On the occasion of the final “RNA BIOLOGY FOREVER Vienna Conference 2021” Andrea Barta talks about the doctoral program (DK) in “RNA Biology” which she led since 2007.
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September 28-29, 2021
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In collaboration with Open Science (https://www.openscience.or.at) and the FH Campus Vienna (https://www.fh-campuswien.ac.at/en/de), the doctoral school in RNA biology made a great video about vaccines against SARS-CoV-2 (in German). ((more…))
Congratulations to Aleksej Drino from Matthias Schäfer Group at the Medical University of Vienna, Center for Anatomy & Cell Biology for successfully defending his PhD thesis “Biochemical identification of protein-tRNA fragment interactions” on March 5th!
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New Publication by Andrea Barta together with Ezequiel Petrillo and Maria Kalyna in Nucleic Acids Research
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„Microsymposium on Small RNA Biology“ organized by IMBA, IMP, GMI and the Max Perutz Labs as well as by the RNA community of the Vienna BioCenter.
Abstract deadline: March 11th 2021
Registration deadline: April 12th 2021
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Congratulations to Philipp Dexheimer from the Cochella lab at IMP for successfully defending his PhD thesis “miRNA requirements in C. elegans embryogenesis” on Jan 19th! ((more…))
Julia Batki, PhD, alumna from Julius Brennecke’s lab at IMBA and former DK RNA Biology associated PhD student, is awarded the Denise P. Barlow Award 2019. ((more…))
A new method developed by researchers of the Vienna BioCenter, SARSeq, will allow testing of thousands of samples for SARS-CoV-2 and other pathogens in just 15 to 24 hours. ((more…))
Scientists from the Vienna BioCenter developed a new SARS-CoV-2 detection method: by rather simple means, their RT-LAMP test is cheaper than PCR testing and achieves results with comparable sensitivity and specificity. ((more…))
The 2020 Nobel Prize for Chemistry is awarded to Emmanuelle Charpentier and Jennifer Doudna for their groundbreaking discoveries on the CRISPR/Cas9 system. Emmanuelle Charpentier was a principal investigator at the Max Perutz Labs (University of Vienna) from 2002 to 2009 and Faculty Member of our doctoral program DK RNA Biology from 2007 to 2010. ((more…))
Congratulations to Stefan Ameres for his promotion to hold a full professorship in RNA Biology at the University of Vienna at the Max Perutz Labs! ((more…))
Congratultions to Raphael Manzenreither from the Ameres Lab (IMBA) for successfully defending his PhD thesis “A central role of the terminal RNA uridylation-mediated processing complex in cytoplasmic RNA quality control and antiviral RNA interference in Drosophila” yesterday! ((more…))
Scientists led by Javier Martinez from the Max Perutz Labs, a joint venture of the Medical University of Vienna and the University of Vienna, have identified a unique chemical reaction at the end of RNA molecules for the first time in human cells. Their findings are now published in “Science”. ((more…))
The new FWF-funded Special Research Program (SFB) RNA-DECO presents itself in its brand-new website: www.rna-deco.org
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Congratulations to Pooja Bhat from the Ameres lab (IMBA) for successfully defending her PhD Defense “Dissecting gene expression dynamics during maternal to zygotic transition in Zebrafish” today! ((more…))
Congratulations to Lucy Sneezum from the Kovarik Lab (Max Perutz Labs, UniWien) for successfully defending her PhD thesis “Context-dependent regulation of immune homeostasis by TTP” yesterday! ((more…))
Congratulations to Sabrina Summer from the Rossmanith Lab (MedUni Vienna) for successfully defending her PhD thesis “YBEY is an essential biogenesis factor for mitochondrial ribosomes” today! ((more…))
It is our pleasure to host Prof. Giovanni Capranico from the University of Bologna for an invited seminar about genome instability induced by G-quadruplex binders on 20 May 2020, 11:00 a.m.
Due to the current situation, the seminar will be held as virtual seminar online. ((more…))
Congratulations to Noémi Mészáros, previously in the Köhler at the Max Perutz Labs, for successfully defending her PhD thesis “A direct link between the nuclear basket and the nuclear envelope” today! ((more…))
RNA researchers Stefan Ameres and Julius Brennecke, both at IMBA and participating in the Vienna COVID-19 Diagnostics Initiative (VCDI), explain for the general German-speaking public the different SARS-CoV-2 testing possibilities in a podcast of the Austrian Academy of Sciences (ÖAW). ((more…))
From this month until further notice our RNA community is continuing its internal regular seminars virtually as interactive online seminars. Members of the RNA community & associates will received the details of each virtual seminars by email.
The acceleration of the CRISPR/Cas technology and all its potential applications have created a media hype that the general public is confronted with. ((more…))
Boris Görke and his group at the Max Perutz Labs Vienna have revealed the mechanisms of a multifunctional sRNA‐binding protein that dynamically regulates the synthesis of an important precursor of the bacterial cell envelope. Their finidings are now published in the EMBO Journal: ((more…))
Congratulations to Stefan Ameres at IMBA for receiving the prestigious European Research Council (ERC) Consolidator Grant worth 2 million Euros! It’s the third ERC grant for Stefan Ameres after having been awarded the ERC Starting Grant in 2013 and the ERC Proof of Concept Grant in 2018. ((more…))
A consortium of RNA researchers led by Michael Jantsch (MedUni Vienna) has been awarded one of the prestigious Special Research Program grants (SFB) of the Austrian Science Fund (FWF): “RNA-DECO – decorating RNA for a purpose” ((more…))
Jürgen Knoblich, scientific director of IMBA, gave an intriguing talk yesterday in the frame of the “Wiener Vorlesungen” about recent innovations in biotechnology and their potential to revolutionize basic biomedical research. Our CRISPR/Cas interactive station was also part of the event and could be visited by participants before and after the lecture. ((more…))
Congratulations to Florian Pflug from the von Haeseler group, who successfully defended his PhD thesis “Correctly counting molecules using unique molecular identifiers” today! ((more…))
The video of our stand at the European Researchers’ Night 2019 is out: Watch our vividly visited station featuring our CRISPR Game, developed by our Doctoral Program in RNA Biology and Open Science. ((more…))
Everyone is invited to join our next guest seminar by
Ashish Lal (NIH NCI Center for Cancer Research):
To be or not to be long noncoding RNA ((more…))
Renée Schroeder’s webinar on Genome Editing, held on 23 October 2019, is now publicly available as an online-video: https://youtu.be/6mrfzx5m8EQ. ((more…))
Congratulations to Chiara Alberti (Cochella Lab, IMP) and Madalena Pinto (Ameres Lab, IMBA) for winning two of the five VBC PhD Awards 2018/2019! ((more…))
We are happy to announce the next dates and speakers of the RNA Lecture Series for WS2019/2020. Everyone is welcome: ((more…))
We’re absolutely proud of yesterday’s webinar, with more than 125 attendees, by Renée Schroeder on the topic of genome editing with all its backgrounds and its implications. ((more…))
We’ve been on tour! After the premier of our hands-on station on CRISPR/Cas together with Open Science at the European Researchers’ Night 2019, last weekend we did some science outreach in Graz for two whole days! ((more…))
After her PhD graduation earlier this year, now Julia Batki from the Brennecke Lab at IMBA was awarded the Kirsten Peter Rabitsch Award 2019 for being this year’s most promising PhD alumna from the IMP or IMBA. Congratulations to Julia! ((more…))
Our RNA Lecture Series for the winter semester 2019/2020 is starting this Friday with lectures by these two successful RNA scientists:
11. October 2019:
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New findings just published by the Schroeder lab on how RNA elements regulate bacterial antisense transcription in cis:
iRAPs curb antisense transcription in E. coli. ((more…))
Congratulations to Utkarsh Kapoor from the M. Jantsch Lab (MedUni Vienna): On Thursday 26 September he successfully defended his PhD thesis “Global Interplay of A-to-I RNA editing & pre-mRNA Splicing“! ((more…))
Our Doctoral Program DK RNA Biology at the Max Perutz Labs has teamed up with Open Science for the European Researchers’ Night on Friday 27 September 2019 to bring the topic of CRISPR/Cas closer to the general public. ((more…))
You are invited to our guest seminar by Heather A. Hundley (Indiana University School pf Medicine):
“Regulation and Impacts of RNA Editing on the Neural Transcriptome“: ((more…))
Congratulations to Svetlana Durica-Mitic from the Görke Lab (Max Perutz Labs) for successfully defending her PhD thesis “Molecular and functional characterization of RNase E adaptor protein RapZ in Escherichia coli” yesterday! ((more…))
Congratulations to the M. Jantsch Lab (MedUni Vienna) on their recent findings on the cotranscriptional regulation between RNA editing and mRNA splicing, published this week in Genome Research: ((more…))
Two new papers from the Brennecke Lab (IMBA), published last week in Cell and in Nature Structural & Molecular Biology, describe “adaptive radiation” of RNA export proteins. ((more…))
The Ameres Lab (IMBA) revealed a comprehensive & quantitative view on the timescales and molecular features of miRNA biogenesis, loading, and turnover in living cells by employing the innovative transcriptomics method SLAMseq on small RNAs. Their work has just been published in Molecular Cell! Congratulation! ((more…))
You are invited to our guest seminar by Prof. Elena Evguenieva-Hackenberg (University Giessen):
“Functions in trans of trp attenuator sRNA and leader peptide” ((more…))
Congratulation to Brian Reichholf from the Ameres Lab at IMBA for successfully defending his PhD thesis “Dissecting the kinetics of microRNA biogenesis and turnover in living cells” today! ((more…))
Research Group: J. Martinez
Email: ameya.khandekar(at)meduniwien.ac.at
Research Group: L. Cochella
Email: paula.gutierrezperez(at)imp.ac.at
Research Group: J. Brennecke
Email: lisa.baumgartner(at)imba.oeaw.ac.at
Research Group: J. Brennecke
Email: veselin.andreev(at)imba.oeaw.ac.at
Research Group: Ivo Hofacker
Email: roman.ochsenreiter(at)univie.ac.at
Research Group: Ivo Hofacker
Email: thiel(at)tbi.ac.at
Congratulation to Poala Pinto from the Martinez Group at the Max Perutz Labs for successfully defending her PhD thesis on “Identification of ANGEL as a novel and unique eukaryotic family of RNA 2’,3’-cyclic phosphatases” today! ((more…))
Congratulations to Prajakta Bajad from the M. Jantsch Lab at the MedUni Vienna: Today she successfully defended her PhD Thesis “Understanding the phenotype of ADAR1 deficient mice“! ((more…))
Congratulation to Andrés Magan Garcia from the Schroeder Lab at the Max Perutz Labs for impressively defending his PhD thesis “The role of RNA polymerase-binding RNA aptamers in Escherichia coli transcription” today! ((more…))
Congratulations to Muna Ayesha Khan from the Görke Lab a the Max Perutz Labs for her successful PhD Defense today on “Signal perception and transduction within the GlmY/GlmZ small RNA cascade in Escherichia coli“. ((more…))
Congrats to Stefan Lutzmayer from the Nodine Lab at the GMI for successfully defending his PhD Thesis entitled “Small interfering RNA dynamics and functions during Arabidopsis embryogenesis” today! ((more…))
Open Science held its first pilot workshops on genome editing this week in schools in Vienna. Guided by a professional visual facilitator, students discussed and dealt with the ethical and social aspects of genome editing with creative methods. This project is part of a public outreach project with our doctoral program in RNA biology. ((more…))
Congratulations to Chiara Alberti from the Cochella Lab at the IMP for successfully defending her PhD Thesis entitled “Dissecting the contribution of microRNAs to nervous system development and function in C. elegans“ today! ((more…))
Congratulations to Julia Batki from the Brennecke Lab at IMBA for successfully defending her PhD thesis “Nuclear small RNA-guided silencing of transposable elements in Drosophila melanogaster” on Fri, 8th March 2019! ((more…))
The Microsymposium on Small RNA was founded over a decade ago as the major small RNA meeting in Europe, and since recent years is featuring exciting research also from broader RNA fields as well. The 14th Microsymposiums takes place 15th – 17th May 2019 at the Vienna BioCenter: see here. ((more…))
Next Monday, 25th February 2019, at 9:30 in VBC5 Seminar Room A: ((more…))
You are cordially invited to the seminar by our guest speaker: ((more…))
Research Group: A. Stark
Email: oliver.hendy(at)imp.ac.at
Research Group: I. Moll
Email: tanino.albanese(at)univie.ac.at
Research Group: M. Nodine
Email: michael.schon(at)gmi.oeaw.ac.at
Research Group: W. Rossmanith
Email: enxhi.hazisllari(at)meduniwien.ac.at
Research Group: Ivo Hofacker
Email: maria.waldl(at)univie.ac.at
Research Group: B. Görke
Email: florian.sikora(at)univie.ac.at
Research Group: S. Ameres
Email: moritz.staltner(at)imba.oeaw.ac.at
The Annual RNA Retreat 2019 takes a very special format as a co-organized meeting with the Swiss RNA community NCCR RNA & Disease. ((more…))
Current Position: Postdoc @ CIBIV, Max Perutz Labs
Open Science is a non-profit scientific association that stands for dialogue between science and the public. Together with our doctoral program in RNA Biology, Open Science has come up with a public outreach concept on the highly topical subject of genome editing with CRISPR/Cas. ((more…))
Congratulations to Laura D. Gallego Valle for winning one of the VBC PhD Awards 2018 ! ((more…))
The Vienna RNA Meeting 2018 took place 17-19 October at the Vienna Biocenter and was a big success – both in terms of the outstanding line-up of internationally renowned RNA expert as speakers, as well as the international echo of the meeting. ((more…))
Congratulations to Madalena Reimao Pinto (Ameres Lab, IMBA) for successfully defending today her PhD thesis “Molecular basis and biological functions of RNA 3′ end uridylation in Drosophila melanogaster“! ((more…))
You are cordially invited to two our guest seminars on Tue 23 October: ((more…))
Congratulations to IMBA group leader Stefan Ameres, faculty member in DK RNA Biology and SFB RNA-REG, for receiving an ERC Proof of Concept Grant to explore the commercial potential of his newly developed sequencing technology SLAMseq. ((more…))
You are cordially invited to our guest seminars: ((more…))
Congratulation to Laura Gallego Valle (group Köhler, MFPL) for successfully defending with excellence her PhD thesis “Molecular Mechanism of Histone H2B Monoubiquitination” on 28th August 2018!
