proteins coded for by mitochondrial DNA&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Reeves&as_ylo=1992&as_allsubj=all&hl=en&c2coff=1


Ribone PA, Capella M, Arce AL, Chan RL (2015a) What do we know about homeodomain-leucine zipper I transcription factors?Functional and biotechnological considerations. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects (Eds:González, DH) Elsevier, Amsterdam, The Netherlands, pP 343-356


Ribone PA, Capella M, Chan, RL (2015b) Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13reveals a crucial role in Arabidopsis development. J Exp Bot 66:5929-5943


Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Romani F, Ribone PA, Capella M, Miguel VN, Chan RL (2015) A matter of quantity: common features in the drought response oftransgenic plants overexpressing HD-Zip I transcription factors. Plant Sci 251:139-154


Sakuma S, Pourkheirandish M, Hensel G, Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma JF, Sassa H, Koba T, et al. (2013) Divergence ofexpression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol 197:939-948


Saul H, Elharrar E, Gaash R, Eliaz D, Valenci M, Akua T, Avramov M, Frankel N, Berezin I, Gottlieb D, Elazar M, David-Assael O,Tcherkas V, Mizrachi K, Shaul O (2009) The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact ontranscript accumulation through the nonsense-mediated mRNA decay pathway. Plant J 60:1031-1042


Schubert D, Lechtenberg B, Forsbach A, Gils M, Bahadur S, Schmidt R (2004) Silencing in Arabidopsis T-DNA Transformants: Thepredominant role of a gene-specific RNA sensing mechanism versus position effects. Plant Cell 16:2561-2572


Somers J, Pöyry T, Willis AE (2013) A perspective on mammalian upstream open reading frame function. Int J Biochem Cell Biol45:1690-1700


Takahashi H, Takahashi A, Naito S, Onouchi, H (2012) BAIUCAS: A novel BLAST-based algorithm for the identification of upstream openreading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome. Bioinformatics 28:2231-2241


Tanaka M, Sotta N, Yamazumi Y, Yamashita Y, Miwa K, Murota K, Chiba Y, Hirai MY, Akiyama T, Onouchi H, Naito S, Fujiwara T (2016)The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation. Plant Cell28:2830-2849


Thorvaldsdottir H, Robinson JT, Mesirov JP (2012) Integrative Genomics Viewer (IGV): High-performance genomics data visualizationand exploration. Briefings in Bioinformatics 14:178-192


Tran Vdu T, Souiai O, Romero-Barrios N, Crespi M, Gautheret D (2016) Detection of generic differential RNA processing events fromRNA-seq data. RNA Biol 13:59-67



http://www.ncbi.nlm.nih.gov/pubmed?term=Ribone PA%2C Capella M%2C Arce AL%2C Chan RL %282015a%29 What do we know about homeodomain%2Dleucine zipper I transcription factors%3F Functional and biotechnological considerations%2E In Plant Transcription Factors%3A Evolutionary%2C Structural and Functional Aspects %28Eds%3A Gonz�lez%2C DH%29 Elsevier%2C Amsterdam%2C The Netherlands%2C pP 343%2D356&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ribone PA, Capella M, Arce AL, Chan RL (2015a) What do we know about homeodomain-leucine zipper I transcription factors? Functional and biotechnological considerations. In Plant Transcription Factors: Evolutionary, Structural and Functional Aspects (Eds: Gonz�lez, DH) Elsevier, Amsterdam, The Netherlands, pP 343-356

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ribone&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=What do we know about homeodomain-leucine zipper I transcription factors? Functional and biotechnological considerations.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=What do we know about homeodomain-leucine zipper I transcription factors? Functional and biotechnological considerations.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ribone&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Ribone PA%2C Capella M%2C Chan%2C RL %282015b%29 Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development%2E J Exp Bot 66%3A5929%2D5943&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Ribone PA, Capella M, Chan, RL (2015b) Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development. J Exp Bot 66:5929-5943

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Ribone&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Ribone&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Rice P%2C Longden I%2C Bleasby A %282000%29 EMBOSS%3A the European Molecular Biology Open Software Suite%2E Trends Genet 16%3A276%2D277&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16:276-277

