RNA Retreat 2017

20 – 22 April 2017

DK RNA Biology SFB RNA Reg

Hotel Resort Kothmühle

Kothmühle 1, 3364 Neuhofen an der Ybbs Tel.: +43 7475 52112 www.kothmuehle.at

Day1

THURSDAY, 20th April 2017 09:30 Departure from Vienna Biocenter Bus (company Dr.Richard) at corner of Viehmarktgasse/Dr.-Bohr-Gasse 12:00 LUNCH at Kothmühle Hotel Restaurant 13:00 Welcome in Seminar Room “Dorschbirne+Landbirne” Chair: Andrea Barta

13:10 Martin Leeb (MFPL) Dissecting the genetic complexity of embryonic stem cell differentiation

13:40 Mamduh A. Zabidi (group Stark) Enhancer-responsiveness and -specificity of core promoters in gene

transcription

14:00 Luis Paulis Paz (group Von Haeseler) Modeling the read count distribution of RNA-sequencing

14:20 Andrea Tanzer (group Hofacker) RNALands: Novel approaches towards coarse-grained RNA folding

kinetics

14:40 Aleksandra Plotnikova (group Nodine) Characterization of microRNA-mediated cleavage events in Arabidopsis

embryos

15:00 BREAK + ROOM CHECK IN

Chair: Michael Jantsch

15:40 Manfred Ogris (Center for Pharmaceutical Sciences, Uni Wien) Nucleic acid based therapeutics: synthetic delivery systems and in vivo

bioimaging

16:10 Julia Batki (group Brennecke) A nuclear export factor (Nxf) variant is required for small RNA-guided

transcriptional silencing of transposable elements in Drosophila melanogaster

16:30 Brian Reichholf (group Ameres) Dissecting intracellular kinetics of miRNA biogenesis and turnover

16:50 Philipp Dexheimer (group Cochella) Two miRNAs are sufficient for morphologically-normal embryogenesis of

C. elegans

17:10 Poster Teaser Talks for Poster Session I 18:10 Hang up posters

18:30 DINNER at hotel restaurant 20: 00 Poster Session I Discussions & Socialising

Day2

FRIDAY, 21st April 2017

Chair: Renée Schroeder

09:00 Alexandra Lusser (Medical University of Innsbruck) 5-methylcytosine as an epitranscriptomic mark on murine mRNA

09:30 Elisa Vilardo (group Rossmanith) Understanding position-9 methylation of nucleocytosolic tRNAs

09:50 Aleksej Drino (group Schäfer) Identification of protein-tRNA fragment interactions

10:10 Prajakta Bajad (group Jantsch) Deciphering the molecular consequences of ADAR1 deficiency

10:30 BREAK

Chair: Boris Görke

11:00 Hanna Engelberg-Kulka (Hebrew University of Jerusalem) A stress-induced hidden secret of the genetic code

11:30 Heather Beck (group Moll) Ribosomal recognition of leaderless mRNA in Escherichia coli

11:50 Nadia Sedlyarova (group Schroeder) Rethinking the concept of RNA-based thermosensing in bacteria

12:10 Elisabeth Sonnleitner (group Bläsi) How to choose the right food - dissecting the interaction between the

catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa

12:30 LUNCH

Chair: Julius Brennecke

14:00 David Ish-Horowicz (UCL London & Oxford University) Regulated mRNA stability and the termination of Drosophila neurogenesis 14:30 Poster Teaser Talks for Poster Session II

15:20 BREAK

15:30 Poster Session II & project discussions with Drinks & Snacks

17:00 Faculty Meeting (2 h)

19:00 “Mostverkostung” + Dinner Socializing at “Retrobar” & “Kegeln”

Day3

SATURDAY, 22nd April 2017 Until 09:00 Room check-out! Chair: Luisa Cochella

09:00 Karel Riha (CEITEC, Brno) Refining the role of nonsense mediated RNA decay in translation and

transcriptome regulation in Arabidopsis

09:30 Igor Asanovic (group Martinez) Characterization of PYROXD1 and its involvement in the redox-regulation

of the tRNA splicing 09:50 Svetlana Durica-Mitic (group Görke) Structural and functional characterization of an adaptor protein for a major

endoribonuclease in Escherichia coli 10:10 Florian Ebner (group Kovarik) The RNA-binding protein tristetraprolin schedules Mcl1-controlled

apoptosis of pathogen-engaged neutrophils during bacterial infection 10:30 Christa Schleper (Dept. Ecogenomics & Systemsbiology, Uni Wien) CRISPR Systems and their Application in Archaea 11:15 Bus 1 leaving (before lunch, with lunch packs/sandwiches) 12:45 Bus 2 leaving (after lunch at Hotel Restaurant)