You are cordially invited to the seminar by our guest speaker: ((more…))
The Vienna RNA Meeting 2018 “RNA-REG: Regulatory Circuits in RNA Biology” will take place in October 17-19, 2018, at the Vienna Biocenter in the IMP Lecture Hall, bringing together researchers studying diverse RNA-regulated processes in all areas of biology. ((more…))
Congratulations to DK RNA Biology student Tanino Albanese and associated students Elena Galimberti, Lucy Sneezum & Aleksej Drino for winning prizes at this years retreat of the Vienna Doctoral School (VDS) Molecules of Life! ((more…))
The 23rd Annual Meeting of the RNA Society, “RNA 2018”, took place in Berkeley, CA, USA, from 29 May to 3 June – of course with participation of members of our doctoral program. ((more…))
Congratulations to Milica Krunic (group Arndt von Haeseler) for successfully defending her PhD thesis “NGS Data Analysis in Resolving Disease Etiology” today! ((more…))
Congratulations to Stefan Hammer for successfully defending his PhD thesis “Design of context-sensitive, multi-stable RNA molecules” on 26th April 2018! ((more…))
You are cordially invited to the following seminar by our guest speaker: ((more…))
Our doctoral program on RNA Biology, together with three other FWF-funded doctoral programs on Chromosome Dynamics, Integrative Structural Biology and Signaling Mechanisms in Cellular Homeostasis, participates in the biggest research-
Congratulations to Celine Prakash (group Arndt von Haeseler) ((more…))
Research Group: U. Bläsi
Email: branislav.lilic(at)univie.ac.at
Research Group: U. Bläsi
Email: anastasia.cianciullo.sesso(at)univie.ac.at
Research Group: A. Köhler /co-supervised A. Barta
Email: katarina.radisavljevic(at)meduniwien.ac.at
Research Group: L. Cochella
Email: philipp.dexheimer(at)imp.ac.at
Congratulations to Muralidhar Tata (group Bläsi) for successfully defending his PhD Thesis “Identification and characterization of novel regulatory RNAs in Pseudomonas aeruginosa during anaerobiosis” today 2nd February 2018. ((more…))
Research Group: A. von Haeseler
Email: cassius.perez(at)univie.ac.at
Research Group: M. Jantsch
Email: renata.kleinova(at)meduniwien.ac.at
You are cordially invited to the following seminar by our guest speaker: ((more…))
Congratulations to Maximilan Radtke (group Schroeder) for successfully defending today his PhD Thesis “Exploring Intra-splicing and its regulatory potential”! ((more…))
Congratulations to Ana Krolo (group Köhler) for successfully defending today her PhD thesis “Identification and characterization of the TREX-2 complex in evolutionary divergent organism Trypanosoma brucei“! ((more…))
Congratulations to M. Mamduh bin A. Zabidi, a DK RNA alumnus, for winning one of the VBC PhD Awards 2017! ((more…))
Everyone is cordially invited to our guest seminar next week by Prof. Erez Levanon (Bar-Ilan University): ((more…))
Congratulations to Luisa Cochella for being selected into the EMBO Young Investigator Programme! ((more…))
It is with deep regret, that we have to report the untimely death of our colleague at the CeMM (Austrian Academy of Sciences), Prof. Dr. Denise P. Barlow. She passed away on October 21st, 2017 at the age of 67 after severe illness. ((more…))
SLAMseq is an innovative sequencing method developed by the Ameres Lab (IMBA) in collaboration with Arndt von Haeseler’s group (CIBIV/MFPL) and other researchers at the Vienna Biocenters. This novel technology opens up new possibilities for medical screening and testing medication on live cells, as reported in the journal Nature Methods. The Viennese RNA community congratulates its members to their work:
Thiol-linked alkylation of RNA to assess expression dynamics. ((more…))
Congratulations to Isabella Moll for her successful promotion to hold a full professorship at the University of Vienna! ((more…))
Congratulations to DK RNA fellow Dhaarsini Koneswarakantha (group Martinez, MFPL) for receiving the prize for Best Elevator Talk at the EMBO Conference on Redox Biology 2017. ((more…))
One more award for a DK RNA-associated student: Laura Gallego Valle (group A. Köhler, MFPL) received the L’Oreal Austria Fellowship for Young Female Scientists in Basic Research! ((more…))
Research Group: M. Schäfer
Email: aleksej.drino(at)univie.ac.at
Research Group: J. Martinez
Email: igor.asanovic(at)meduniwien.ac.at
Research Group: S. Ameres
Congratulations to DK RNA fellows Aleksej Drino (MedUni Wien, group Schäfer) and Mostafa Elmaghray (IMBA, group Brennecke) for receiving the DOC Fellowship from the Austrian Academy of Sciences (ÖAW)! ((more…))
The Schroeder lab has discovered a novel layer of transcription regulation in bacteria. The new findings have recently been published in the journal Molecular Cell:
Natural RNA Polymerase Aptamers Regulate Transcription in E. coli. ((more…))
We cordially invite you to the following seminar on July 7th, by our guest speaker: ((more…))
We cordially invite you to the following seminar on Friday by our guest speaker: ((more…))
We are happy to announce a rather special seminar next week by our guest speaker Takekazu Kunieda, who investigates the survival mechanisms of one of the most resilient animals known: ((more…))
Congratulations to Julia Batki from the Brennecke lab! ((more…))
Andrea Barta, coordinator of our Doctoral Program in RNA Biology, was scientific organizer of this year’s 22nd Annual Meeting of the RNA Society, “RNA 2017”. ((more…))
You are cordially invited to the following guest seminar: ((more…))
Congratulations to M. Mamduh bin A. Zabidi (group Alex Stark) ((more…))
Tomorrow Wed, 17th May 2017, at 10 a.m. in the IMP Lecture Hall: ((more…))
The VBC Ubiquitin and Friends Club invites all VBC members to their annual symposium: This year on 13th May 2017 in the Josephinum in Vienna. ((more…))
We cordially invite you to the following guest talk in the frame of the next RNA Tuesday Seminar: ((more…))
We cordially invite you to the following seminar next week by our guest speaker: ((more…))
E-mail: michael.kiebler(at)med.uni-muenchen.de
Research Group: www.zellbio.anatomie.med.uni-muenchen.de/about_us/prof_kiebler
Institution: LMU Munich, Department for Cell Biology (Head of Dept)
Member of the DoktoratsKolleg RNA Biology from 2007 until 2013.
Member of the Focus Regulatory RNA (SFB RNA-REG) from 2011 until 2013.
Michael Kiebler moved to LMU Munich in 2012 to head there the newly founded Department for Cell Biology.
DK PhD alumni:
Jacki Heraud: “Functional characterisation of novel neuronal Staufen2 target RNAs”
Foong yee Ang: “Biochemical characterization of Staufen2-, Barentsz- and Pumilio2-containing neuronal ribonucleoprotein particles from rat brain“
You are cordially invited to the following guest seminar: ((more…))
Congratulations to Armin Fuchs who successfully defended his PhD thesis ((more…))
We cordially invite you to the following seminar next week by our guest speaker: ((more…))
Congratulations Maja Stulic, PhD! ((more…))
The RNA Lecture Series, starting 2nd December 2016, covers diverse aspects in RNA Research. Please find the schedule here. ((more…))
Congratulations to Jörg Fallman, PhD, and Florian Eggenhofer, PhD, for their successful PhD graduation, both on 17th November 2016! ((more…))
Congratulations to Faculty Member Stefan Ameres for being selected into the EMBO Young Investigator Programme! ((more…))
Congratulations to Michael Jantsch on his appointment as Professor for Cell and Developmental Biology at the Medical University of Vienna. As such, he is now head of the Center for Anatomy and Cell Biology at the MedUni Vienna. ((more…))
Congratulations to Faculty Member Javier Martinez for his successful appointment to a full professorship at the Medical University of Vienna! ((more…))
You are cordially invited to the guest talk by ((more…))
Congratulations to Adam Weiss, PhD! ((more…))
We cordially invite you to the following seminar next week by our guest speaker : ((more…))
Andrea Barta, Coordinator of the Doctoral Program in RNA Biology, is awarded one of the highest honours of the Province of Vienna: ((more…))
You are cordially invited to the guest talk by ((more…))
Research Group: J. Brennecke
Email: jakob.schnabl(a)imba.oeaw.ac.at
Research Group: J. Brennecke
Email: mostafa.elmaghraby(a)imba.oeaw.ac.at
Research Group: U. Bläsi
Email: marlena.rozner(at)univie.ac.at
Current Position: Postdoc @ Alex Schier Lab (Harvard Universtiy / Biozentrum Uni Basel)
Current Position: Senior Consultant, Strategy, Life Sciences @ EY-Parthenon, Munich
Andrea Barta, Coordinator of the Doctoral Program in RNA Biology, has received the 2016 Service Award of the RNA Society ((more…))
Congratulations to Alexandra Kornienko, PhD! ((more…))
You are cordially invited to the guest talk by ((more…))
Congratulations to our DK Alumnus Dr. Krzysztof Chylinski for 2 notable prizes he was awarded this year: ((more…))
We kindly invite to the following seminar by our guest speaker ((more…))
We kindly invite you to the following seminar by our guest speaker ((more…))
We kindly invite you to our guest talk by ((more…))
You are cordially invited to the guest talk by ((more…))
Current Position: Postdoc @ Cancer Research Malaysia
Graduation: 15 May 2017
Thesis: Enhancer-responsiveness and –specificity of Core Promoters in Gene Transcription
Supervisor: Alex Stark (IMP)
Graduation: 18 June 2020
Thesis: Context-dependent regulation of immune homeostasis by TTP
Supervisor: Pavel Kovarik
Congratulations to Jan Henrik Suhren, PhD! ((more…))
Congratulations to Dr. Krzysztof Chylinski who won one of the four annual VBC PhD Awards for his thesis “The type II CRISPR-Cas adaptive immunity in bacteria: molecular mechanisms and evolution!” which he defended in October 2014. The awards were presented within the VBC PhD Symposium “Communication – Let’s talk about it”.
Research Group: J. Martinez
Email: dhaarsini.koneswarakantha(a)imba.oeaw.ac.at
Research Group: J. Martinez
Email: paola.pinto(a)imba.oeaw.ac.at
Congratulations to Nadia Sedlyarova from Renée Schroeder’s group!!! She successfully defended her thesis “Novel concepts of RNA-based transcription regulation in E.coli” on Thursday 29th October 2016.
We welcome you to our DK RNA Alumni Club!
Research Group: B. Görke
Email: muna.khan(a)univie.ac.at
Research Group: B. Görke
Email: svetlana.durica(a)nivie.ac.at
We would like to invite you to our guest talk by ((more…))
We would like to invite you to our guest talk by ((more…))
E-mail: pavel.kovarik(at)univie.ac.at
Phone: 0043 1 4277 54608
Research Group: http://www.mfpl.ac.at/kovarik.html
Institution: MFPL/UniWien
Full member of the Focus Regulatory RNA (SFB RNA-Reg) since 2015, with students associated to the DK.
PhD students associated to the DK:
Lucy Sneezum
Martina Borroni
For complete list of group members please visit the Kovarik group website.
Our research:
Inflammation can be viewed as stereotypical set of reactions to protect cells and entire organisms against environmental insults such as invading pathogens or tissue injuries. One of the key features of inflammatory responses is the precise and multilayered control of their magnitude and duration, which are adjusted such that hyper- or chronic inflammation is avoided yet a protective response is generated. We investigate the regulation of immune homeostasis at the level of transcriptional and posttranscriptional control of gene expression. In the field of posttranscriptional mechanisms we focus on the mRNA-destabilizing protein TTP and how TTP regulates inflammatory mRNA degradation to re-install immune and tissue homeostasis. We employ systems biology approaches combining high content approaches such as PAR-CLIP, RNA-seq and GRO-seq with cellular as well as animal models of infection and inflammation.
Publications: (since 2015)
Competition of Candida glabrata against Lactobacillus is Hog1 dependent.
Beyer R, Jandric Z, Zutz C, Gregori C, Willinger B, Jacobsen ID, Kovarik P, Strauss J, Schüller C.
Cell Microbiol. 2018 Aug 15:e12943.
The Bicarbonate Transporter SLC4A7 Plays a Key Role in Macrophage Phagosome Acidification.
Sedlyarov V, Eichner R, Girardi E, Essletzbichler P, Goldmann U, Nunes-Hasler P, Srndic I, Moskovskich A, Heinz LX, Kartnig F, Bigenzahn JW, Rebsamen M, Kovarik P, Demaurex N, Superti-Furga G.
Cell Host Microbe. 2018 Jun 13;23(6):766-774.e5.
Natural killer cell-intrinsic type I IFN signaling controls Klebsiella pneumoniae growth during lung infection.
Ivin M, Dumigan A, de Vasconcelos FN, Ebner F, Borroni M, Kavirayani A, Przybyszewska KN, Ingram RJ, Lienenklaus S, Kalinke U, Stoiber D, Bengoechea JA, Kovarik P.
PLoS Pathog. 2017 Nov 7;13(11):e1006696.
The RNA-binding protein tristetraprolin schedules apoptosis of pathogen-engaged neutrophils during bacterial infection.
Ebner F, Sedlyarov V, Tasciyan S, Ivin M, Kratochvill F, Gratz N, Kenner L, Villunger A, Sixt M, Kovarik P.
J Clin Invest. 2017 Jun 1;127(6):2051-2065.
HuR Small-Molecule Inhibitor Elicits Differential Effects in Adenomatosis Polyposis and Colorectal Carcinogenesis.
Lang M, Berry D, Passecker K, Mesteri I, Bhuju S, Ebner F, Sedlyarov V, Evstatiev R, Dammann K, Loy A, Kuzyk O, Kovarik P, Khare V, Beibel M, Roma G, Meisner-Kober N, Gasche C.
Cancer Res. 2017 May 1;77(9):2424-2438.
Posttranscriptional regulation of cytokine expression.
Kovarik P, Ebner F, Sedlyarov V.
Cytokine. 2017 Jan;89:21-26
Type I Interferons in Bacterial Infections: A Balancing Act.
Kovarik P, Castiglia V, Ivin M, Ebner F.
Front Immunol. 2016 Dec 26;7:652.
The Influence of Programmed Cell Death in Myeloid Cells on Host Resilience to Infection with Legionella pneumophila or Streptococcus pyogenes.
Gamradt P, Xu Y, Gratz N, Duncan K, Kobzik L, Högler S, Kovarik P, Decker T, Jamieson AM.
PLoS Pathog. 2016 Dec 14;12(12):e1006032.
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution.
Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, Kovarik P.
Mol Syst Biol. 2016 May 13;12(5):868
Type I Interferon Signaling Prevents IL-1β-Driven Lethal Systemic Hyperinflammation during Invasive Bacterial Infection of Soft Tissue.
Castiglia V, Piersigilli A, Ebner F, Janos M, Goldmann O, Damböck U, Kröger A, Weiss S, Knapp S, Jamieson AM, Kirschning C, Kalinke U, Strobl B, Müller M, Stoiber D, Lienenklaus S, Kovarik P.
Cell Host Microbe. 2016 Mar 9;19(3):375-87.
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
Fallmann J, Sedlyarov V, Tanzer A, Kovarik P, Hofacker IL.
Nucleic Acids Res. 2016 Jan 4;44(D1):D90-5.
Tristetraprolin Limits Inflammatory Cytokine Production in Tumor-Associated Macrophages in an mRNA Decay-Independent Manner.
Kratochvill F, Gratz N, Qualls JE, Van De Velde LA, Chi H, Kovarik P, Murray PJ.
Cancer Res. 2015 Aug 1;75(15):3054-64.
Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2.
Fieber C, Janos M, Koestler T, Gratz N, Li XD, Castiglia V, Aberle M, Sauert M, Wegner M, Alexopoulou L, Kirschning CJ, Chen ZJ, von Haeseler A, Kovarik P.
PLoS One. 2015 Mar 10;10(3):e0119727.
Promoter occupancy of STAT1 in interferon responses is regulated by processive transcription.
Wiesauer I, Gaumannmüller C, Steinparzer I, Strobl B, Kovarik P.
Mol Cell Biol. 2015 Feb;35(4):716-27.
E-mail: luisa.cochella(a)imp.ac.at
Phone: +43 1 79730
Research Group: www.imp.ac.at/groups/luisa-cochella
Institution: Research Institute of Molecular Pathology (IMP)
Full member of the Focus Regulatory RNA (SFB RNA Reg) since 2015 and of the DoktoratsKolleg (DK) RNA Biology since 2017.
PhD students within/associated to the DK:
Philipp Dexheimer
Paula Gutierrez Perez
DK RNA Biology Alumni:
Chiara Alberti: “Dissecting the contribution of microRNAs to nervous system development and function in C. elegans”
For complete list of group members please visit the Cochella group website.
Spatio-temporal specificity of miRNA biogenesis and function
As a single-cell zygote divides and its daughters continue to do so, the patterns of gene expression in each cell change due to intrinsic and external cues. These changes in gene expression have been primarily studied at the transcriptional level, with a number of transcription factor and chromatin associated proteins being implicated in driving many of the changes required for the developmental process. However, the role of post-transcriptional regulation in this process is much less understood. We are currently studying how transcriptional and post-transcriptional mechanisms integrate into gene regulatory networks that define different cell types during development. We are also interested in how the different mechanisms of gene regulation have contributed to the evolution of cell-type complexity.
With the discovery of microRNAs, short RNAs that can act as specific repressors of gene expression at the post-transcriptional level, we have a very good entry point to understand the impact of post-transcriptional regulation of gene expression to development and evolution. To do so, we use as a model system the nematode Caenorhabditis elegans, which is well known for the availability of extremely powerful genetic tools for its study. But in addition, C. elegans offers an invariant body plan where the lineage history and identity of every one of its ~950 cells – as well as a lot about the function of every cell – is known. Moreover, a growing group of Caenorhabditis sp. as well as other out groups have had their genomes fully sequenced and are also tractable with genetic approaches, making these species useful for comparative studies. Together, this makes “the worms” ideally suited model organisms to ask our questions of interest.
Combining genetic approaches, next generation sequencing and in vivo strategies that allow us to follow miRNA expression and function with single-cell resolution, we are currently dissecting the roles of miRNAs in providing specific cell types with their functional properties. We have found that many miRNAs are themselves expressed with very high spatio-temporal specificity, with an extreme case being a miRNA that is made and acts in a single neuron out of the 302 neurons that make up the C. elegans nervous system. This not only allows us to generate hypotheses about the roles of these miRNAs during cell-type specification but also leads us into understanding how their expression is regulated and therefore how this class of regulators is integrated in the cascade of events that unfolds from that totipotent one-cell zygote.
Selected publications: (since 2015)
Cell-type specific sequencing of microRNAs from complex animal tissues.
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.
Nat Methods. 2018 Apr;15(4):283-289.