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Rice&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=EMBOSS: the European Molecular Biology Open Software Suite&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=EMBOSS: the European Molecular Biology Open Software Suite&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Rice&as_ylo=2000&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Romani F%2C Ribone PA%2C Capella M%2C Miguel VN%2C Chan RL %282015%29 A matter of quantity%3A common features in the drought response of transgenic plants overexpressing HD%2DZip I transcription factors%2E Plant Sci 251%3A139%2D154&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Romani F, Ribone PA, Capella M, Miguel VN, Chan RL (2015) A matter of quantity: common features in the drought response of transgenic plants overexpressing HD-Zip I transcription factors. Plant Sci 251:139-154

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Romani&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A matter of quantity: common features in the drought response of transgenic plants overexpressing HD-Zip I transcription factors&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A matter of quantity: common features in the drought response of transgenic plants overexpressing HD-Zip I transcription factors&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Romani&as_ylo=2015&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Sakuma S%2C Pourkheirandish M%2C Hensel G%2C Kumlehn J%2C Stein N%2C Tagiri A%2C Yamaji N%2C Ma JF%2C Sassa H%2C Koba T%2C et al%2E %282013%29 Divergence of expression pattern contributed to neofunctionalization of duplicated HD%2DZip I transcription factor in barley%2E New Phytol 197%3A939%2D948&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Sakuma S, Pourkheirandish M, Hensel G, Kumlehn J, Stein N, Tagiri A, Yamaji N, Ma JF, Sassa H, Koba T, et al. (2013) Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley. New Phytol 197:939-948

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Sakuma&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Divergence of expression pattern contributed to neofunctionalization of duplicated HD-Zip I transcription factor in barley&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Sakuma&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Saul H%2C Elharrar E%2C Gaash R%2C Eliaz D%2C Valenci M%2C Akua T%2C Avramov M%2C Frankel N%2C Berezin I%2C Gottlieb D%2C Elazar M%2C David%2DAssael O%2C Tcherkas V%2C Mizrachi K%2C Shaul O %282009%29 The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense%2Dmediated mRNA decay pathway%2E Plant J 60%3A1031%2D1042&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Saul H, Elharrar E, Gaash R, Eliaz D, Valenci M, Akua T, Avramov M, Frankel N, Berezin I, Gottlieb D, Elazar M, David-Assael O, Tcherkas V, Mizrachi K, Shaul O (2009) The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway. Plant J 60:1031-1042

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Saul&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The upstream open reading frame of the Arabidopsis AtMHX gene has a strong impact on transcript accumulation through the nonsense-mediated mRNA decay pathway&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Saul&as_ylo=2009&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Schubert D%2C Lechtenberg B%2C Forsbach A%2C Gils M%2C Bahadur S%2C Schmidt R %282004%29 Silencing in Arabidopsis T%2DDNA Transformants%3A The predominant role of a gene%2Dspecific RNA sensing mechanism versus position effects%2E Plant Cell 16%3A2561%2D2572&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Schubert D, Lechtenberg B, Forsbach A, Gils M, Bahadur S, Schmidt R (2004) Silencing in Arabidopsis T-DNA Transformants: The predominant role of a gene-specific RNA sensing mechanism versus position effects. Plant Cell 16:2561-2572

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Schubert&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Silencing in Arabidopsis T-DNA Transformants: The predominant role of a gene-specific RNA sensing mechanism versus position effects&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Silencing in Arabidopsis T-DNA Transformants: The predominant role of a gene-specific RNA sensing mechanism versus position effects&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Schubert&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Somers J%2C P�yry T%2C Willis AE %282013%29 A perspective on mammalian upstream open reading frame function%2E Int J Biochem Cell Biol 45%3A1690%2D1700&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Somers J, P�yry T, Willis AE (2013) A perspective on mammalian upstream open reading frame function. Int J Biochem Cell Biol 45:1690-1700

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Somers&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A perspective on mammalian upstream open reading frame function&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A perspective on mammalian upstream open reading frame function&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Somers&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Takahashi H%2C Takahashi A%2C Naito S%2C Onouchi%2C H %282012%29 BAIUCAS%3A A novel BLAST%2Dbased algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome%2E Bioinformatics 28%3A2231%2D2241&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Takahashi H, Takahashi A, Naito S, Onouchi, H (2012) BAIUCAS: A novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome. Bioinformatics 28:2231-2241

