17-19 October 2018

REGULATORY CIRCUITS IN RNA BIOLOGY

vIenna

bIologyrna

RNA ProcessingRNA Turnover Regulatory RNARNA Networks

Vienna Biocenter · IMP Lecture HallCampus-Vienna-Biocenter 1 · A-1030 Vienna

Organizers: Michael Jantsch, head of SFB RNA-REG Andrea Barta, head of DK RNA Biology

www.vienna-rna-meeting.at

Meeting coordinators: Christine Hatwieger-Ertl, SFB RNA-REG

Zahra Ayatollahi, DK RNA Biology SFB RNA-REG and DK RNA Biology are funded by:

Meeting sponsors:

Special thanks to the IMP, in particular Manuela Steurer, to the IMP/IMBA Graphics Department & to the Cafeteria Team.

Vienna RNA Meeting 2018 RNA-REG: Regulatory Circuits in RNA Biology

IMP Lecture Hall, Vienna Biocenter Campus-Vienna-Biocenter 1, 1030 Vienna, Austria

WEDNESDAY, 17th OCTOBER 2018 12:00 - 13:45 Registration (IMP Foyer) & Poster set-up (IMBA/GMI Atrium) 13:45 Welcome & introduction Session 1: RNA synthesis (Chair: Renée Schroeder) 14:00 - 14:30 Patrick Cramer (MPI for Biophysical Chemistry, Göttingen) Mechanisms to regulate mRNA synthesis 14:30 - 15:00 Torben Heick Jensen (Aarhus University) Balancing RNA levels 15:00 - 15:20 Renée Schroeder (MFPL, Vienna Biocenter) Riboregulation of transcription 15:20 - 15:40 Vanja Haberle (group Stark, IMP, Vienna Biocenter) Transcriptional cofactors display core promoter class-specificity 15:40 - 16:10 Coffee break Session 2: tRNAs (Chair: Walter Rossmanith) 16:10 - 16:40 Eric Westhof (University of Strasbourg)

tRNA modifications and control over translation 16:40 - 17:10 Stewart Shuman (Sloan Kettering Institute, New York)

Structures and mechanisms of tRNA splicing enzymes 17:10 - 17:30 Javier Martinez (MFPL, Vienna Biocenter)

Discovery of a unique 2’, 3’-cyclic phosphatase in human cells 17:30 - 17:50 Matthias Schäfer (Medical University of Vienna)

tRNA-derived small RNAs: Acting alone or through protein association?

18:00 - 21:45 Poster session & Buffet dinner at the IMBA/GMI Atrium

THURSDAY, 18th OCTOBER 2018 Session 3: RNA processing (Chair: Andrea Barta) 09:00 - 09:30 Reinhard Lührmann (MPI for Biophysical Chemistry, Göttingen)

Novel mechanistic insights into the inner workings of the spliceosome by combined biochemical and Cryo-EM studies

09:30 - 10:00 Benjamin Blencowe (University of Toronto)

Systematic characterization of alternative splicing regulatory networks 10:00 - 10:20 Konstantin Licht (group Jantsch, Medical University of Vienna)

A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing

10:20 - 10:50 Coffee break 10:50 - 11:20 Mihaela Zavolan (University of Basel)

Transcriptome-wide interference of translation parameters in eukaryotic cells

11:20 - 11:40 Stefan Ameres (IMBA, Vienna Biocenter)

Dissecting gene-regulatory mechanisms by time-resolved RNA sequencing

11:40 - 12:10 Sebastian Falk (MPI of Biochemistry, Martinsried/Munich)

Structural and functional insights into the nuclear RNA Exosome 12:10 - 12:30 Sebastian Will (group Hofacker, TBI, University of Vienna)

Detection and rational design of RNA switches 12:30 - 14:00 Lunch (IMP Cafeteria) & Posters (IMBA/GMI Atrium)

Session 4: Translation (Chair: Isabella Moll) 14:00 - 14:30 Nenad Ban (ETH Zurich)

Protein synthesis: from ribosome assembly to targeting of membrane proteins

14:30 - 15:00 Marina Rodnina (MPI for Biophysical Chemistry, Göttingen)

Ribosome dynamics during mRNA recoding 15:00 - 15:20 Andrea Pauli (IMP, Vienna Biocenter)

Small proteins with big roles – Bouncer is necessary and sufficient for species-specific fertilization

15:20 - 15:40 Tanino Albanese (group Moll, MFPL, Vienna Biocenter)