A framework for understanding the roles of miRNAs in animal development.
Alberti C, Cochella L.
Development. 2017 Jul 15;144(14):2548-2559.
Neuron type-specific miRNA represses two broadly expressed genes to modulate an avoidance behavior in C. elegans.
Drexel T, Mahofsky K, Latham R, Zimmer M, Cochella L.
Genes Dev. 2016 Sep 15;30(18):2042-2047.
The Vienna RNA Meeting 2015 is all about RNA in Disease and Development and will take place from 22 – 24 October in the Van-Swieten-Saal in Vienna’s 9th district (easily reachable from Schottentor). ((more…))
Graduation: 4 June 2020
Thesis: YBEY is an essential biogenesis factor for mitochondrial ribosomes
Supervisor: Walter Rossmanith (MedUni Vienna)
Current Position: Postdoc @ CIBIV, MFPL
Graduation: 25 May 2018
Current Position: Postdoc @ MPI for Evolutionary Biology
Graduation: 9 April 2018
Research Group: I. Moll
Email: christian_mueller@univie.ac.at
Research Group: I. Moll
Email: folke.ebert@univie.ac.at
Congratulations to Janett Göhring, PhD! She was awarded the ÖGMBT prize for her dissertation “Imaging of Endogenous mRNA Splice Variants in Living Plant Cells” during the ÖGMBT Annual Meeting in Salzburg. ((more…))
We are happy to announce our new alumnus: Michael Wildauer, PhD ((more…))
We congratulate Mansoureh to the successful defense of her PhD thesis “Impact of inverted SINEs on gene expression”. ((more…))
Foong yee ANG (supervisors M. Jantsch & M. Kiebler) will be defending her PhD thesis entitled
“Biochemical characterization of Staufen2-, Barentsz- and Pumilio2-containing neuronal ribonucleoprotein particles from rat brain.”
on Thursday 16th April 2015 at 9:30 in the seminar room 3, MFPL 6th floor.
It’s the 10-year celebration of the Microsymposium on Small RNAs with an outstanding speaker line-up! Even if you’re only remotely interested in RNA Biology, you’ll love it! ((more…))
Congratulations Martina & Hannes! ((more…))
Martina Sauert (group Isabella Moll) will be defending her PhD thesis entitled
“Selective translation of leaderless mRNAs by specialized ribosomes upon MazF-mediated stress response in Escherichia coli.”
on Friday 27th March 2015 at 12:30 in the seminar room 1/2, MFPL 6th floor.
Hannes Temmel (group Isabella Moll) will be defending his PhD thesis entitled
“The novel E. coli RNA ligase RtcB: Elucidation of its physiological function”
on Friday 27th March 2015 at 11:00 a.m. in the seminar room 1/2, MFPL 6th floor.
We invite you to our eXtra RNA Seminar on Wednesday 18th March 2015 at 10:30 a.m. in the IMP lecture hall: ((more…))
We invite you to our eXtra RNA Seminar on Tuesday 17th March 2015 at 9:00 a.m. in the IMP lecture hall: ((more…))
We invite you to our eXtra RNA Seminar on Tuesday 20th January 2015 at 9:00 a.m. in the IMP lecture hall: ((more…))
We want to wish all of you a HAPPY NEW YEAR –
2015 shall be a healthy and successful year for you!
We invite you to our eXtra RNA Seminar on Tuesday 16th December 2014 at 9:00 a.m. in the IMP lecture hall: ((more…))
We invite you to our eXtra RNA Seminar on Tuesday 9th December 2014 at 9:00 a.m. in the IMP lecture hall: ((more…))
We kindly invite you to our following extra RNA Seminar: ((more…))
Please download the schedules for each individual lecture day: ((more…))
Congratulations Janett & Chris! We proudly present our 2 new alumni of the DoktoratsKolleg RNA Biology: ((more…))
We would like to invite you to 2 very interesting talks on Tuesday 7th October 2014: ((more…))
Janett Göhring from Andrea Barta’s group will defend her PhD thesis entitled“Imaging of Endogenous mRNA Splice Variants in Living Plant Cells”
on Thursday 2nd October 2014 at 11:30 a.m. in the seminar room 1 of the Vienna Competence Center (VCC), Lazarettgasse 19, A-1090 Wien ((more…))
We would like to invite you to our eXtra RNA Seminar on Monday 22 September 2014 at 10:00 a.m. (in MFPL sr 1/2): ((more…))
Save these dates: 24 October, 21 November, 12 December 2014! ((more…))
Philip, a PhD candidate from the University of Florida, spent 2 months working in the lab of Renée Schroeder at the Max. F. Perutz Laboratories. ((more…))
The former faculty member of the DoktoratsKolleg RNA Biology Dr. Emmanuelle Charpentier (now Hannover Medical School and Helmholtz Centre for Infection Research) wins the 2014 Dr. Paul Janssen Award for Biomedical Research together with Dr. Jennifer Doudna (Univ. of California at Berkeley and Howard Hughes Medical Institute). ((more…))
We would like to invite you to following extra RNA Seminar:
From marsupials to microorganisms: With Bioinformatics into the world of microRNAs ((more…))
Yamile Marquez from Andrea Barta’s group will defend her PhD thesis entitled
“The alternative splicing landscape of Arabidopsis thaliana”
on Wednesday, May 7th at 11 a.m. in the MFPL seminar room 1/2.
The journal RNA Biology presents a Special Issue devoted to Carl Woese, the famous American microbiologist and biophysicist, who has become known for defining the third kingdom of life – Archaea -, and originating the RNA world hypothesis (to name just two of his many accomplishments). The articles contained in this Special Issue ((more…))
We would like to invite you to following extra RNA Seminar:
Engineering of ribozymes with useful activities in the ancient RNA world ((more…))
We would like to invite you to following extra RNA Seminar:
Bacterial apoptotic cell death and its biological relevance ((more…))
Silpi Banerjee from Michael Jantsch’ group will defend her PhD thesis
“Nuclear import by an ADAR1 double stranded RNA binding domain”
on Friday 25th April 2014 at 14:30 in the 3rd floor seminar room (MFPL).
Our doctoral programme in RNA Biology recruits new PhD students through the MFPL International PhD Program. Please note that the application deadline for the current summer selection 2014 ends on Sunday 16th March!
Great minds from the Eric Greene Lab (Columbia University) and the Jennifer Doudna Lab (University of California) have released an educational video describing how Cas9 searches DNA for target sites: ((more…))
The Austrian Mint has now made its Silver Niobium series richer by introducing the new EVOLUTION coin. It was issued on 22nd January 2014 and shows ((more…))
The MFPL International PhD Program has just started its Spring Call 2014! All informations on the program and detailed application information can be found on the program’s website. ((more…))
E-mail: walter.rossmanith(at)meduniwien.ac.at
Phone: 0043 1 40160 37512
Research Group: www.meduniwien.ac.at/wrlab/
Institution: MedUniWien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2014.
PhD students within/associated to the DK:
Sabrina Summer
Enxhi Hazisllari
For complete list of group members please visit the Rossmanith group website.
tRNA biology & mitochondria
We are interested in the biogenesis of tRNA molecules, and the structure, function, and evolution of the enzymes involved in this multistep process. Though we now use and study various eukaryal model systems, the origin and focus of our research is the human mitochondrial system. In this small genetic subsystem, the tRNAs have non-canonical structures and are frequently involved in the pathogenesis of a heterogeneous group of diseases. We are interested in structure-function relationships of mitochondrial tRNAs, their biogenesis, and their role in disease. We employ a variety of experimental approaches and model systems for our studies.
Publications: (since 2014)
Deciphering the “m6A Code” via Antibody-Independent Quantitative Profiling.
Garcia-Campos MA, Edelheit S, Toth U, Safra M, Shachar R, Viukov S, Winkler R, Nir R, Lasman L, Brandis A, Hanna JH, Rossmanith W, Schwartz S.
Cell. 2019 Jul 25;178(3):731-747.e16.
A subcomplex of human mitochondrial RNase P is a bifunctional methyltransferase – extensive moonlighting in mitochondrial tRNA biogenesis.
Vilardo E, Nachbagauer C, Buzet A, Taschner A, Holzmann J, Rossmanith W.
Nucleic Acids Res. 2018 Nov 16;46(20):11126-11127.
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF, Quattrone A, O’Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.
RNA Biol. 2018 May 9:1-3.
Minimal and RNA-free RNase P in Aquifex aeolicus.
Nickel AI, Wäber NB, Gößringer M, Lechner M, Linne U, Toth U, Rossmanith W, Hartmann RK.
Proc Natl Acad Sci U S A. 2017 Oct 17;114(42):11121-11126.
The m1A landscape on cytosolic and mitochondrial mRNA at single-base resolution.
Safra M, Sas-Chen A, Nir R, Winkler R, Nachshon A, Bar-Yaacov D, Erlacher M, Rossmanith W, Stern-Ginossar N, Schwartz S.
Nature. 2017 Nov 9;551(7679):251-255.
Protein-only RNase P function in Escherichia coli: viability, processing defects and differences between PRORP isoenzymes.
Gößringer M, Lechner M, Brillante N, Weber C, Rossmanith W, Hartmann RK.
Nucleic Acids Res. 2017 Jul 7;45(12):7441-7454.
Repairing tRNA termini: News from the 3′ end.
Rammelt C, Rossmanith W.
RNA Biol. 2016 Dec;13(12):1182-1188.
Analysis of the Cleavage Mechanism by Protein-Only RNase P Using Precursor tRNA Substrates with Modifications at the Cleavage Site.
Walczyk D, Gößringer M, Rossmanith W, Zatsepin TS, Oretskaya TS, Hartmann RK.
J Mol Biol. 2016 Dec 4;428(24 Pt B):4917-4928.
A novel HSD17B10 mutation impairing the activities of the mitochondrial RNase P complex causes X-linked intractable epilepsy and neurodevelopmental regression.
Falk MJ, Gai X, Shigematsu M, Vilardo E, Takase R, McCormick E, Christian T, Place E, Pierce EA, Consugar M, Gamper HB, Rossmanith W, Hou YM.
RNA Biol. 2016 May 3;13(5):477-85.
Substrate recognition and cleavage-site selection by a single-subunit protein-only RNase P.
Brillante N, Gößringer M, Lindenhofer D, Toth U, Rossmanith W, Hartmann RK.
Nucleic Acids Res. 2016 Mar 18;44(5):2323-36.
Mitochondrial poly(A) polymerase is involved in tRNA repair.
Fiedler M, Rossmanith W, Wahle E, Rammelt C.
Nucleic Acids Res. 2015 Nov 16;43(20):9937-49.
Distribution of Ribonucleoprotein and Protein-Only RNase P in Eukarya.
Lechner M, Rossmanith W, Hartmann RK, Thölken C, Gutmann B, Giegé P, Gobert A.
Mol Biol Evol. 2015 Dec;32(12):3186-93.
Molecular insights into HSD10 disease: impact of SDR5C1 mutations on the human mitochondrial RNase P complex.
Vilardo E, Rossmanith W.
Nucleic Acids Res. 2015 May 26;43(10):5112-9.
Playing RNase P evolution: swapping the RNA catalyst for a protein reveals functional uniformity of highly divergent enzyme forms.
Weber C, Hartig A, Hartmann RK, Rossmanith W.
PLoS Genet. 2014 Aug 7;10(8):e1004506.
MFPL Scientific Advisory Board’s Meeting took place on the 16th and 17th December 2013.
((more…))
Congratulations to Hermann Hämmerle! From now on an Alumni of the DoktoratsKolleg RNA Biology … ((more…))
Hermann Hämmerle from Udo Bläsi’s group will defend his PhD Thesis
“Functional Studies on Hfq Proteins of Escherichia coli and Bacillus subtilis”
on Monday 9th December 2013 at 12:00 in the MFPL seminar room 1 (6th floor).
The first of our 3 lecture days starts today – a lecture series with total of 12 lectures each 90 min. ((more…))
We congratulate our new PhD graduate Dr. Conny Vesely!!! ((more…))
We would like to invite you to our guest talk by ((more…))
We are happy to announce this guest talk to which you are cordially invited:
Alfredo Castello Palomares, PhD (EMBL Heidelberg)
“Insights into Biology and Disease from the first in vivo atlas of RNA-binding proteins” ((more…))
The Vienna RNA Meeting 2013 will take place from 13-15 October 2013 in the IMBA/GMI Lecture Hall. ((more…))
Stulic M, Jantsch MF.
RNA Biol. 2013 Sep 4.
We are happy to announce this guest talk to which you are cordially invited: ((more…))
E-mail: boris.goerke(a)univie.ac.at
Phone: 0043 1 4277 54603
Research Group: https://www.maxperutzlabs.ac.at/research/research-groups/goerke
Institution: Max Perutz Labs/UniWien
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2015.
Full member of the DoktoratsKolleg (DK) RNA Biology since 2017.
PhD students within/associated to the DK RNA Biology:
Svetlana Durica
Florian Sikora
DK RNA Biology Alumni & their theses:
Muna Ayesha Khan: “Signal perception and transduction within the GlmY/GlmZ small RNA cascade in E.coli”
For complete list of group members please visit the Görke group website.
Signal Transduction and post-transcriptional regulation in model bacteria
In recent years post-transcriptional control of gene expression by small regulatory RNAs (sRNAs) has emerged as a major principle of gene regulation in bacteria. Due to their central regulatory roles in virtually all physiological circuits, sRNA activities must be tightly controlled. This might occur either at the level of their biogenesis or turn-over. Using the GlmY/GlmZ sRNA circuit of E. coli as a model system we aim to obtain insight into these important questions. In particular, we are interested to (I) unravel the various factors and conditions controlling expression of sRNAs and (II) to identify the components of the machineries specifically controlling the decay of sRNAs.
Publications: (since 2015)
Feedback regulation of small RNA processing by the cleavage product.
Durica-Mitic S, Görke B.
RNA Biol. 2019 Aug;16(8):1055-1065.
Interaction of lipoprotein QseG with sensor kinase QseE in the periplasm controls the phosphorylation state of the two-component system QseE/QseF in Escherichia coli.
Göpel Y, Görke B.
PLoS Genet. 2018 Jul 24;14(7):e1007547.
Carbohydrate Utilization in Bacteria: Making the Most Out of Sugars with the Help of Small Regulatory RNAs.
Durica-Mitic S, Göpel Y, Görke B.
Microbiol Spectr. 2018 Mar;6(2).
Structural insights into RapZ-mediated regulation of bacterial amino-sugar metabolism.
Gonzalez GM, Durica-Mitic S, Hardwick SW, Moncrieffe MC, Resch M, Neumann P, Ficner R, Görke B, Luisi BF.
Nucleic Acids Res. 2017 Oct 13;45(18):10845-10860.
Non-canonical activation of histidine kinase KdpD by phosphotransferase protein PtsN through interaction with the transmitter domain.
Mörk-Mörkenstein M, Heermann R, Göpel Y, Jung K, Görke B.
Mol Microbiol. 2017 Oct;106(1):54-73.
Synthesis and antimicrobial activity of 6-sulfo-6-deoxy-D-glucosamine and its derivatives.
Skarbek K, Gabriel I, Szweda P, Wojciechowski M, Khan MA, Görke B, Milewski S, Milewska MJ.
Carbohydr Res. 2017 Aug 7;448:79-87.
Roles of Regulatory RNAs for Antibiotic Resistance in Bacteria and Their Potential Value as Novel Drug Targets.
Dersch P, Khan MA, Mühlen S, Görke B.
Front Microbiol. 2017 May 5;8:803.
Two Small RNAs Conserved in Enterobacteriaceae Provide Intrinsic Resistance to Antibiotics Targeting the Cell Wall Biosynthesis Enzyme Glucosamine-6-Phosphate Synthase.
Khan MA, Göpel Y, Milewski S, Görke B.
Front Microbiol. 2016 Jun 15;7:908.
Domain swapping between homologous bacterial small RNAs dissects processing and Hfq binding determinants and uncovers an aptamer for conditional RNase E cleavage.
Göpel Y, Khan MA, Görke B.
Nucleic Acids Res. 2016 Jan 29;44(2):824-37.
Cross-Talk between the Canonical and the Nitrogen-Related Phosphotransferase Systems Modulates Synthesis of the KdpFABC Potassium Transporter in Escherichia coli.
Lüttmann D, Göpel Y, Görke B.
J Mol Microbiol Biotechnol. 2015;25(2-3):168-77.