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Takahashi&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=BAIUCAS: A novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=BAIUCAS: A novel BLAST-based algorithm for the identification of upstream open reading frames with conserved amino acid sequences and its application to the Arabidopsis thaliana genome&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Takahashi&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tanaka M%2C Sotta N%2C Yamazumi Y%2C Yamashita Y%2C Miwa K%2C Murota K%2C Chiba Y%2C Hirai MY%2C Akiyama T%2C Onouchi H%2C Naito S%2C Fujiwara T %282016%29 The Minimum Open Reading Frame%2C AUG%2DStop%2C Induces Boron%2DDependent Ribosome Stalling and mRNA Degradation%2E Plant Cell 28%3A2830%2D2849&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tanaka M, Sotta N, Yamazumi Y, Yamashita Y, Miwa K, Murota K, Chiba Y, Hirai MY, Akiyama T, Onouchi H, Naito S, Fujiwara T (2016) The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation. Plant Cell 28:2830-2849

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tanaka&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tanaka&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Thorvaldsdottir H%2C Robinson JT%2C Mesirov JP %282012%29 Integrative Genomics Viewer %28IGV%29%3A High%2Dperformance genomics data visualization and exploration%2E Briefings in Bioinformatics 14%3A178%2D192&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Thorvaldsdottir H, Robinson JT, Mesirov JP (2012) Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration. Briefings in Bioinformatics 14:178-192

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Thorvaldsdottir&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Integrative Genomics Viewer (IGV): High-performance genomics data visualization and exploration&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Thorvaldsdottir&as_ylo=2012&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Tran Vdu T%2C Souiai O%2C Romero%2DBarrios N%2C Crespi M%2C Gautheret D %282016%29 Detection of generic differential RNA processing events from RNA%2Dseq data%2E RNA Biol 13%3A59%2D67&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Tran Vdu T, Souiai O, Romero-Barrios N, Crespi M, Gautheret D (2016) Detection of generic differential RNA processing events from RNA-seq data. RNA Biol 13:59-67

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Tran&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Detection of generic differential RNA processing events from RNA-seq data&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Detection of generic differential RNA processing events from RNA-seq data&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Tran&as_ylo=2016&as_allsubj=all&hl=en&c2coff=1


Uchiyama-Kadokura N, Murakami K, Takemoto M, Koyanagi N, Murota K, Naito S, Onouchi H (2014) Polyamine-responsive ribosomalarrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense-mediated mRNA decay inArabidopsis thaliana. Plant Cell Physiol 55:1556-1567


Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17:29-35Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

von Armin AG, Jia Q, Vaughn JN (2014) Regulation of plant translation by upstream open reading frames. Plant Sci 214:1-12Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title

Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, Gan X, Hajheidari M, Hay A, Smith RS, et al. (2014) Leaf shapeevolution through duplication, regulatory diversification, and loss of a homeobox gene. Science 343:780-783


Wang L, Wessler SR (1998) Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression ofthe maize R Gene. Plant Cell 10:1733-1746


Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering forstress tolerance. Planta 218:1-14


Wiese A, Elzinga N, Wobbes B, Smeekens S (2004) A conserved upstream open reading frame mediates sucrose-induced repression oftranslation. Plant Cell 16:1717-1729


Yang Z (1993) Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol BiolEvol 10:1396-1401


Zur H, Tuller T (2013) New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol 9:e1003136Pubmed: Author and TitleCrossRef: Author and TitleGoogle Scholar: Author Only Title Only Author and Title


http://www.ncbi.nlm.nih.gov/pubmed?term=Uchiyama%2DKadokura N%2C Murakami K%2C Takemoto M%2C Koyanagi N%2C Murota K%2C Naito S%2C Onouchi H %282014%29 Polyamine%2Dresponsive ribosomal arrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense%2Dmediated mRNA decay in Arabidopsis thaliana%2E Plant Cell Physiol 55%3A1556%2D1567&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Uchiyama-Kadokura N, Murakami K, Takemoto M, Koyanagi N, Murota K, Naito S, Onouchi H (2014) Polyamine-responsive ribosomal arrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense-mediated mRNA decay in Arabidopsis thaliana. Plant Cell Physiol 55:1556-1567

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Uchiyama-Kadokura&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Polyamine-responsive ribosomal arrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense-mediated mRNA decay in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Polyamine-responsive ribosomal arrest at the stop codon of an upstream open reading frame of the AdoMetDC1 gene triggers nonsense-mediated mRNA decay in Arabidopsis thaliana&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Uchiyama-Kadokura&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Vaucheret H%2C Fagard M %282001%29 Transcriptional gene silencing in plants%3A targets%2C inducers and regulators%2E Trends Genet 17%3A29%2D35&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Vaucheret H, Fagard M (2001) Transcriptional gene silencing in plants: targets, inducers and regulators. Trends Genet 17:29-35