Unconventional regulatory circuits in bacteria: from endonucleases cleavage to protein splicing

15:40 - 16:10 Coffee break Session 5: RNA turnover (Chair: Pavel Kovarik) 16:10 - 16:40 Elena Conti (MPI of Biochemistry, Martinsried/Munich)

Mechanistic studies of polyA-tail control 16:40 - 17:10 Narry Kim (Seoul National University)

RNA tails come in more than one flavor 17:10 - 17:40 Antonio Giraldez (Yale University, New Haven)

Deciphering the regulatory code shaping mRNA stability and translation during embryogenesis

17:40 - 18:00 Lucy Sneezum (group Kovarik, MFPL, Vienna Biocenter)

Phsyiology and mechanism of interleukin-1 signalling regulation by Tristetraprolin

Free evening/ Speakers’ dinner

FRIDAY, 19th OCTOBER 2018 Session 6: Regulatory RNAs (Chair: Michael Nodine) 09:00 - 09:30 David Bartel (MIT, Cambridge, USA)

MicroRNAs and other regulatory RNAs 09:30 - 10:00 Yukihide Tomari (University of Tokyo)

Biochemical and biophysical dissection of RNA silencing 10:00 - 10:20 Peter R. Andersen (group Brennecke, IMBA, Vienna Biocenter)

A dedicated RNA export pathway facilitates piRNA production in Drosophila

10:20 - 10:40 Luisa Cochella (IMBA, Vienna Biocenter)

Roles of miRNAs in animal development: lessons from C. elegans 10:40 - 11:10 Coffee break 11:10 - 11:30 Ranjith Papareddy (group Nodine, GMI, Vienna Biocenter)

Small RNA regulation of DNA methylation dynamics during early plant embryogenesis

11:30 - 12:00 Ben Luisi (University of Cambridge, UK)

The versatile machinery of bacterial riboregulation 12:00 - 12:20 Boris Görke (MFPL, Vienna Biocenter)

Post-transcriptional control of cell envelope biosynthesis in Escherichia coli

12:20 - 12:40 Elisabeth Sonnleitner (MFPL, Vienna Biocenter)

Harnessing RNA based metabolic regulation to increase the antibiotic susceptibility of Pseudomonas aeruginosa

12:40 - 14:10 Lunch (IMP Cafeteria) & Posters (IMBA/GMI Attrium)

Session 7: RNA modifications (Chair: Michael Jantsch) 14:10 - 14:40 Ann Ehrenhofer-Murray (Humboldt University of Berlin)

Queuine links translational control in eukaryotes to a micronutrient from bacteria

14:40 - 15:10 Samie Jaffrey (Cornell University, New York)

The dynamic epitranscriptome: Control of mRNA fate and function by internal and cap-associated RNA modifications

15:10 - 15:40 Coffee break 15:40 - 16:10 Rupert Fray (University of Nottingham)

Writing and consequences of methylation marks in the model plant Arabidopsis thaliana

16:10 - 16:40 Mark Helm (Johannes Gutenberg-University of Mainz)

Fast profiling of modification content and composition of total tRNA 16:40 Concluding remarks 18:30 Conference Dinner at MARX Restauration/Palast Address: Maria-Jacobi-Gasse 2 (3 min walk from the lecture hall)

Vienna RNA Meeting 2018 RNA-REG: Regulatory Circuits in RNA Biology

Posters

Poster session location: IMBA/GMI Atrium (accessible via the IMP Foyer)

# Poster presenter

Poster title

#1 Britt Ardal Box C/D snoRNP autoregulation by a cis-acting snoRNA in the NOP56 pre-mRNA

#2 Maria Gockert Analysis of the transcriptome upon rapid depletion of RNA turnover factors

#3 Laura Arribas-Hernandez New insights into the mechanisms and functions of the m6A-YTH module: lessons to learn from plants

#4 Nikolaos Balatsos An alternative splice variant of Poly(A)-specific ribonuclease in lung cancer

#5 Bodhisattwa Banerjee Transcriptomic profiling of novel lncRNAs in specific regions of hypoxic zebrafish brain: Predictive role in neurodegenerative diseases

#6 Livia Caizzi Global two-step RNA splicing kinetics in human cells

#7 Tom Dendooven Architectural principles for Hfq/Crc-mediated regulation of gene expression

#8 Philipp Dexheimer Dissecting the essential requirements for microRNAs in embryonic development of Caenorhabditis elegans

#9 Laura Diaz Saez Targeting RNA metabolism in cancer and immunology: Adenosine deaminases