The department of Biochemistry and Cell Biology of the University of Vienna is currently seeking an outstanding scientist with research expertise in the field of RNA Biochemistry. ((more…))
We have great pleasure informing you that Prof. W. Filipowicz is currently on a sabbatical in the frame of the SFB Regulatory RNAs here at MFPL until the end of June 2013. ((more…))
On Monday 24th June 2013 at 4 p.m. Federica will defend her PhD thesis in the 8th floor seminar room in CeMM:“Onset and maintenance of Airn non-coding RNA mediated imprinted expression in an in vitro embryonic stem cell model” ((more…))
We are happy to announce this guest talk to which you are cordially invited:
Prof.Dr. Nicola Abrescia (Univ. of Basque Country, Spain)
“Structural studies of large macromolecular assemblies: from viruses to enzymatic machines” ((more…))
Research Group: U. Bläsi
Email: petra.pusic@univie.ac.at
Research Group: A. Köhler
Email: laura.gallego.valle(at)univie.ac.at
Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity.
Bannikova, Olga; Zywicki, Marek; Marquez, Yamile; Skrahina, Tatsiana; Kalyna, Maria; Barta, Andrea (2013).
Nucleic Acids Res. 2013 Feb 1;41(3):1783-96. doi: 10.1093/nar/gks1252. Epub 2012 Dec 16.
Current Position: Postdoc/Staff Scientist @ Bioinformatics Leipzig
Graduation: 26 April 2018
Thesis: Design of context-sensitive, multi-stable RNA molecules
Supervisor: Ivo Hofacker (TBI, UniWien)
PhD with: R. Schroeder
We are happy to announce this guest talk to which you are cordially invited:
Prof.Dr. Karine Lapouge (Univ. of Lausanne) ((more…))
We invite you all to Alessandra Romeo’s PhD defense entitled “Characterisation of the small regulatory non-coding RNA NalA in the opportunistic pathogen Pseudomonas aeruginosa” ((more…))
After Ursula’s successful defense of her PhD Thesis “Nucleus-specific biogenesis of noncoding RNAs in Tetrahymena thermophila” on 16th January 2013, we may now address her as Dr. Ursula Schöberl! ((more…))
Mss116p: a DEAD-box protein facilitates RNA folding.
Sachsenmaier N, Waldsich C.
RNA Biol. 2013 Jan;10(1):71-82. doi: 10.4161/rna.22492. Epub 2012 Oct 12.
The Austrian Federal Minister for Science & Research Dr. Karlheinz Töchterle and the president of the Austrian Science Fund (FWF) Christoph Kratky visited MFPL on Thursday 24th January 2013 to give a press talk and ((more…))
On Monday 21st January 2013 it’s the 3rd day of our RNA LECTURE SERIES, this time in the IMBA lecture hall (IMBA, Dr.-Bohr-Gasse 3, A-1030 Wien).
The schedule is ((more…))
On Monday 14th January 2013 it’s the 2nd day of our RNA LECTURE SERIES, this time in the IMBA lecture hall (IMBA, Dr.-Bohr-Gasse 3, A-1030 Wien).
The schedule is ((more…))
This year’s VBC PhD Awards were announced on 9th November and we are very proud to congratulate Martina Dötsch and Johannes Popow to their success! ((more…))
“Gene regulation in the Lyme disease bacterium” ((more…))
The new RNA Lecture Series consists of 13 talks from invited guest speakers and is held on 3 days: 19th Nov., 14th Jan., and 21st Jan. 2013. (PhD and Master students can register via MedCampus and UniVis to receive 2 ECTS credits for participation.). You can download the schedule from our download area or read it below. ((more…))
On 17th October 2012 we had the chance to dine with Nobel Laureates from the RNA World. The RNA Biology DK/SFB organized a dinner for the students and post docs with Elizabeth Blackburn and Thomas Steitz at the Vestibül. The dinner and the discussions were excellent. It was an unforgettable evening. ((more…))
Current Position: Regulatory CMC Associate Manager @ Sandoz
The Plant RNA Workshop will be held on 8 & 9 July 2012 in the Institute of Molecular Biotechnology (IMBA), Vienna – following the 23rd International Conference on Arabidopsis Research (ICAR), 3-7 July 2012. ((more…))
Jan Suhren: “The HP1-like protein Coi6 is involved in RNAi mediated DNA elimination in Tetrahymena thermophila” ((more…))
“Naked and pregnant: Cell wall deficient Listeria monocytogenes reveal a novel mode of division and multiplication” ((more…))
Peter Kerpedjiev: Coarse grained 3D RNA folding ((more…))
Stefan Badelt and Florian Huber ((more…))
“Evolution of long non-coding RNAs: conservation and flexibility” ((more…))
Current Position:
After the successful defense of her PhD Thesis “Functional characterisation of novel neuronal Staufen2 target RNAs” this morning, we may now address her as Dr. Heraud! ((more…))
“A novel apoptotic-like cell death pathway in bacteria and its biological significance” ((more…))
E-mail: michael.nodine(@)gmi.oeaw.ac.at
Phone: 0043 1 79044 9822
Research Group: www.gmi.oeaw.ac.at/research-groups/michael-nodine
Institution: Gregor Mendel Institute (GMI)
Full member of the DoktoratsKolleg (DK) RNA Biology since 2014 and of the Focus Regulatory RNA (SFB RNA Reg) since 2015.
PhD students within/associated with the DK RNA:
Aleksandra Plotnikova
Michael Schon
DK RNA Biology alumni & their thesis:
Stefan Lutzmayer: “Small interferring RNA dynamics and functions during Arabidopsis embryogenesis”
For complete list of group members please visit the Nodine group website.
Small RNA functions in plant embryos
The basic plant body plan is established during embryogenesis. However, despite its fundamental importance to both agriculture and developmental biology, the molecular mechanisms that regulate plant embryogenesis remain mostly uncharacterized. Studying the embryonic functions of regulatory RNAs will not only yield significant insights into the mechanistic basis of plant embryo development, but will also contribute to our general understanding of how regulatory RNAs influence cellular differentiation. For example, a class of ~21 nucleotide RNAs called microRNAs (miRNAs) play essential roles during plant embryo pattern formation and developmental timing. Interestingly, most plant embryonic miRNAs repress transcripts encoding transcription factors and other key developmental regulators. Our goal is to understand how small regulatory RNAs, including miRNAs, shape the gene regulatory networks that control plant embryogenesis. We will use a combination of cutting-edge experimental and computational approaches to achieve this aim.
Publications: (since 2014)
Transcriptional Activation of Arabidopsis Zygotes Is Required for Their Initial Division. (preprint)
Kao P and Nodine MD.
bioRivx:679035. 2019 June 21
MicroRNA Dynamics and Functions during Arabidopsis Embryogenesis. (preprint)
Plotnikova A, Kellner M, Mosiolek M, Schon M, Nodine MD.
bioRxiv:633735 2019 May 9
The embryonic transcriptome of Arabidopsis thaliana.
Hofmann F, Schon MA, Nodine MD.
Plant Reprod. 2019 Mar;32(1):77-91.
Stage-specific transcriptomes and DNA methylomes indicate an early and transient loss of transposon control in Arabidopsis shoot stem cells. (preprint)
Gutzat R, Rembart K, Nussbaumer T, Pisupati R, Hofmann Falko, Bradamante G, Daubel N, Gaidora A, Lettner N, Donà M, Nordborg M, Nodine MD, Mittelsten Scheid O.
bioRxiv:430447. 2018 Oct 5
NanoPARE: parallel analysis of RNA 5′ ends from low-input RNA.
Schon MA, Kellner MJ, Plotnikova A, Hofmann F, Nodine MD.
Genome Res. 2018 Dec;28(12):1931-1942.
Whole Mount in situ Localization of miRNAs and mRNAs During Somatic Embryogenesis in Arabidopsis.
Wójcik AM, Mosiolek M, Karcz J, Nodine MD, Gaj MD.
Front Plant Sci. 2018 Sep 4;9:1277.
A Common Pathway of Root Growth Control and Response to CLE Peptides Through Two Receptor Kinases in Arabidopsis.
Racolta A, Nodine MD, Davies K, Lee C, Rowe S, Velazco Y, Wellington R, Tax FE.
Genetics. 2018 Feb;208(2):687-704.
miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
Wójcik AM, Nodine MD, Gaj MD1.
Front Plant Sci. 2017 Dec 11;8:2024.
Novel small RNA spike-in oligonucleotides enable absolute normalization of small RNA-Seq data.
Lutzmayer S, Enugutti B, Nodine MD.
Sci Rep. 2017 Jul 19;7(1):5913.
Widespread Contamination of Arabidopsis Embryo and Endosperm Transcriptome Data Sets.
Schon MA, Nodine MD.
Plant Cell. 2017 Apr;29(4):608-617.
Sensitive whole mount in situ localization of small RNAs in plants.
Ghosh Dastidar M, Mosiolek M, Bleckmann A, Dresselhaus T, Nodine MD, Maizel A.
Plant J. 2016 Nov;88(4):694-702.
Mobile small RNAs: Sperm-companion communication.
Nodine MD.
Nat Plants. 2016 Apr 5;2:16041.
MicroRNA functions in plant embryos.
Vashisht D, Nodine MD.
Biochem Soc Trans. 2014 Apr;42(2):352-7
E-mail: stefan.ameres(at)imba.oeaw.ac.at, stefan.ameres@univie.ac.at
Phone: 0043 1 79044-4740
Research Group: www.imba.oeaw.ac.at/research/stefan-ameres
https://www.maxperutzlabs.ac.at/research/research-groups/ameres
Institution: IMBA, Max Perutz Labs
Full member of the DoktoratsKolleg (DK) RNA Biology since 2014 and of the Focus Regulatory RNA (SFB RNA Reg) since 2015.
PhD students within/associated to the DK:
Pooja Bhat
Moritz Staltner
DK RNA Biology alumni & their PhD theses:
Madalena Reimão-Pinto: “Molecular basis and biological functions of RNA 3′ end uridylation in Drosophila melanogaster”
Brian Reichholf: “Dissecting the kinetics of miRNA biogenesis and turnover in living cells”
For complete list of group members please visit the Ameres group website.
Mechanism and Biology of RNA Silencing
Small silencing RNAs regulate animal physiology and development, enhance target gene discovery in pharmacological industry and serve as next-generation therapy for human disease. In RNA silencing pathways, ~22 nucleotide small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), guide ribonucleoprotein complexes to complementary sequences within messenger RNAs to mediate their post-transcriptional silencing.
We are interested in molecular mechanisms that govern small RNA silencing pathways in flies and mammals. Our focus lies on processes that regulate the production of small RNAs, their assembly into ribonucleoprotein complexes, and the disassembly thereof in response to synthetic and natural triggers, such as target mRNAs. Our goal is to define the principles that establish and maintain small RNA profiles in a given tissue or cell type. To do so, we are using a combination of biochemical, genetic and bioinformatic approaches using Drosophila melanogaster as a model organism. The hypotheses emerging from our studies in flies are directly tested for their conservation in mammals.
Publications: (since 2014)
Time-Resolved Small RNA Sequencing Unravels the Molecular Principles of MicroRNA Homeostasis.
Reichholf B, Herzog VA, Fasching N, Manzenreither RA, Sowemimo I, Ameres SL.
Mol Cell. 2019 Jul 9. pii: S1097-2765(19)30474-5. [Epub ahead of print]
Sequencing cell-type-specific transcriptomes with SLAM-ITseq. Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Nat Protoc. 2019 Jun 26. doi: 10.1038/s41596-019-0179-x. [Epub ahead of print] Erratum in: Nat Protoc. 2019 Jul 11;:.
Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.
Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P.
BMC Bioinformatics. 2019 May 20;20(1):258.
Structural basis for acceptor RNA substrate selectivity of the 3′ terminal uridylyl transferase Tailor.
Kroupova A, Ivascu A, Reimão-Pinto MM, Ameres SL, Jinek M.
Nucleic Acids Res. 2019 Jan 25;47(2):1030-1042.
Small RNAs Are Trafficked from the Epididymis to Developing Mammalian Sperm.
Sharma U, Sun F, Conine CC, Reichholf B, Kukreja S, Herzog VA, Ameres SL, Rando OJ.
Dev Cell. 2018 Aug 20;46(4):481-494.e6.
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF, Quattrone A, O’Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.
RNA Biol. 2018 May 9:1-3.
Analysis of 3′ End Modifications in microRNAs by High-Throughput Sequencing.
Reimão-Pinto MM, Rodrigues-Viana AM, Ameres SL.
Methods Mol Biol. 2018;1823:115-139.
SLAM-ITseq: sequencing cell type-specific transcriptomes without cell sorting.
Matsushima W, Herzog VA, Neumann T, Gapp K, Zuber J, Ameres SL, Miska EA.
Development. 2018 Jul 11;145(13).
SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.
Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J.
Science. 2018 May 18;360(6390):800-805.
Cell-type specific sequencing of microRNAs from complex animal tissues.
Alberti C, Manzenreither RA, Sowemimo I, Burkard TR, Wang J, Mahofsky K, Ameres SL, Cochella L.
Nat Methods. 2018 Apr;15(4):283-289.
Thiol-linked alkylation of RNA to assess expression dynamics.
Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL.
Nat Methods. 2017 Dec;14(12):1198-1204.
Genetic and mechanistic diversity of piRNA 3′-end formation.
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J.
Nature. 2016 Nov 24;539(7630):588-592.
Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.
Reimão-Pinto MM, Manzenreither RA, Burkard TR, Sledz P, Jinek M, Mechtler K, Ameres SL.
EMBO J. 2016 Nov 15;35(22):2417-2434.
Uridylation of RNA Hairpins by Tailor Confines the Emergence of MicroRNAs in Drosophila.
Reimão-Pinto MM, Ignatova V, Burkard TR, Hung JH, Manzenreither RA, Sowemimo I, Herzog VA, Reichholf B, Fariña-Lopez S, Ameres SL.
Mol Cell. 2015 Jul 16;59(2):203-16.
Selective Suppression of the Splicing-Mediated MicroRNA Pathway by the Terminal Uridyltransferase Tailor.
Bortolamiol-Becet D, Hu F, Jee D, Wen J, Okamura K, Lin CJ, Ameres SL, Lai EC.
Mol Cell. 2015 Jul 16;59(2):217-28.
Approaching the Golden Fleece a Molecule at a Time: Biophysical Insights into Argonaute-Instructed Nucleic Acid Interactions.
Herzog VA, Ameres SL.
Mol Cell. 2015 Jul 2;59(1):4-7.
Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of a normalized cDNA library which resulted in a high coverage transcriptome map of Arabidopsis. ((more…))
Some pictures & videos of us, visits, our events and science communication activities.
((more…))
The biggest network event of the Viennese RNA community is the annual RNA Retreat – usually a combined event of the two Vienna-based RNA programmes: the SFB RNA REG and the DK RNA Biology.
((more…))
E-mail: arndt.von.haeseler(at)univie.ac.at
Phone: 0043 1 4277 24007
Research Group: http://www.cibiv.at
https://www.maxperutzlabs.ac.at/research/research-groups/von-haeseler
Institution: CIBIV/Max Perutz Labs
Full member of the DoktoratsKolleg (DK) RNA Biology since 2014.
PhD students within/associated to the DK:
Florian Pflug
Cassius M. Perez de los Cobos Hermosa
DK RNA Biology Alumni& their PhD thesis:
Luis Felipe Paulin Paz: “Understanding the sampling properties of high throughput sequencing technologies”
Milica Krunic: “NGS Data Analysis in Resolving Disease Etiology”
Celine Prakash: “Enumerative Combinatorics Models for Fragmentation Pattern in RNA Sequencing Provides Insights into the Expected Coverage Profile”
(Philipp Rescheneder)
For complete list of group members please visit the von Haeseler group website.
Arndt is Head of CIBIV (Center for Integrative Bioinformatics Vienna) at the Max Perutz Labs, and the Bioinformatics Coordinator for the SFB Special Research Focus Regulatory RNAs.
Publications: (since 2014)
Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets.
Neumann T, Herzog VA, Muhar M, von Haeseler A, Zuber J, Ameres SL, Rescheneder P.
BMC Bioinformatics. 2019 May 20;20(1):258.
Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.
Schrempf D, Minh BQ, von Haeseler A, Kosiol C.
Mol Biol Evol. 2019 Jun 1;36(6):1294-1301.
Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase.
Schenk S, Bannister SC, Sedlazeck FJ, Anrather D, Minh BQ, Bileck A, Hartl M, von Haeseler A, Gerner C, Raible F, Tessmar-Raible K.
Elife. 2019 Feb 15;8. pii: e41556.
VARIFI-Web-Based Automatic Variant Identification, Filtering and Annotation of Amplicon Sequencing Data.
Krunic M, Venhuizen P, Müllauer L, Kaserer B, von Haeseler A.
J Pers Med. 2019 Feb 1;9(1).