PostersI

Poster Session I Thursday 20th April 2017

#1 Petra Pusic (group Bläsi): Competition for Hfq by CrcZ cross-regulates Hfq-dependent physiological processes unrelated to

carbon metabolism

#2 Marlena Rozner (group Bläsi): Capturing the dynamics of carbon catabolite repression and the regulatory impact of Hfq/CrcZ during diauxic growth in Pseudomonas aeruginosa

#3 Mostafa ElMaghraby (group Brennecke): Hijacking nuclear RNA export: a dedicated export pathway for piRNA precursors in Drosophila

#4 Jakob Schnabl (group Brennecke): Genetic and mechanistic diversity of piRNA 3' end formation

#5 Merrit Romeike (group Bücker): Mapping heterogeneity in the exit from naive pluripotency

#6 Yvonne Göpel (group Görke): Identification of adapter proteins for global endoribonucleases in Escherichia coli

#7 Muna Ayesha Khan (group Görke): A hunt for the sensor of metabolite Glucosamine-6-phosphate within the sRNA GlmY/GlmZ cascade in E. coli

#8 Markus Mörk-Mörkenstein (group Görke): Modulation of histidine kinase activity by interaction with an accessory protein in Escherichia coli

#9 Mariam Farman (group Hofacker): Interspecies coexpression networks

#10 Veerendra Gadekar (group Hofacker): Identification of functional antisense lncRNAs in plant genomes

#11 Roman Ochsenreiter (group Hofacker): Detecting ncRNAs across all viral domains

#12 Christina Wagner (group Hofacker): Modelling transcriptional elongation

#13 Maria Waldl (group Hofacker): Conservation in RNA folding trajectories

#14 Sebastian Will (group Hofacker): RNA alignment and folding variations in and around the LocARNA package

#15 Utkarsh Kapoor (group Jantsch): Global interplay of A-to-I RNA editing & pre-mRNA splicing

#16 Philipp Czermak (group Jantsch): Spatio-temporal profiling of Filamin B RNA-editing in mouse

#17 Masa Ivin (group Kovarik): Inflammation-associated mRNA-decay is a key determinant of host resistance and resilience against bacterial pneumonia

#18 Lucy Sneezum (group Kovarik): Physiology and mechanism of interleukin-1 regulation by RNA-binding protein tristetraprolin

#19 Elena Galimberti (group Leeb): Role of nonsense-mediated mRNA decay in the exit from pluripotency

PostersII

Poster Session II Friday 21th April 2017

#20 Dhaarsini Koneswarakantha (group Martinez): Redox regulation of the mammalian tRNA ligase complex

#21 Paola Pinto (group Martinez): Identification of a novel mammalian RNA 2’,3’ cyclic phosphatase

#22 Christan Müller (group Moll): The RNA ligase RtcB in Escherichia coli

#23 Mykola Roiuk (group Moll): Ribosome profiling as a tool to analyze the MazF-mediated stress response

#24 Manon Thomet (group Moll): 16S rRNA methylations and stress response

#25 Stefan Lutzmayer (group Nodine): siRNAs regulate protein-coding genes in Arabidopsis embryogenesis

#26 Michael Schon (group Nodine): Bookend: novel transcript discovery through end-guided transcriptome reconstruction

#27 Luis Enrique Cabrera Quio (group Pauli): What is the role of uORFs during the maternal-to-zygotic transition?

#28 Jessica Stock (group Pauli): Characterizing the role of toddler during zebrafish embryogenesis

#29 Sabrina Summer (group Rossmanith): Characterisation of human YBEY, a potential new player in mitochondrial ribosomal RNA metabolism

#30 Bianca Genenncher (group Schäfer): Is there a link between (cytosine-5) tRNA methylation and TE silencing?

#31 Cynthia Wollner (group Schäfer): Tissue-specific mapping of the NSUN6-mediated RNA methylome using miCLiP and RNA-BisSeq in Drosophila melanogaster

#32 Andrés Magan Garcia (group Schroeder): Interfering with antisense transcription: the role of RNA polymerase-binding RNA aptamers in transcriptional interference

#33 Milica Krunic (group Von Haeseler): Gene expression profile of osteoarthritis affected fingers

#34 Celine Prakash (group Von Haeseler): Modelling transcript fragmentation to understand RNA-Seq gene coverage

#35 Florian Pflug (group Von Haeseler): Correcting for unobserved molecules in quantitative NGS experiments

#36 Isabelle Zink (group Schleper): Silencing of essential genes via a type III CRISPR system in the hyperthermophilic Archaeon Sulfolobus solfataricus

#37 Benedikt Hagen (group Indik): A novel GFP-based reporter for the detection of cis-acting RNA export elements

#38 Stan Indik (group Indik): Rate of DNA polymerization during reverse transcription governs APOBEC3G-mediated G-to-A mutagenesis of retroviruses