Xiu-Jie Wang

Institute of Genetics and Developmental

Biology

Chinese Academy of Sciences

Computational Identification of Natural

Antisense Transcripts in Arabidopsis

thaliana

Natural antisense transcripts

(NATs)

• Two classes of NATs

cis-NATs

trans-NATs

• Commonly seen in prokaryotes

A

• Also exist broadly in eukaryotes

B

Cis-encoded antisense transcripts

• Sense and antisense transcripts originated from

the samethe same genomic locus but in opposite directions.

senseantisens

e

dsRNAdsRNA

Trans-encoded antisense transcripts

small trans-NATs (microRNA, siRNA, etc.) long trans-NATs

• A pair of overlapping transcripts originated from differentdifferent genomic loci.

antisense

sense

dsRNAdsRNA

NATs participate in many gene expression regulatory processes

• Transcription control

• RNA processing and transport

• RNA stability and translation

- eye development of mouse

- cancer cell proliferation

- plant stress responses

- other unknown functions

A. transcription exclusion

Sense gene

Antisense gene

B. genomic imprinting (Air RNA)

Sleutels et al., Nature, 415, 810-813.

The maternal imprinting of Igf2r, Slc22a2, Slc22a3 are maintained by antisense Air RNA.

Functions of NATs at transcriptional level

C. X-chromosome inactivation (Xist)

D. DNA methylation

Functions of NATs at transcriptional level

Functions of NATs at post-transcriptional level

• RNA processing and transport

alternative splicing

RNA editing

RNA interference

• RNA stability and translation

translation regulation

Prediction and analysis of Arabidopsis NATs

- cis-NATs

- trans-NATs

Prediction of Arabidopsis cis-NATs

1340 total cis-NAT pairs were predicted957 pairs have expression evidence for both

strandsWang et al. Genome Biol. (2005)

Most Arabidopsis cis-NAT pairs overlap at 3’ end

Wang et al. Genome Biol. (2005)

Most sense and antisense transcripts of the same cis-NAT pairs were expressed in different tissues

Wang et al. Genome Biol. (2005)

Function speculation of Arabidopsis cis-NATs

11 Arabidopsis cis-NAT pairs have siRNA evidence

• gene silencing by RNAi

• genomic imprinting

three of six Arabidopsis imprinted genes have cis-antisense transcripts

FIS2, FIE and FWA Wang et al. Genome Biol. (2005)

Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. (2005) Cell 1279-1291.

Some cis-NAT originated siRNAs are induced by stress

Conservation of Arabidopsis cis-NAT pairs in rice

Wang et al. Genome Biol. (2005)

Conclusions of cis-NATs

• Predicted 1340 putative cis-NAT pairs in Arabidopsis

• Expression evidence for both transcripts were found for 957 cis-NAT pairs

• Most cis-NAT pairs have tissue-specific expression profile

• The biological function of Arabidopsis cis-NATs includes RNA interference, genomic imprinting and gene regulation under certain conditions

- trans-NATs

Prediction and analysis of Arabidopsis NATs

- cis-NATs

Prediction of trans-NATs in Arabidopsis

High-coverage

100 nt

More than 90% of trans-NAT pairs are predicted to hybrid to each other basing on the results of RNA hybride program

Wang et al. Genome Biol. (2006)

Trans-NAT pairs tend to co-express in the same tissue

 ID

LibrariesCAF INF LEF ROF SIF API AP3 AGM INS ROS SAP SO4 S52 LES GSE CAS SIS

Pair A  At1g50020 0 18 6 1 0 12 22 1 17 0 0 0 0 0 73 0 0At1g04820 0 0 0 0 0 19 13 8 13 1 3 0 0 0 0 0 0

Pair B  At5g02370 0 0 0 0 0 36 15 20 16 0 56 1 19 29 21 28 39At3g09390 0 0 0 0 0 60 36 27 14 0 55 8 4 28 362 0 0

Sense transcript:

At3g23260F-box protein

Antisense transcript:

At3g21580Expressed protein

Wang et al. Genome Biol. (2006)

Functional Analysis of Trans-NATs

Wang et al. Genome Biol. (2006)

Over-represented gene families in trans-NAT pairs

Wang et al. Genome Biol. (2006)

Antisense networks of UDP-glucosyl transferase family genes

Some cis- and trans-NATs form complex regulatory networks

UDP transcripts involved in trans-NAT pairs

UDP transcripts involved in cis-NAT pairs UDP transcripts involved in cis- and trans- NAT pairs Transcripts from other protein families

Wang et al. Genome Biol. (2006)

Potential roles of Arabidopsis trans-NATs

• Induce gene silencing

- generate siRNAs

148 trans-NAT associated siRNAs were found

• Regulate alternative splicing

Alternative splicing rate

All annotated genes 11.59%

Trans-NAT pairs 19.76%

Conclusions of trans-NATs

• Identified 1320 putative trans-NAT pairs

• Trans-NATs tend to co-exist in the same tissue

• Transcripts from function classes with catalytic activity, signal transducer activity and transporter activities were slightly over-represented

• Cis- and trans- NATs could form complex regulatory networks

• Potential functions of trans-NATs include inducing gene silencing and regulate alternative splicing

Xiujie WangInvestigator, Group LeaderQi Zheng

Graduate student

Guanglin LiGraduate student

Huajun WuVisiting student

Yingtao ZhaoGraduate student Xudong Wu

Graduate student

Huan WangGraduate student

Guanzheng LuoGraduate student

Jun LiuVisiting student

Ying ChenVisiting student

Zhijun ZhenResearch asistant

Acknowledgments

IGDB, CAS

Ms. Huan Wang

The Rockefeller University

Prof. Terry Gaasterland

Prof. Nam-Hai Chua

National Natural Science Foundation of China