The Evolutionary Traceability of a Protein.
Jain A, Perisa D, Fliedner F, von Haeseler A, Ebersberger I.
Genome Biol Evol. 2019 Feb 1;11(2):531-545.
Accurate detection of complex structural variations using single-molecule sequencing.
Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC.
Nat Methods. 2018 Jun;15(6):461-468.
SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis.
Muhar M, Ebert A, Neumann T, Umkehrer C, Jude J, Wieshofer C, Rescheneder P, Lipp JJ, Herzog VA, Reichholf B, Cisneros DA, Hoffmann T, Schlapansky MF, Bhat P, von Haeseler A, Köcher T, Obenauf AC, Popow J, Ameres SL, Zuber J.
Science. 2018 May 18;360(6390):800-805.
Germline Variants in the POT1-Gene in High-Risk Melanoma Patients in Austria.
Müller C, Krunic M, Wendt J, von Haeseler A, Okamoto I.
G3 (Bethesda). 2018 May 4;8(5):1475-1480.
Complex Models of Sequence Evolution Require Accurate Estimators as Exemplified with the Invariable Site Plus Gamma Model.
Nguyen LT, von Haeseler A, Minh BQ.
Syst Biol. 2018 May 1;67(3):552-558.
In vivo insertion pool sequencing identifies virulence factors in a complex fungal-host interaction.
Uhse S, Pflug FG, Stirnberg A, Ehrlinger K, von Haeseler A, Djamei A.
PLoS Biol. 2018 Apr 23;16(4):e2005129.
Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes.
Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C.
Nat Commun. 2018 Apr 17;9(1):1517.
TRUmiCount: Correctly counting absolute numbers of molecules using unique molecular identifiers.
Pflug FG, von Haeseler A.
Bioinformatics. 2018 Apr 16.
MPBoot: fast phylogenetic maximum parsimony tree inference and bootstrap approximation.
Hoang DT, Vinh LS, Flouri T, Stamatakis A, von Haeseler A, Minh BQ.
BMC Evol Biol. 2018 Feb 2;18(1):11.
UFBoot2: Improving the Ultrafast Bootstrap Approximation.
Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS.
Mol Biol Evol. 2018 Feb 1;35(2):518-522.
Thiol-linked alkylation of RNA to assess expression dynamics.
Herzog VA, Reichholf B, Neumann T, Rescheneder P, Bhat P, Burkard TR, Wlotzka W, von Haeseler A, Zuber J, Ameres SL.
Nat Methods. 2017 Dec;14(12):1198-1204.
ModelFinder: fast model selection for accurate phylogenetic estimates.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS.
Nat Methods. 2017 Jun;14(6):587-589.
HIV-1 full-genome phylogenetics of generalized epidemics in sub-Saharan Africa: impact of missing nucleotide characters in next-generation sequences.
Ratmann O, Wymant C, Colijn C, Danaviah S, Essex M, Frost SDW, Gall A, Gaiseitsiwe S, Grabowski M, Gray R, Guindon S, von Haeseler A, Kaleebu P, Kendall M, Kozlov A, Manasa J, Minh BQ, Moyo S, Novitsky V, Nsubuga R, Pillay S, Quinn TC, Serwadda D, Ssemwanga D, Stamatakis A, Trifinopoulos J, Wawer M, Leigh Brown A, de Oliveira T, Kellam P, Pillay D, Fraser C.
AIDS Res Hum Retroviruses. 2017 May 25.
The genomic basis of circadian and circalunar timing adaptations in a midge.
Kaiser TS, Poehn B, Szkiba D, Preussner M, Sedlazeck FJ, Zrim A, Neumann T, Nguyen LT, Betancourt AJ, Hummel T, Vogel H, Dorner S, Heyd F, von Haeseler A, Tessmar-Raible K.
Nature. 2016 Dec 1;540(7631):69-73.
Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices.
Chernomor O, von Haeseler A, Minh BQ.
Syst Biol. 2016 Nov;65(6):997-1008.
Reversible polymorphism-aware phylogenetic models and their application to tree inference.
Schrempf D, Minh BQ, De Maio N, von Haeseler A, Kosiol C.
J Theor Biol. 2016 Oct 21;407:362-370.
W-IQ-TREE: a fast online phylogenetic tool for maximum likelihood analysis.
Trifinopoulos J, Nguyen LT, von Haeseler A, Minh BQ.
Nucleic Acids Res. 2016 Jul 8;44(W1):W232-5.
Next-generation sequencing diagnostics of bacteremia in septic patients.
Grumaz S, Stevens P, Grumaz C, Decker SO, Weigand MA, Hofer S, Brenner T, von Haeseler A, Sohn K.
Genome Med. 2016 Jul 1;8(1):73.
A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha.
Gesson K, Rescheneder P, Skoruppa MP, von Haeseler A, Dechat T, Foisner R.
Genome Res. 2016 Apr;26(4):462-73.
Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance.
Jagut M, Hamminger P, Woglar A, Millonigg S, Paulin L, Mikl M, Dello Stritto MR, Tang L, Habacher C, Tam A, Gallach M, von Haeseler A, Villeneuve AM, Jantsch V.
PLoS Biol. 2016 Mar 24;14(3):e1002412.
Consequences of Common Topological Rearrangements for Partition Trees in Phylogenomic Inference.
Chernomor O, Minh BQ, von Haeseler A.
J Comput Biol. 2015 Dec;22(12):1129-42.
Teaser: Individualized benchmarking and optimization of read mapping results for NGS data.
Smolka M, Rescheneder P, Schatz MC, von Haeseler A, Sedlazeck FJ.
Genome Biol. 2015 Oct 22;16:235.
The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways.
Tscherner M, Zwolanek F, Jenull S, Sedlazeck FJ, Petryshyn A, Frohner IE, Mavrianos J, Chauhan N, von Haeseler A, Kuchler K.
PLoS Pathog. 2015 Oct 16;11(10):e1005218.
Decreased expression of endogenous feline leukemia virus in cat lymphomas: a case control study.
Krunic M, Ertl R, Hagen B, Sedlazeck FJ, Hofmann-Lehmann R, von Haeseler A, Klein D.
BMC Vet Res. 2015 Apr 10;11:90.
Innate immune response to Streptococcus pyogenes depends on the combined activation of TLR13 and TLR2.
Fieber C, Janos M, Koestler T, Gratz N, Li XD, Castiglia V, Aberle M, Sauert M, Wegner M, Alexopoulou L, Kirschning CJ, Chen ZJ, von Haeseler A, Kovarik P.
PLoS One. 2015 Mar 10;10(3):e0119727.
The phylogenetic likelihood library.
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A.
Syst Biol. 2015 Mar;64(2):356-62.
Split diversity in constrained conservation prioritization using integer linear programming.
Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A.
Methods Ecol Evol. 2015 Jan;6(1):83-91.
IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies.
Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ.
Mol Biol Evol. 2015 Jan;32(1):268-74.
The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima.
Chipman AD, Ferrier DE, Brena C, Qu J, Hughes DS, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JC, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJ, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JH, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S.
PLoS Biol. 2014 Nov 25;12(11):e1002005.
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.
Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF.
Nucleic Acids Res. 2014 Oct 29;42(19):12155-68.
Discovery of the first light-dependent protochlorophyllide oxidoreductase in anoxygenic phototrophic bacteria.
Kaschner M, Loeschcke A, Krause J, Minh BQ, Heck A, Endres S, Svensson V, Wirtz A, von Haeseler A, Jaeger KE, Drepper T, Krauss U.
Mol Microbiol. 2014 Sep;93(5):1066-78.
A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity.
Sengoelge G, Winnicki W, Kupczok A, von Haeseler A, Schuster M, Pfaller W, Jennings P, Weltermann A, Blake S, Sunder-Plassmann G.
BMC Genomics. 2014 Aug 27;15:725.
SNP2GO: functional analysis of genome-wide association studies.
Szkiba D, Kapun M, von Haeseler A, Gallach M.
Genetics. 2014 May;197(1):285-9.
The evolution of the ribosome biogenesis pathway from a yeast perspective.
Ebersberger I, Simm S, Leisegang MS, Schmitzberger P, Mirus O, von Haeseler A, Bohnsack MT, Schleiff E.
Nucleic Acids Res. 2014 Feb;42(3):1509-23.
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects.
Dell’Ampio E, Meusemann K, Szucsich NU, Peters RS, Meyer B, Borner J, Petersen M, Aberer AJ, Stamatakis A, Walzl MG, Minh BQ, von Haeseler A, Ebersberger I, Pass G, Misof B.
Mol Biol Evol. 2014 Jan;31(1):239-49.
Current Position: Postdoc @ MedUni, Vienna
Current Position: tba
Current Position: Postdoc @ Dept. of Molecular Evolution and Development (Univ. Vienna)
Current Position: Postdoc @ CCRI, Vienna
Current Position: Global Associate Program Director @ Novartis
Current Position: Postdoc @ EMBL Heidelberg
Current Position: Postdoc @ IMP (Pavri lab)
Current Position: Christian Doppler Laboratory for Med. Radiation Research @ MedUni Wien
Current Position: Senior Professional @ Shire Austria
Current Position: Head of Genome Engineering Services @ VBCF GmbH, Vienna
Current Position: Product Manager @ Lexogen, Vienna
Current Position:
Current Position: Postdoc @ University of Siena, Italy
Current Position: Postdoc @ University of Texas Health Science Center at Houston
Current Position: @ Marinomed Biotech AG, Vienna
Research Group: M. Nodine
Email: a.plotnikova(at)gmi.oeaw.ac.at
Current Position: Postdoc @ MedUni, Vienna
Current Position: @ VBCF GmbH, Vienna
Current Position: Acquisitions Editor @ Taylor & Francis Group
Current Position: Postdoc @ MFPL
Current Position: Postdoc @ Caltech, Pasadena
PhD supervisor: I. Hofacker
Current Position: Postdoc @ Uni Freiburg
PhD supervisor: I. Hofacker
Current Position: Postdoc @ Bioinformatics Uni Leipzig
Email: pkerpedjiev(at)gmail.com
Current Position: Postdoc @ Harvard Medical School
Current Position: Scientific Staff @ Laboratory of RNA Biology and Functional Genomics, PAS, Warsaw
Current Position: Postdoc @ GMI, Vienna
Current Position: Postdoc @ Karolinska Institutet, Stockholm
Current Position: Postdoc @ CRG, Barcelona
Current Position: Postdoc @ Technical Univ. Vienna
Current Position: Postdoc @ MFPL
Current Position: Scientist @ Allcyte GmbH
Graduation: 12 May 2020
Thesis: A direct link between nuclear basket and the nuclear envelope
Supervisor: Alwin Köhler (Max Perutz Labs Vienna)
Current Position: @ LBI for Rare and Undiagnosed Diseases, Vienna
E-mail: alex.stark(at)imp.ac.at
Phone: 0043 1 4277 79730
Research Group: www.imp.ac.at/groups/alexander-stark
Institution: Research Institute of Molecular Pathology (IMP)
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2011.
Full member of the DoktoratsKolleg (DK) RNA Biology since 2014.
PhD students within/associated to the DK RNA Biology:
Oliver HENDY
Leonid SEREBRENI
DK RNA Biology Alumni:
M. Mamduh A. ZABIDI: “Enhancer-responsiveness and -specificity of core promorters on gene transcription”
For complete list of group members please visit the Stark group website.
Joint research project J. Brennecke and A. Stark:
We propose to perform an unbiased study of RNA-abundance and post-transcriptional regulation in the female Drosophila germ line. Drosophila oogenesis serves as a paradigm for regulation of gene expression at the RNA-level, as all 3 known small RNA pathways (miRNAs, siRNAs, PiRNAs) are employed and it is the key system in which control of RNA localization, translation and transport have been established and are actively studied.
Specifically, we will establish and employ ribosome foot-printing (Ingolia et al. 2009) to determine ribosome occupancy and translation rates of mRNAs and RNA-PAR-CLIP (Hafner et al, 2010) to identify the specific target RNAs of three key protein factors involved in post-transcriptional regulation (Pumilio, Staufen, and Argonaute 1). We will couple these genom-wide approaches to bioninformatics analyses established in our or the Hofacker groups to determine the cis-regulatory motifs of RNAs at the level of sequence and secondary structure. We anticipate gaining significant insight into the post-transcriptional control of RNA fate in a complex in vivo context.
In a broader perspective, both technologies will proof extremely useful for the scientific progress within the Brennecke/Stark labs, which are focusing on small RNAs and cis-regulatory motifs. Finally, we believe that multiple groups within this SFB (e.g. Kiebler, Dorner, Mochizuki, Martinez) and a number of labs at the Vienna Biocenter Campus will benefit strongly from the establishment of the two technologies.
Publications: (since 2011)
Transcriptional cofactors display specificity for distinct types of core promoters.
Haberle V, Arnold CD, Pagani M, Rath M, Schernhuber K, Stark A.
Nature. 2019 Jun;570(7759):122-126
A high-throughput method to identify trans-activation domains within transcription factor sequences.
Arnold CD, Nemčko F, Woodfin AR, Wienerroither S, Vlasova A, Schleiffer A, Pagani M, Rath M, Stark A.
EMBO J. 2018 Aug 15;37(16).
Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle V, Stark A.
Nat Rev Mol Cell Biol. 2018 Jun 26.
Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation.
Catarino RR, Stark A.
Genes Dev. 2018 Feb 1;32(3-4):202-223.
Resolving systematic errors in widely used enhancer activity assays in human cells.
Muerdter F, Boryń ŁM, Woodfin AR, Neumayr C, Rath M, Zabidi MA, Pagani M, Haberle V, Kazmar T, Catarino RR, Schernhuber K, Arnold CD, Stark A.
Nat Methods. 2018 Feb;15(2):141-149.
A reversible haploid mouse embryonic stem cell biobank resource for functional genomics.
Elling U, Wimmer RA, Leibbrandt A, Burkard T, Michlits G, Leopoldi A, Micheler T, Abdeen D, Zhuk S, Aspalter IM, Handl C, Liebergesell J, Hubmann M, Husa AM, Kinzer M, Schuller N, Wetzel E, van de Loo N, Martinez JAZ, Estoppey D, Riedl R, Yang F, Fu B, Dechat T, Ivics Z, Agu CA, Bell O, Blaas D, Gerhardt H, Hoepfner D, Stark A, Penninger JM.
Nature. 2017 Oct 5;550(7674):114-118.
Promoting transcription over long distances.
Catarino RR, Neumayr C, Stark A.
Nat Genet. 2017 Jun 28;49(7):972-973.
Probing the canonicity of the Wnt/Wingless signaling pathway.
Franz A, Shlyueva D, Brunner E, Stark A, Basler K.
PLoS Genet. 2017 Apr 3;13(4):e1006700.
Combinatorial function of transcription factors and cofactors.
Reiter F, Wienerroither S, Stark A.
Curr Opin Genet Dev. 2017 Apr;43:73-81.
Genome-wide assessment of sequence-intrinsic enhancer responsiveness at single-base-pair resolution.
Arnold CD, Zabidi MA, Pagani M, Rath M, Schernhuber K, Kazmar T, Stark A.
Nat Biotechnol. 2017 Feb;35(2):136-144.
Regulatory Enhancer-Core-Promoter Communication via Transcription Factors and Cofactors.
Zabidi MA, Stark A.
Trends Genet. 2016 Dec;32(12):801-814.
RNA-binding profiles of Drosophila CPEB proteins Orb and Orb2.
Stepien BK, Oppitz C, Gerlach D, Dag U, Novatchkova M, Krüttner S, Stark A, Keleman K.
Proc Natl Acad Sci U S A. 2016 Oct 24.
Gene Regulation: Activation through Space.
Muerdter F, Stark A.
Curr Biol. 2016 Oct 10;26(19):R895-R898.
Genome-Wide Ultrabithorax Binding Analysis Reveals Highly Targeted Genomic Loci at Developmental Regulators and a Potential Connection to Polycomb-Mediated Regulation.
Shlyueva D, Meireles-Filho AC, Pagani M, Stark A.
PLoS One. 2016 Aug 30;11(8):e0161997.
Transcriptional regulators form diverse groups with context-dependent regulatory functions.
Stampfel G, Kazmar T, Frank O, Wienerroither S, Reiter F, Stark A.
Nature. 2015 Dec 3;528(7580):147-51.
Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.
Rathert P, Roth M, Neumann T, Muerdter F, Roe JS, Muhar M, Deswal S, Cerny-Reiterer S, Peter B, Jude J, Hoffmann T, Boryń ŁM, Axelsson E, Schweifer N, Tontsch-Grunt U, Dow LE, Gianni D, Pearson M, Valent P, Stark A, Kraut N, Vakoc CR, Zuber J.