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vaucheret&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Transcriptional gene silencing in plants: targets, inducers and regulators&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Transcriptional gene silencing in plants: targets, inducers and regulators&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vaucheret&as_ylo=2001&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=von Armin AG%2C Jia Q%2C Vaughn JN %282014%29 Regulation of plant translation by upstream open reading frames%2E Plant Sci 214%3A1%2D12&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=von Armin AG, Jia Q, Vaughn JN (2014) Regulation of plant translation by upstream open reading frames. Plant Sci 214:1-12

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=von&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Regulation of plant translation by upstream open reading frames&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Regulation of plant translation by upstream open reading frames&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=von&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Vlad D%2C Kierzkowski D%2C Rast MI%2C Vuolo F%2C Dello Ioio R%2C Galinha C%2C Gan X%2C Hajheidari M%2C Hay A%2C Smith RS%2C et al%2E %282014%29 Leaf shape evolution through duplication%2C regulatory diversification%2C and loss of a homeobox gene%2E Science 343%3A780%2D783&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Vlad D, Kierzkowski D, Rast MI, Vuolo F, Dello Ioio R, Galinha C, Gan X, Hajheidari M, Hay A, Smith RS, et al. (2014) Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene. Science 343:780-783

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Vlad&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Leaf shape evolution through duplication, regulatory diversification, and loss of a homeobox gene&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Vlad&as_ylo=2014&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wang L%2C Wessler SR %281998%29 Inefficient reinitiation is responsible for upstream open reading frame%2Dmediated translational repression of the maize R Gene%2E Plant Cell 10%3A1733%2D1746&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wang L, Wessler SR (1998) Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression of the maize R Gene. Plant Cell 10:1733-1746

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression of the maize R Gene&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Inefficient reinitiation is responsible for upstream open reading frame-mediated translational repression of the maize R Gene&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=1998&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wang W%2C Vinocur B%2C Altman A %282003%29 Plant responses to drought%2C salinity and extreme temperatures%3A towards genetic engineering for stress tolerance%2E Planta 218%3A1%2D14&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wang W, Vinocur B, Altman A (2003) Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta 218:1-14

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wang&as_ylo=2003&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Wiese A%2C Elzinga N%2C Wobbes B%2C Smeekens S %282004%29 A conserved upstream open reading frame mediates sucrose%2Dinduced repression of translation%2E Plant Cell 16%3A1717%2D1729&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Wiese A, Elzinga N, Wobbes B, Smeekens S (2004) A conserved upstream open reading frame mediates sucrose-induced repression of translation. Plant Cell 16:1717-1729

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Wiese&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=A conserved upstream open reading frame mediates sucrose-induced repression of translation&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=A conserved upstream open reading frame mediates sucrose-induced repression of translation&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Wiese&as_ylo=2004&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Yang Z %281993%29 Maximum%2Dlikelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites%2E Mol Biol Evol 10%3A1396%2D1401&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Yang Z (1993) Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 10:1396-1401

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Yang&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Yang&as_ylo=1993&as_allsubj=all&hl=en&c2coff=1

http://www.ncbi.nlm.nih.gov/pubmed?term=Zur H%2C Tuller T %282013%29 New universal rules of eukaryotic translation initiation fidelity%2E PLoS Comput Biol 9%3Ae1003136&dopt=abstract

http://search.crossref.org/?page=1&rows=2&q=Zur H, Tuller T (2013) New universal rules of eukaryotic translation initiation fidelity. PLoS Comput Biol 9:e1003136

http://scholar.google.com/scholar?as_q=&num=10&as_occt=any&as_sauthors=Zur&hl=en&c2coff=1

http://scholar.google.com/scholar?as_q=New universal rules of eukaryotic translation initiation fidelity.&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_publication=&as_yhi=&as_allsubj=all&hl=en&lr=&c2coff=1

http://scholar.google.com/scholar?as_q=New universal rules of eukaryotic translation initiation fidelity.&num=10&btnG=Search+Scholar&as_occt=any&as_sauthors=Zur&as_ylo=2013&as_allsubj=all&hl=en&c2coff=1


Documents

Short title: CPuORF33 represses AtHB1 translation Corresponding … · 2017. 9. 27. · 80 two-hybrid and in vitro pull-down assays (Capella et al., 2014). ... 90 when rdr6-12 mutant