#10 Svetlana Durica-Mitic Molecular characterization of an adaptor protein for a major endoribonuclease in Escherichia coli

#11 Muna Ayesha Khan The mechanism of glucosamine-6-phosphate sensing by the small RNA GlmY/GlmZ cascade in Escherichia coli

#12 Alexandra Schilder Role of small RNA 5´-phosphorylation status for target RNA decay in Escherichia coli

#13 Florian Sikroa Regulation of ptsN expression and its effect on TCA cycle flux in Escherichia coli

#14 Marc R. Friedländer miRTrace reveals the organismal origins of microRNA sequencing data

#15 Marcel Tabier Causes and putative functions of gene expression covariances in single mammalian cells #16 Bastian Fromm The metazoan microRNA complement

#17 Mattia Furlan Transcriptional and post-transcriptional dynamics from total RNA-seq datasets #18 Boris Fürtig Ribosome induced riboswitch structure melting #19 Elena Galimberti mRNA regulation during ES cell differentiation

#20 Antoni Gañez Zapater SWI/SNF subunits Brg1 and Brm affect alternative splicing by regulating the recruitment of splicing associated factors

#21 Catherine Goh Phenovault: An open-access resource for RNAi and CRISPR screening data

#22 Marion Goldeck The RNA 3'-terminal phosphate cyclase RTCA generates 2', 3'-cyclic phosphate substrates for the human tRNA ligase complex in vitro #23 Paola Pinto Discovery of a unique 2’, 3’-cyclic phosphatase in human cells #24 Joao Guimaraes A rare codon-based translational program drives cell proliferation

#25 Ileana Guzzetti A structural and functional investigation of microRNA-34a and the Notch targetome #26 Utkarsh Kapoor Global Interplay of A-to-I RNA Editing & pre-mRNA Splicing #27 Svetlana Lebedeva Long non-coding RNAs in neuronal differentiation

#28 Stefan Lutzmayer Small interfering RNA dynamics and functions during Arabidopsis embryogenesis

#29 Alexandra Plotnikova MicroRNA-mediated repression of transcription factors is required for embryo morphogenesis in Arabidopsis

#30 Christian Müller The RNA-Ligase RtcB and Motility in Escherichia coli

#31 Sowndarya Muthukumar Assembly and regulation of the human decapping machinery: insights from biochemical reconstitution

#32 Danny Nedialkova An improved workflow for quantitative tRNA transcriptomics

#33 Jonas Nørskov Søndergaard Identifying functional long noncoding RNAs in hepatocellular carcinoma

#34 Vera Oberbauer tRNA-derived small RNAs: How to find protein binding partners?

#35 Vladimir Ovchinnikov

Extracellular vesicles transported microRNAs of F. hepatica and S. mansoni: potential mechanisms of host–parasite intercellular communication

#36 Emanuele Parisi BioSeq-Zip: a tool for collapsing recurrent reads in high throughput sequencing datasets

#37 Gianvito Urgese isomiR-SEA: miRNA and isomiR expression level detection from RNA-Seq datasets

#38 Petra Pusic CrcZ RNA cross-regulates Hfq-mediated oprD repression and leads to increased susceptibility to carbapenems

#39 Jaclyn Quin Changes in levels of A-to-I RNA editing in the Fulani, an ethnic group less susceptible to malaria #40 Jiří Sedmík Activation of innate immunity by mitochondrial dsRNA in p53-/- cell lines #41 Veronika Rajecka RNA demethylase FTO influences nuclear pre-mRNA processing events

#42 Nandan Varadarajan Examining factors mediating oligo uridylation and degradation of Eukaryotic aberrant RNAs

#43 Marlene Reichel Global identification of RNA-binding proteins in Arabidopsis using mRNA interactome capture #44 Aldema Sas-Chen Systematic dissection of snoRNA mediated RNA modifications

#45 Jakob Schnabl A nuclear RNA export factor variant licenses piRNA-guided heterochromatin formation

#46 Sabrina Summer The human homolog of a bacterial endonuclease is essential for mitochondrial gene expression

#47 Henry Fabian Thomas Activation of the Fgf5 enhancer cluster during mouse embryonic stem cell differentiation

#48 Elisa Vilardo Characterization of the human TRM10 family of tRNA methyltransferases

#49 Sung-Hui Yi Characterization of eIF3 binding to mRNA-implications for global translation initiation #50 Xiangfu Zhong Mining miRBase: what's in a miRBase entry?

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