Nature. 2015 Sep 24;525(7570):543-547.
Coordinating the human looks.
Haberle V, Stark A.
Cell. 2015 Sep 24;163(1):24-6.
Enhancer-core-promoter specificity separates developmental and housekeeping gene regulation.
Zabidi MA, Arnold CD, Schernhuber K, Pagani M, Rath M, Frank O, Stark A.
Nature. 2015 Feb 26;518(7540):556-9.
The RNA-binding protein Arrest (Bruno) regulates alternative splicing to enable myofibril maturation in Drosophila flight muscle.
Spletter ML, Barz C, Yeroslaviz A, Schönbauer C, Ferreira IR, Sarov M, Gerlach D, Stark A, Habermann BH, Schnorrer F.
EMBO Rep. 2015 Feb;16(2):178-91.
Genomics: Hiding in plain sight.
Muerdter F, Stark A.
Nature. 2014 Aug 28;512(7515):374-5.
Genome-scale functional characterization of Drosophila developmental enhancers in vivo.
Kvon EZ, Kazmar T, Stampfel G, Yáñez-Cuna JO, Pagani M, Schernhuber K, Dickson BJ, Stark A.
Nature. 2014 Aug 7;512(7512):91-5.
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution.
Arnold CD, Gerlach D, Spies D, Matts JA, Sytnikova YA, Pagani M, Lau NC, Stark A.
Nat Genet. 2014 Jul;46(7):685-92.
Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features.
Yáñez-Cuna JO, Arnold CD, Stampfel G, Boryń LM, Gerlach D, Rath M, Stark A.
Genome Res. 2014 Jul;24(7):1147-56.
Hormone-responsive enhancer-activity maps reveal predictive motifs, indirect repression, and targeting of closed chromatin.
Shlyueva D, Stelzer C, Gerlach D, Yáñez-Cuna JO, Rath M, Boryń ŁM, Arnold CD, Stark A.
Mol Cell. 2014 Apr 10;54(1):180-192.
Transcriptional enhancers: from properties to genome-wide predictions.
Shlyueva D, Stampfel G, Stark A.
Nat Rev Genet. 2014 Apr;15(4):272-86.
A conserved role for Snail as a potentiator of active transcription.
Rembold M, Ciglar L, Yáñez-Cuna JO, Zinzen RP, Girardot C, Jain A, Welte MA, Stark A, Leptin M, Furlong EE.
Genes Dev. 2014 Jan 15;28(2):167-81.
cis-regulatory requirements for tissue-specific programs of the circadian clock.
Meireles-Filho ACA, Bardet AF, Yáñez-Cuna JO, Stampfel G, Stark A.
Curr Biol. 2014 Jan 6;24(1):1-10.
Identification of transcription factor binding sites from ChIP-seq data at high resolution.
Bardet AF, Steinmann J, Bafna S, Knoblich JA, Zeitlinger J, Stark A.
Bioinformatics. 2013 Nov 1;29(21):2705-13.
Regulatory Genomics – Decoding Drosophila Regulatory Sequences.
Stark A.
Biomed Tech (Berl). 2013 Sep 7.
Genome-wide quantitative enhancer activity maps identified by STARR-seq.
Arnold CD, Gerlach D, Stelzer C, Boryń ŁM, Rath M, Stark A.
Science. 2013 Mar 1;339(6123):1074-7.
Deciphering the transcriptional cis-regulatory code.
Yáñez-Cuna JO, Kvon EZ, Stark A.
Trends Genet. 2013 Jan;29(1):11-22.
A histone deacetylase adjusts transcription kinetics at coding sequences during Candida albicans morphogenesis.
Hnisz D, Bardet AF, Nobile CJ, Petryshyn A, Glaser W, Schöck U, Stark A, Kuchler K.
PLoS Genet. 2012;8(12):e1003118.
Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding.
Yáñez-Cuna JO, Dinh HQ, Kvon EZ, Shlyueva D, Stark A.
Genome Res. 2012 Oct;22(10):2018-30.
HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature.
Kvon EZ, Stampfel G, Yáñez-Cuna JO, Dickson BJ, Stark A.
Genes Dev. 2012 May 1;26(9):908-13.
A computational pipeline for comparative ChIP-seq analyses.
Bardet AF, He Q, Zeitlinger J, Stark A.
Nat Protoc. 2011 Dec 15;7(1):45-61.
Forward and reverse genetics through derivation of haploid mouse embryonic stem cells.
Elling U, Taubenschmid J, Wirnsberger G, O’Malley R, Demers SP, Vanhaelen Q, Shukalyuk AI, Schmauss G, Schramek D, Schnuetgen F, von Melchner H, Ecker JR, Stanford WL, Zuber J, Stark A, Penninger JM.
Cell Stem Cell. 2011 Dec 2;9(6):563-74.
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team, Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team, Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University, Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M.
Nature. 2011 Oct 12;478(7370):476-82.
Neural-specific elongation of 3′ UTRs during Drosophila development.
Hilgers V, Perry MW, Hendrix D, Stark A, Levine M, Haley B.
Proc Natl Acad Sci U S A. 2011 Sep 20;108(38):15864-9.
A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors.
Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J.
EMBO J. 2011 Aug 23;30(19):3977-93.
High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species.
He Q, Bardet AF, Patton B, Purvis J, Johnston J, Paulson A, Gogol M, Stark A, Zeitlinger J.
Nat Genet. 2011 May;43(5):414-20.
E-mail: julius.brennecke(at)imba.oeaw.ac.at
Phone: 0043 1 79044
Research Group: www.imba.oeaw.ac.at/research/julius-brennecke
Institution: IMBA
Full member of the DoktoratsKolleg RNA Biology since 2014 and of the SFB RNA Reg since 2011.
PhD students within/associated to the DK:
Jakob Schnabl
Mostafa Elmaghraby
Lisa Baumgartner
Veselin Andreev
DK RNA Biology alumni & their PhD theses:
Julia Batki: “Nuclear small RNA-guided silencing of transposable elements in Drosophila melanogaster”
For complete list of group members please visit the Brennecke group website.
Joint SFB research project J. Brennecke and A. Stark:
We propose to perform an unbiased study of RNA-abundance and post-transcriptional regulation in the female Drosophila germ line. Drosophila oogenesis serves as a paradigm for regulation of gene expression at the RNA-level, as all 3 known small RNA pathways (miRNAs, siRNAs, PiRNAs) are employed and it is the key system in which control of RNA localization, translation and transport have been established and are actively studied.
Specifically, we will establish and employ ribosome foot-printing (Ingolia et al. 2009) to determine ribosome occupancy and translation rates of mRNAs and RNA-PAR-CLIP (Hafner et al, 2010) to identify the specific target RNAs of three key protein factors involved in post-transcriptional regulation (Pumilio, Staufen, and Argonaute 1). We will couple these genom-wide approaches to bioninformatics analyses established in our or the Hofacker groups to determine the cis-regulatory motifs of RNAs at the level of sequence and secondary structure. We anticipate gaining significant insight into the post-transcriptional control of RNA fate in a complex in vivo context.
In a broader perspective, both technologies will proof extremely useful for the scientific progress within the Brennecke/Stark labs, which are focusing on small RNAs and cis-regulatory motifs. Finally, we believe that multiple groups within this SFB (e.g. Kiebler, Dorner, Mochizuki, Martinez) and a number of labs at the Vienna Biocenter Campus will benefit strongly from the establishment of the two technologies.
Publications: (since 2011)
A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production.
ElMaghraby MF, Andersen PR, Pühringer F, Hohmann U, Meixner K, Lendl T, Tirian L, Brennecke J.
Cell. 2019 Aug 8;178(4):964-979.e20.
The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J.
Nat Struct Mol Biol. 2019 Aug;26(8):720-731. Epub 2019 Aug 5.
A heterochromatin-dependent transcription machinery drives piRNA expression.
Andersen PR, Tirian L, Vunjak M, Brennecke J.
Nature. 2017 Sep 7;549(7670):54-59.
Genetic and mechanistic diversity of piRNA 3′-end formation.
Hayashi R, Schnabl J, Handler D, Mohn F, Ameres SL, Brennecke J.
Nature. 2016 Nov 24;539(7630):588-592.
Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery.
Sienski G, Batki J, Senti KA, Dönertas D, Tirian L, Meixner K, Brennecke J.
Genes Dev. 2015 Nov 1;29(21):2258-71.
piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire.
Senti KA, Jurczak D, Sachidanandam R, Brennecke J.
Genes Dev. 2015 Aug 15;29(16):1747-62.
Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis.
Mohn F, Handler D, Brennecke J.
Science. 2015 May 15;348(6236):812-817.
Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi’s genomic targets still not identified.
Marinov GK, Wang J, Handler D, Wold BJ, Weng Z, Hannon GJ, Aravin AA, Zamore PD, Brennecke J, Toth KF.
Dev Cell. 2015 Mar 23;32(6):765-71.
The exon junction complex is required for definition and excision of neighboring introns in Drosophila.
Hayashi R, Handler D, Ish-Horowicz D, Brennecke J.
Genes Dev. 2014 Aug 15;28(16):1772-85.
Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex.
Dönertas D, Sienski G, Brennecke J.
Genes Dev. 2013 Aug 1;27(15):1693-705.
The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila.
Mohn F, Sienski G, Handler D, Brennecke J.
Cell. 2014 Jun 5;157(6):1364-79.
The genetic makeup of the Drosophila piRNA pathway.
Handler D, Meixner K, Pizka M, Lauss K, Schmied C, Gruber FS, Brennecke J.
Mol Cell. 2013 Jun 6;50(5):762-77.
Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression.
Sienski G, Dönertas D, Brennecke J.
Cell. 2012 Nov 21;151(5):964-80.
Preparation of small RNA libraries for high-throughput sequencing.
Malone C, Brennecke J, Czech B, Aravin A, Hannon GJ.
Cold Spring Harb Protoc. 2012 Oct 1;2012(10):1067-77.
The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila.
Olivieri D, Senti KA, Subramanian S, Sachidanandam R, Brennecke J.
Mol Cell. 2012 Sep 28;47(6):954-69.
A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors.
Handler D, Olivieri D, Novatchkova M, Gruber FS, Meixner K, Mechtler K, Stark A, Sachidanandam R, Brennecke J.
EMBO J. 2011 Aug 23;30(19):3977-93.
A genome-scale shRNA resource for transgenic RNAi in Drosophila.
Ni JQ, Zhou R, Czech B, Liu LP, Holderbaum L, Yang-Zhou D, Shim HS, Tao R, Handler D, Karpowicz P, Binari R, Booker M, Brennecke J, Perkins LA, Hannon GJ, Perrimon N.
Nat Methods. 2011 May;8(5):405-7.
E-mail: ivo(at)tbi.univie.ac.at
Phone: 0043 1 4277 52738
Research Group: http://www.tbi.univie.ac.at/~ivo/
Institution: UniWien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2010.
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2011.
PhD students within/associated to the DK RNA Biology:
Bernhard Thiel
Roman Ochsenreiter
Mariam Farman
Gregor Entzian
Maria Waldl
DK RNA Biology Alumni & their PhD theses:
Stefan Hammer: “Design of context-sensitive, multi-stable RNA molecules”
Stefan Badelt: “Control of RNA function by conformational design”
Florian Eggenhofer: “Conservation and interaction of RNA in regulatory networks”
Joerg Fallmann: “RNA-protein interactions in RNA decay”
Peter Kerpedjiev: “Coarse grained 3D RNA folding”
For complete list of group members please visit the website of the Theoretical Biochemistry (TBI) Group.
Research:
My scientific interests fit mostly under the computational biology umbrella. Much of my work focuses on RNA Bioinformatics, the most visible part perhaps being the Vienna RNA Package for prediction and comparison of RNA secondary structures, which my coworkers and I have developed for over 15 years.
For a description of the individual projects in our group see the TBI Research page, or browse though my list of publications. Our preprint server contains working papers and downloadable preprints for most papers for the really curious.
Publications: (since 2011)
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements.
Thiel BC, Beckmann IK, Kerpedjiev P, Hofacker IL.
Version 2. F1000Res. 2019 Mar 14 [revised 2019 Jan 1];8. pii: ISCB Comm J-287.
Conserved Secondary Structures in Viral mRNAs.
Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D.
Viruses. 2019 Apr 29;11(5).
Functional RNA Structures in the 3’UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses.
Ochsenreiter R, Hofacker IL, Wolfinger MT.
Viruses. 2019 Mar 24;11(3).
Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs.
Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Hart-Smith G, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y.
Plant Physiol. 2019 May;180(1):305-322.
RNA modifications in structure prediction – Status quo and future challenges.
Tanzer A, Hofacker IL, Lorenz R.
Methods. 2019 Mar 1;156:32-39.
MSF: Modulated Sub-graph Finder.
Farman MR, Hofacker IL, Amman F.
Version 3. F1000Res. 2018 Aug 29 [revised 2019 Jan 1];7:1346.
Comparative genomics of Czech vaccine strains of Bordetella pertussis.
Dienstbier A, Pouchnik D, Wildung M, Amman F, Hofacker IL, Parkhill J, Holubova J, Sebo P, Vecerek B.
Pathog Dis. 2018 Oct 1;76(7).
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.
Thiel BC, Ochsenreiter R, Gadekar VP, Tanzer A, Hofacker IL.
Genes (Basel). 2018 Aug 1;9(8).
CMV: visualization for RNA and protein family models and their comparisons.
Eggenhofer F, Hofacker IL, Backofen R, Höner Zu Siederdissen C.
Bioinformatics. 2018 Aug 1;34(15):2676-2678.
Efficient computation of co-transcriptional RNA-ligand interaction dynamics.
Wolfinger MT, Flamm C, Hofacker IL.
Methods. 2018 Jul 1;143:70-76.
In silico design of ligand triggered RNA switches.
Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL.
Methods. 2018 Jul 1;143:90-101.
Comparative RNA Genomics.
Backofen R, Gorodkin J, Hofacker IL, Stadler PF.
Methods Mol Biol. 2018;1704:363-400.
RNAblueprint: flexible multiple target nucleic acid sequence design.
Hammer S, Tschiatschek B, Flamm C, Hofacker IL, Findeiß S.
Bioinformatics. 2017 Sep 15;33(18):2850-2858.
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.
Alkan F, Wenzel A, Palasca O, Kerpedjiev P, Rudebeck AF, Stadler PF, Hofacker IL, Gorodkin J.
Nucleic Acids Res. 2017 May 5;45(8):e60.
NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations.
Helmling C, Wacker A, Wolfinger MT, Hofacker IL, Hengesbach M, Fürtig B, Schwalbe H.
J Am Chem Soc. 2017 Feb 22;139(7):2647-2656.
RNAlien – Unsupervised RNA family model construction.
Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.
Nucleic Acids Res. 2016 Sep 30;44(17):8433-41.
Predicting RNA secondary structures from sequence and probing data.
Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL.
Methods. 2016 Jul 1;103:86-98.
RNA folding with hard and soft constraints.
Lorenz R, Hofacker IL, Stadler PF.
Algorithms Mol Biol. 2016 Apr 23;11:8.
Computational Design of a Circular RNA with Prionlike Behavior.
Badelt S, Flamm C, Hofacker IL.
Artif Life. 2016 Spring;22(2):172-84.
Pseudoknots in RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J.
Bioinformatics. 2016 Jan 15;32(2):187-94.
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.
Fallmann J, Sedlyarov V, Tanzer A, Kovarik P, Hofacker IL.
Nucleic Acids Res. 2016 Jan 4;44(D1):D90-5.
SHAPE directed RNA folding.
Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT.
Bioinformatics. 2016 Jan 1;32(1):145-7.
RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure.
Theis C, Zirbel CL, Zu Siederdissen CH, Anthon C, Hofacker IL, Nielsen H, Gorodkin J.
PLoS One. 2015 Oct 28;10(10):e0139900.
Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams.
Kerpedjiev P, Hammer S, Hofacker IL.
Bioinformatics. 2015 Oct 15;31(20):3377-9.
Optimizing RNA structures by sequence extensions using RNAcop.
Hecker N, Christensen-Dalsgaard M, Seemann SE, Havgaard JH, Stadler PF, Hofacker IL, Nielsen H, Gorodkin J.
Nucleic Acids Res. 2015 Sep 30;43(17):8135-45.
Predicting RNA 3D structure using a coarse-grain helix-centered model.
Kerpedjiev P, Höner Zu Siederdissen C, Hofacker IL.
RNA. 2015 Jun;21(6):1110-21.
Model-Free RNA Sequence and Structure Alignment Informed by SHAPE Probing Reveals a Conserved Alternate Secondary Structure for 16S rRNA.
Lavender CA, Lorenz R, Zhang G, Tamayo R, Hofacker IL, Weeks KM.
PLoS Comput Biol. 2015 May 20;11(5):e1004126.
Product Grammars for Alignment and Folding.
Höner Zu Siederdissen C, Hofacker IL, Stadler PF.
IEEE/ACM Trans Comput Biol Bioinform. 2015 May-Jun;12(3):507-19.
Thermodynamic and kinetic folding of riboswitches.
Badelt S, Hammer S, Flamm C, Hofacker IL.
Methods Enzymol. 2015;553:193-213.
Basin Hopping Graph: a computational framework to characterize RNA folding landscapes.
Kucharík M, Hofacker IL, Stadler PF, Qin J.
Bioinformatics. 2014 Jul 15;30(14):2009-17.
Challenges in RNA virus bioinformatics.
Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A.
Bioinformatics. 2014 Jul 1;30(13):1793-9.
TSSAR: TSS annotation regime for dRNA-seq data.
Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S.
BMC Bioinformatics. 2014 Mar 27;15:89
Energy-directed RNA structure prediction.
Hofacker IL.
Methods Mol Biol. 2014;1097:71-84.
Concepts and introduction to RNA bioinformatics.
Gorodkin J, Hofacker IL, Ruzzo WL.
Methods Mol Biol. 2014;1097:1-31.
Predicting RNA structure: advances and limitations.
Hofacker IL, Lorenz R.
Methods Mol Biol. 2014;1086:1-19.
Computational design of RNAs with complex energy landscapes.
Höner zu Siederdissen C, Hammer S, Abfalter I, Hofacker IL, Flamm C, Stadler PF.
Biopolymers. 2013 Dec;99(12):1124-36.
Automated identification of RNA 3D modules with discriminative power in RNA structural alignments.
Theis C, Höner Zu Siederdissen C, Hofacker IL, Gorodkin J.
Nucleic Acids Res. 2013 Dec;41(22):9999-10009.
2D meets 4G: G-quadruplexes in RNA secondary structure prediction.
Lorenz R, Bernhart SH, Qin J, Höner zu Siederdissen C, Tanzer A, Amman F, Hofacker IL, Stadler PF.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Jul-Aug;10(4):832-44.
CMCompare webserver: comparing RNA families via covariance models.
Eggenhofer F, Hofacker IL, Höner Zu Siederdissen C.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W499-503.
The RNAsnp web server: predicting SNP effects on local RNA secondary structure.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.
Nucleic Acids Res. 2013 Jul;41(Web Server issue):W475-9
Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics.
Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S.
J Proteomics. 2013 Jun 28;86:27-42.
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs.
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J.
Hum Mutat. 2013 Apr;34(4):546-56.
Folding RNA/DNA hybrid duplexes.
Lorenz R, Hofacker IL, Bernhart SH.
Bioinformatics. 2012 Oct 1;28(19):2530-1.
RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.
Washietl S, Hofacker IL, Stadler PF, Kellis M.
Nucleic Acids Res. 2012 May;40(10):4261-72
LocARNA-P: accurate boundary prediction and improved detection of structural RNAs.
Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R.
RNA. 2012 May;18(5):900-14.
ViennaRNA Package 2.0.
Lorenz R, Bernhart SH, Höner Zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL.
Algorithms Mol Biol. 2011 Nov 24;6:26.
Animal snoRNAs and scaRNAs with exceptional structures.
Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF.
RNA Biol. 2011 Nov-Dec;8(6):938-46.
From structure prediction to genomic screens for novel non-coding RNAs.
Gorodkin J, Hofacker IL.
PLoS Comput Biol. 2011 Aug;7(8):e1002100.
Fast accessibility-based prediction of RNA-RNA interactions.
Tafer H, Amman F, Eggenhofer F, Stadler PF, Hofacker IL.
Bioinformatics. 2011 Jul 15;27(14):1934-40.
A folding algorithm for extended RNA secondary structures.
Höner zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL.
Bioinformatics. 2011 Jul 1;27(13):i129-36.
RNApredator: fast accessibility-based prediction of sRNA targets.
Eggenhofer F, Tafer H, Stadler PF, Hofacker IL.
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W149-54.
Next-generation sequencing of the Chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering.
Hackl M, Jakobi T, Blom J, Doppmeier D, Brinkrolf K, Szczepanowski R, Bernhart SH, Höner Zu Siederdissen C, Bort JA, Wieser M, Kunert R, Jeffs S, Hofacker IL, Goesmann A, Pühler A, Borth N, Grillari J.
J Biotechnol. 2011 Apr 20;153(1-2):62-75.
RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Washietl S, Findeiss S, Müller SA, Kalkhof S, von Bergen M, Hofacker IL, Stadler PF, Goldman N.
RNA. 2011 Apr;17(4):578-94.
RNA Accessibility in cubic time.
Bernhart SH, Mückstein U, Hofacker IL.
Algorithms Mol Biol. 2011 Mar 9;6(1):3.
AREsite: a database for the comprehensive investigation of AU-rich elements.
Gruber AR, Fallmann J, Kratochvill F, Kovarik P, Hofacker IL.
Nucleic Acids Res. 2011 Jan;39(Database issue):D66-9.
E-mail: javier.martinez(at)meduniwien.ac.at
Phone: 0043-1-4277-61803
Research Group: https://www.maxperutzlabs.ac.at/research/research-groups/martinez
Institution: Max Perutz Labs/MedUni Wien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2007.
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2015.
PhD students within/associated to the DK:
Dhaarsini Koneswarakantha
Igor Asanovic
Ameya Khandekar
DK RNA Biology Alumni:
Paola Hentges Pinto: “Identification of ANGEL as a novel and unique eukaryotic family of RNA 2′, 3′-cyclic phosphatases”
Johannes Popow: “Identification and characterization of a human tRNA ligase complex”
Sabrina Bandini: “Characterization of the cellular function of the 5′ polinucleotide kinase NOL9”
Theresa Henkel: “Cytoplasmic functions of the tRNA ligase complex in health and disease”
For complete list of group members please visit the Martinez group website.
Our research:
Our laboratory combines biochemistry, bioinformatics, PAR-CLIP and mouse knockout models to study novel enzymes that phosphorylate RNA molecules and ligate pre-tRNAs and pre-mRNAs during non-canonical splicing.
In vitro and in silico approaches allow a profound mechanistic and structural understanding of these enzymatic activities.
In vivo analysis promises to reveal connections between RNA metabolism and disease.
Publications:
The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli.
Temmel H, Müller C, Sauert M, Vesper O, Reiss A, Popow J, Martinez J, Moll I.
Nucleic Acids Res. 2017 May 5;45(8):4708-4721.
A code within a code: how codons influence mRNA stability.
Martinez J, Zagrovic B.
EMBO J. 2016 Oct 4;35(19):2064-2065.
CLP1 as a novel player in linking tRNA splicing to neurodegenerative disorders.
Weitzer S, Hanada T, Penninger JM, Martinez J.
Wiley Interdiscip Rev RNA. 2015 Jan-Feb;6(1):47-63.
The mammalian tRNA ligase complex mediates splicing of XBP1 mRNA and controls antibody secretion in plasma cells.
Jurkin J, Henkel T, Nielsen AF, Minnich M, Popow J, Kaufmann T, Heindl K, Hoffmann T, Busslinger M, Martinez J.
EMBO J. 2014 Dec 17;33(24):2922-36.
Analysis of orthologous groups reveals archease and DDX1 as tRNA splicing factors.
Popow J, Jurkin J, Schleiffer A, Martinez J.
Nature. 2014 Jul 3;511(7507):104-7.
Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function.
Karaca E, Weitzer S, Pehlivan D, Shiraishi H, Gogakos T, Hanada T, Jhangiani SN, Wiszniewski W, Withers M, Campbell IM, Erdin S, Isikay S, Franco LM, Gonzaga-Jauregui C, Gambin T, Gelowani V, Hunter JV, Yesil G, Koparir E, Yilmaz S, Brown M, Briskin D, Hafner M, Morozov P, Farazi TA, Bernreuther C, Glatzel M, Trattnig S, Friske J, Kronnerwetter C, Bainbridge MN, Gezdirici A, Seven M, Muzny DM, Boerwinkle E, Ozen M; Baylor Hopkins Center for Mendelian Genomics, Clausen T, Tuschl T, Yuksel A, Hess A, Gibbs RA, Martinez J, Penninger JM, Lupski JR.
Cell. 2014 Apr 24;157(3):636-50.
Intron excision from precursor tRNA molecules in mammalian cells requires ATP hydrolysis and phosphorylation of tRNA-splicing endonuclease components.
Mair B, Popow J, Mechtler K, Weitzer S, Martinez J.
Biochem Soc Trans. 2013 Aug;41(4):831-7.
miR-100 suppresses IGF2 and inhibits breast tumorigenesis by interfering with proliferation and survival signaling.
Gebeshuber CA, Martinez J.
Oncogene. 2013 Jul 4;32(27):3306-10.
Focal segmental glomerulosclerosis is induced by microRNA-193a and its downregulation of WT1.
Gebeshuber CA, Kornauth C, Dong L, Sierig R, Seibler J, Reiss M, Tauber S, Bilban M, Wang S, Kain R, Böhmig GA, Moeller MJ, Gröne HJ, Englert C, Martinez J, Kerjaschki D.
Nat Med. 2013 Apr;19(4):481-7.
CLP1 links tRNA metabolism to progressive motor-neuron loss.
Hanada T, Weitzer S, Mair B, Bernreuther C, Wainger BJ, Ichida J, Hanada R, Orthofer M, Cronin SJ, Komnenovic V, Minis A, Sato F, Mimata H, Yoshimura A, Tamir I, Rainer J, Kofler R, Yaron A, Eggan KC, Woolf CJ, Glatzel M, Herbst R, Martinez J, Penninger JM.
Nature. 2013 Mar 28;495(7442):474-80.
Diversity and roles of (t)RNA ligases.
Popow J, Schleiffer A, Martinez J.
Cell Mol Life Sci. 2012 Aug;69(16):2657-70.
HSPC117 is the essential subunit of a human tRNA splicing ligase complex.
Popow J, Englert M, Weitzer S, Schleiffer A, Mierzwa B, Mechtler K, Trowitzsch S, Will CL, Lührmann R, Söll D, Martinez J.
Science. 2011 Feb 11;331(6018):760-4.
Nol9 is a novel polynucleotide 5′-kinase involved in ribosomal RNA processing.
Heindl K, Martinez J.
EMBO J. 2010 Dec 15;29(24):4161-71.
MicroRNAs cross the line: the battle for mRNA stability enters the coding sequence.
Nielsen AF, Gloggnitzer J, Martinez J.
Mol Cell. 2009 Jul 31;35(2):139-40.
Ars2 and the Cap-Binding Complex Team up for Silencing.
Nielsen AF, Gloggnitzer J, Martinez J.
Cell. 2009 Jul 23;138(2):224-6.
The TLR-independent DNA recognition pathway in murine macrophages: Ligand features and molecular signature.
Karayel E, Bürckstümmer T, Bilban M, Dürnberger G, Weitzer S, Martinez J, Superti-Furga G.
Eur J Immunol. 2009 Jul;39(7):1929-36.
miR-29a suppresses tristetraprolin, which is a regulator of epithelial polarity and metastasis.
Gebeshuber CA, Zatloukal K, Martinez J.
EMBO Rep. 2009 Apr;10(4):400-5.
Target site effects in the RNA interference and microRNA pathways.
Obernosterer G, Tafer H, Martinez J.
Biochem Soc Trans. 2008 Dec;36(Pt 6):1216-9.
The impact of target site accessibility on the design of effective siRNAs.
Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.
Nat Biotechnol. 2008 May;26(5):578-83.
E-mail: kazufumi.mochizuki(at)imba.oeaw.ac.at
Institution: previously at IMBA until end of 2016, then:
Kazufumi Mochizuki & his group moved to IGH Montpellier
Full member of the DoktoratsKolleg RNA Biology since 2007 until 2016.
Full member of the Focus Regulatory RNA (SFB RNA-REG) from 2011 until 2015.
PhD students within/associated to the DK:
Quentin Rahms
DK RNA Alumni:
Sophie Soyka: “Characterization of a novel gene from Tetrahymena thermophila involved in RNA directed DNA elimination”
Jan Henrik Suhren: “Small RNA-directd heterochromatin formtion in Tetrahymena thermophila”
Ursula Schöberl: “RNA-directed DNA elimination in Tetrahymena thermophila”
Research:
Transgenerational epigenetic inheritance has been observed in a wide variety of eukaryotes from plants to mammals while its molecular mechanism is still unclear. Our group studies such an epigenetic inheritance process that regulates programmed DNA elimination in the ciliated protozoan Tetrahymena. Nuclear-acting small RNAs mediate the communication between the parental and gremlin genomes and we try to understand how these small RNAs are utilized to establish the epigenetic inheritance.
E-mail: dbarlow(at)cemm.oeaw.ac.at
Research Group: www.cemm.oeaw.ac.at
Institution: CeMM
Full member of the DoktoratsKolleg RNA Biology from 2007 until 2013.
Full member of the Focus Regulatory RNA (SFB RNA-REG) from 2011 until 2015.
DK RNA Biology Alumni:
Daniel Andergassen: “Mapping the mouse Allelome reveals tissue-specific regulation”
Alexandra Kornienko: “Identification and variabilitiy analysis of long non-coding RNAs in human primary granulocytes”
Tomasz Kulinski: “Genomic imprinting in mouse extra-embryonic cell lineage in vitro and in vivo”
Federica Santoro: “Onset and maintenance of Airn non-coding RNA mediated imprinted expression in an in vitro embryonic stem cell model”
Philipp Günzl: “Macro lncRNA hallmarks analyzed by RNAseq”
Genomic imprinting – an entry point for the unexpected:
All mammals including human beings inherit equal numbers of genes from both their parents, but about 200 of these are ‘imprinted’ by one parent. The consequences of this is that although we have two parental copies of imprinted genes only one copy can be turned on, while the other is locked in a silent state. The study of imprinted genes has uncovered many unpredictable findings about what controls the on/off state of a gene. In particular, the Barlow lab has shown that a special class of inefficiently-spliced long non-coding RNA, known as a ‘macro’ ncRNA, act in cis to initiate silencing of imprinted genes. The human genome is known to contain vast numbers of long ncRNAs that are presumed to play a gene-regulatory role. The Barlow lab is now using RNA-seq combined with a recently developed pipeline to optimize the identification of the whole coding and non-coding transcriptome in mammalian cells, to study the role of long and macro ncRNAs in development and disease.
E-mail: michael.jantsch(at)meduniwien.ac.at
Phone: +43 1 40160 37510
Research Group: Jantsch group
Institution: MedUniWien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2007.
Head of the Focus Regulatory RNA (SFB RNA-REG) since February 2015; full member since 2011.
PhD students within/associated to the DK:
Utkarsh Kapoor
Renata Kleinová
DK RNA Biology alumni:
Prajakta Bajad: “Understanding the phenotype of Adar1-deficient mice”
Maja Stulic: “Impact of pre-mRNA editing on Filamin A function”
Mansoureh Tajaddod: “Impact of SINEs on gene expression”
Conny Vesely: “Impact of ADARs on miRNA abundance and sequence”
Silpi Banerjee: “Nuclear Import and substrate recognition by dsRBDs”
Aamira Tariq: “Identification of inhibitors of A to I editing”
For complete list of group members please visit the Jantsch group website.
Our research:
Publications: (since 2007)
A high resolution A-to-I editing map in the mouse identifies editing events controlled by pre-mRNA splicing.
Licht K, Kapoor U, Amman F, Picardi E, Martin D, Bajad P, Jantsch MF.
Genome Res. 2019 Aug 19. [Epub ahead of print]
Dynamic Interactions Between the Genome and an Endogenous Retrovirus: Tirant in Drosophila simulans Wild-Type Strains.
Fablet M, Jacquet A, Rebollo R, Haudry A, Rey C, Salces-Ortiz J, Bajad P, Burlet N, Jantsch MF, Guerreiro MPG, Vieira C.
G3 (Bethesda). 2019 Mar 7;9(3):855-865.
Inosine induces context-dependent recoding and translational stalling.
Licht K, Hartl M, Amman F, Anrather D, Janisiw MP, Jantsch MF.
Nucleic Acids Res. 2019 Jan 10;47(1):3-14.
RNA editing of Filamin A pre-mRNA regulates vascular contraction and diastolic blood pressure.
Jain M, Mann TD, Stulić M, Rao SP, Kirsch A, Pullirsch D, Strobl X, Rath C, Reissig L, Moreth K, Klein-Rodewald T, Bekeredjian R, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Pablik E, Cimatti L, Martin D, Zinnanti J, Graier WF, Sibilia M, Frank S, Levanon EY, Jantsch MF.
EMBO J. 2018 Aug 7. [Epub ahead of print]
Organ-wide profiling in mouse reveals high editing levels of Filamin B mRNA in the musculoskeletal system.
Czermak P, Amman F, Jantsch MF, Cimatti L.
RNA Biol. 2018 Jul 31:1-9. [Epub ahead of print]
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Jantsch MF, Quattrone A, O’Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.
RNA Biol. 2018 May 9:1-3.
Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells.
Avogaro L, Querido E, Dalachi M, Jantsch MF, Chartrand P, Cusanelli E.
RNA Biol. 2018 Apr 16:1-10.
The Other Face of an Editor: ADAR1 Functions in Editing-Independent Ways.
Licht K, Jantsch MF.
Bioessays. 2017 Nov;39(11).
A to I editing in disease is not fake news.
Bajad P, Jantsch MF, Keegan L, O’Connell M.
RNA Biol. 2017 Sep 2;14(9):1223-1231.
RNA-editing enzymes ADAR1 and ADAR2 coordinately regulate the editing and expression of Ctn RNA.
Anantharaman A, Gholamalamdari O, Khan A, Yoon JH, Jantsch MF, Hartner JC, Gorospe M, Prasanth SG, Prasanth KV.
FEBS Lett. 2017 Sep;591(18):2890-2904.
RNA in Disease and development.
Barta A, Jantsch MF.
RNA Biol. 2017 May 4;14(5):457-459.
Understanding RNA modifications: the promises and technological bottlenecks of the ‘epitranscriptome’.
Schaefer M, Kapoor U, Jantsch MF.
Open Biol. 2017 May;7(5). pii: 170077.
ADAR2 regulates RNA stability by modifying access of decay-promoting RNA-binding proteins.
Anantharaman A, Tripathi V, Khan A, Yoon JH, Singh DK, Gholamalamdari O, Guang S, Ohlson J, Wahlstedt H, Öhman M, Jantsch MF, Conrad NK, Ma J, Gorospe M, Prasanth SG, Prasanth KV.
Nucleic Acids Res. 2017 Apr 20;45(7):4189-4201.
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.
Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I, Jantsch MF.
Genome Biol. 2016 Oct 25;17(1):220.
Paraspeckles modulate the intranuclear distribution of paraspeckle-associated Ctn RNA.
Anantharaman A, Jadaliha M, Tripathi V, Nakagawa S, Hirose T, Jantsch MF, Prasanth SG, Prasanth KV.
Sci Rep. 2016 Sep 26;6:34043.
Adenosine to Inosine editing frequency controlled by splicing efficiency.
Licht K, Kapoor U, Mayrhofer E, Jantsch MF.
Nucleic Acids Res. 2016 Jul 27;44(13):6398-408.
Rapid and dynamic transcriptome regulation by RNA editing and RNA modifications.
Licht K, Jantsch MF.
J Cell Biol. 2016 Apr 11;213(1):15-22.
The dynamic epitranscriptome: A to I editing modulates genetic information.
Tajaddod M, Jantsch MF, Licht K.
Chromosoma. 2016 Mar;125(1):51-63.
The RNA-editing enzyme ADAR1 controls innate immune responses to RNA.
Mannion NM, Greenwood SM, Young R, Cox S, Brindle J, Read D, Nellåker C, Vesely C, Ponting CP, McLaughlin PJ, Jantsch MF, Dorin J, Adams IR, Scadden AD, Ohman M, Keegan LP, O’Connell MA.
Cell Rep. 2014 Nov 20;9(4):1482-94.
ADAR2 induces reproducible changes in sequence and abundance of mature microRNAs in the mouse brain.
Vesely C, Tauber S, Sedlazeck FJ, Tajaddod M, von Haeseler A, Jantsch MF.
Nucleic Acids Res. 2014 Oct 29;42(19):12155-68.
Drosha protein levels are translationally regulated during Xenopus oocyte maturation.
Muggenhumer D, Vesely C, Nimpf S, Tian N, Yongfeng J, Jantsch MF.
Mol Biol Cell. 2014 Jul 1;25(13):2094-104.
A bimodular nuclear localization signal assembled via an extended double-stranded RNA-binding domain acts as an RNA-sensing signal for transportin 1.
Barraud P, Banerjee S, Mohamed WI, Jantsch MF, Allain FH.
Proc Natl Acad Sci U S A. 2014 May 6;111(18):E1852-61.
Spatio-temporal profiling of Filamin A RNA-editing reveals ADAR preferences and high editing levels outside neuronal tissues.
Stulić M, Jantsch MF.
RNA Biol. 2013 Oct;10(10):1611-7.
RNA-interacting proteins act as site-specific repressors of ADAR2-mediated RNA editing and fluctuate upon neuronal stimulation.
Tariq A, Garncarz W, Handl C, Balik A, Pusch O, Jantsch MF.
Nucleic Acids Res. 2013 Feb 1;41(4):2581-93.
A high-throughput screen to identify enhancers of ADAR-mediated RNA-editing.
Garncarz W, Tariq A, Handl C, Pusch O, Jantsch MF.
RNA Biol. 2013 Feb;10(2):192-204.
Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs.
Vesely C, Tauber S, Sedlazeck FJ, von Haeseler A, Jantsch MF.
Genome Res. 2012 Aug;22(8):1468-76.
Transcript diversification in the nervous system: a to I RNA editing in CNS function and disease development.
Tariq A, Jantsch MF.
Front Neurosci. 2012 Jul 9;6:99.
A structural determinant required for RNA editing.
Tian N, Yang Y, Sachsenmaier N, Muggenhumer D, Bi J, Waldsich C, Jantsch MF, Jin Y.
Nucleic Acids Res. 2011 Jul;39(13):5669-81.
Mutations in Caenorhabditis elegans him-19 show meiotic defects that worsen with age.
Tang L, Machacek T, Mamnun YM, Penkner A, Gloggnitzer J, Wegrostek C, Konrat R, Jantsch MF, Loidl J, Jantsch V.
Mol Biol Cell. 2010 Mar 15;21(6):885-96.
Reaching complexity through RNA editing.
Jantsch MF.
RNA Biol. 2010 Mar-Apr;7(2):191.
Proteome diversification by adenosine to inosine RNA editing.
Pullirsch D, Jantsch MF.
RNA Biol. 2010 Mar-Apr;7(2):205-12.
RNA-regulated interaction of transportin-1 and exportin-5 with the double-stranded RNA-binding domain regulates nucleocytoplasmic shuttling of ADAR1.
Fritz J, Strehblow A, Taschner A, Schopoff S, Pasierbek P, Jantsch MF.
Mol Cell Biol. 2009 Mar;29(6):1487-97.
SINE RNA induces severe developmental defects in Arabidopsis thaliana and interacts with HYL1 (DRB1), a key member of the DCL1 complex.
Pouch-Pélissier MN, Pélissier T, Elmayan T, Vaucheret H, Boko D, Jantsch MF, Deragon JM.
PLoS Genet. 2008 Jun 13;4(6):e1000096.
Specificity of ADAR-mediated RNA editing in newly identified targets.
Riedmann EM, Schopoff S, Hartner JC, Jantsch MF.
RNA. 2008 Jun;14(6):1110-8.
RNA chaperones, RNA annealers and RNA helicases.
Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, Jantsch MF, Konrat R, Bläsi U, Schroeder R.
RNA Biol. 2007 Nov;4(3):118-30. Review.
Regulation of glutamate receptor B pre-mRNA splicing by RNA editing.
Schoft VK, Schopoff S, Jantsch MF
Nucleic Acids Res. 2007;35(11):3723-32.
E-mail: isabella.moll(at)univie.ac.at
Phone: 0043 1 4277 54606
Research Group: https://www.maxperutzlabs.ac.at/research/research-groups/moll
Institution: Max Perutz Labs/UniWien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2007.
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2011.
PhD students within/associated to the DK:
Tanino Albanese
Folke Ebert
Christian Müller
DK RNA Biology Alumni & their PhD theses:
Konstantin Byrgazov: “Interaction between ribosomal proteins S1 and S2: a novel target for antimicrobials semi-selective against Gram-negative bacteria”
Martina Sauert: “Modulation of the translational program mediated by the toxin MazF under diverse stress conditions in Escherichia coli”
Hannes Temmel: “Studies on the physiological function of the RNA-Ligase RtcB in Escherichia coli”
For complete list of group members please visit the Moll group website.
Our research:
One of the fundamental processes of life is the translation of mRNA-based information into proteins by the large ribonucleoprotein complex, the ribosome. Traditionally, the ribosome is viewed as a highly conserved machinery with an invariable rRNA and protein complement. Thus, it was not considered to have an intrinsic regulatory capacity, and the efficiency of translation was suggested to be determined either by features inherent to the mRNA or mediated by proteins or RNA regulators. In contrast to this perception, the Moll lab addresses diverse molecular mechanisms of post-transcriptional regulation of gene expression in Bacteria with a special focus on ribosome heterogeneity.
Publications: (since 2011)
Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!
Beck HJ, Moll I.
Microbiol Spectr. 2018 Jul;6(4).
Autoregulation of mazEF expression underlies growth heterogeneity in bacterial populations.
Nikolic N, Bergmiller T, Vandervelde A, Albanese TG, Gelens L, Moll I.
Nucleic Acids Res. 2018 Apr 6;46(6):2918-2931.
Coordinated Control of mRNA and rRNA Processing Controls Embryonic Stem Cell Pluripotency and Differentiation.
Corsini NS, Peer AM, Moeseneder P, Roiuk M, Burkard TR, Theussl HC, Moll I, Knoblich JA.
Cell Stem Cell. 2018 Apr 5;22(4):543-558.e12.
MazF activation promotes translational heterogeneity of the grcA mRNA in Escherichia coli populations.
Nikolic N, Didara Z, Moll I.
PeerJ. 2017 Sep 21;5:e3830.
The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli.
Temmel H, Müller C, Sauert M, Vesper O, Reiss A, Popow J, Martinez J, Moll I.
Nucleic Acids Res. 2017 May 5;45(8):4708-4721.
A Stress-Induced Bias in the Reading of the Genetic Code in Escherichia coli.
Oron-Gottesman A, Sauert M, Moll I, Engelberg-Kulka H.
MBio. 2016 Nov 15;7(6). pii: e01855-16.
The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli.
Sauert M, Wolfinger MT, Vesper O, Müller C, Byrgazov K, Moll I.
Nucleic Acids Res. 2016 Aug 19;44(14):6660-75.
Insights into the Stress Response Triggered by Kasugamycin in Escherichia coli.
Müller C, Sokol L, Vesper O, Sauert M, Moll I.
Antibiotics (Basel). 2016 Jun 1;5(2).
Escherichia coli Quorum-Sensing EDF, A Peptide Generated by Novel Multiple Distinct Mechanisms and Regulated by trans-Translation.
Kumar S, Kolodkin-Gal I, Vesper O, Alam N, Schueler-Furman O, Moll I, Engelberg-Kulka H.
MBio. 2016 Jan 26;7(1):e02034-15.
Heterogeneity of the translational machinery: Variations on a common theme.
Sauert M, Temmel H, Moll I.
Biochimie. 2015 Jul;114:39-47.
Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.
Byrgazov K, Grishkovskaya I, Arenz S, Coudevylle N, Temmel H, Wilson DN, Djinovic-Carugo K, Moll I.
Nucleic Acids Res. 2015 Jan;43(1):661-73.
Ribosome heterogeneity: another level of complexity in bacterial translation regulation.
Byrgazov K, Vesper O, Moll I.
Curr Opin Microbiol. 2013 Apr;16(2):133-9.
Selective translation during stress in Escherichia coli.
Moll I, Engelberg-Kulka H.
Trends Biochem Sci. 2012 Nov;37(11):493-8.
Direct interaction of the N-terminal domain of ribosomal protein S1 with protein S2 in Escherichia coli.
Byrgazov K, Manoharadas S, Kaberdina AC, Vesper O, Moll I.
PLoS One. 2012;7(3):e32702.
Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli.
Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC, Engelberg-Kulka H, Moll I.
Cell. 2011 Sep 30;147(1):147-57.
E-mail: udo.blaesi(at)univie.ac.at
Phone: 0043 1 4277 54609
Research Group: https://www.maxperutzlabs.ac.at/research/research-groups/blaesi
Institution: Max Perutz Labs/UniWien
Full member of the DoktoratsKolleg (DK) RNA Biology since 2007.
Full member of the Focus Regulatory RNA (SFB RNA-REG) since 2011.
PhD students within/associated to the DK:
Petra Pusic
Marlena Rozner
Branisav Lilic
Anastasia Cianciulli Sesso
DK RNA Biology alumni & their thesis:
Muralidhar Tata: “Identification and characterization of novel regulatory RNAs in Pseudomonas aeruginosa during anaerobiosis”
Alessandra Romeo: “Characterization of small non-coding RNA in Pseudomonas aeruginosa”
Hermann Hämmerle: “Function of Hfq protein in different bacteria”
For complete list of group members please visit the Bläsi group website.
Our research:
The opportunistic human pathogen Pseudomonas aeruginosa is a major cause of nosocomial infections. We have previously identified P. aeruginosa regulatory RNAs that impact on virulence gene expression. Some of these sRNAs are expressed in response to nitrogen or oxygen deprivation, whereby the latter condition can become prevalent in Pseudomonas biofilms present in the lung of cystic fibrosis (CF) patients. The main focus of this project is the identification and functional analysis of regulatory RNAs as well as the elucidation of their impact on gene networks under conditions that mimic growth of the clinical Pseudomonas aeruginosa PA14 strain in CF lungs.
Publications: (since 2007)
Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus.
Bassani F, Zink IA, Pribasnig T, Wolfinger MT, Romagnoli A, Resch A, Schleper C, Bläsi U, La Teana A.
RNA Biol. 2019 May;16(5):675-685.
Architectural principles for Hfq/Crc-mediated regulation of gene expression.
Pei XY, Dendooven T, Sonnleitner E, Chen S, Bläsi U, Luisi BF.
Elife. 2019 Feb 13;8.
Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa.
Pusic P, Sonnleitner E, Krennmayr B, Heitzinger DA, Wolfinger MT, Resch A, Bläsi U.
Front Microbiol. 2018 Nov 9;9:2709.
Negative Control of RpoS Synthesis by the sRNA ReaL in Pseudomonas aeruginosa.
Thi Bach Nguyen H, Romero A D, Amman F, Sorger-Domenigg T, Tata M, Sonnleitner E, Bläsi U.
Front Microbiol. 2018 Oct 29;9:2488.
Modification of translation factor aIF5A from Sulfolobus solfataricus.
Bassani F, Romagnoli A, Cacciamani T, Amici A, Benelli D, Londei P, Märtens B, Bläsi U, La Teana A.
Extremophiles. 2018 Sep;22(5):769-780.
Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa.
Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FH, Luisi BF, Urlaub H, Bläsi U.
Nucleic Acids Res. 2018 Feb 16;46(3):1470-1485.
The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14.
Tata M, Amman F, Pawar V, Wolfinger MT, Weiss S, Häussler S, Bläsi U.
Front Microbiol. 2017 Nov 23;8:2312.
The SmAP2 RNA binding motif in the 3’UTR affects mRNA stability in the crenarchaeum Sulfolobus solfataricus.
Märtens B, Sharma K, Urlaub H, Bläsi U.
Nucleic Acids Res. 2017 Sep 6;45(15):8957-8967.
The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts.
Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U.
Nucleic Acids Res. 2017 Jul 27;45(13):7938-7949.
The Pseudomonas aeruginosa CrcZ RNA interferes with Hfq-mediated riboregulation.
Sonnleitner E, Prindl K, Bläsi U.
PLoS One. 2017 Jul 7;12(7):e0180887.
Cross-regulation by CrcZ RNA controls anoxic biofilm formation in Pseudomonas aeruginosa.
Pusic P, Tata M, Wolfinger MT, Sonnleitner E, Häussler S, Bläsi U.
Sci Rep. 2016 Dec 21;6:39621.
RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium.
Tata M, Wolfinger MT, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U.
PLoS One. 2016 Jan 28;11(1):e0147811.
Binding of the 5′-Triphosphate End of mRNA to the γ-Subunit of Translation Initiation Factor 2 of the Crenarchaeon Sulfolobus solfataricus.
Arkhipova V, Stolboushkina E, Kravchenko O, Kljashtorny V, Gabdulkhakov A, Garber M, Nikonov S, Märtens B, Bläsi U, Nikonov O.
J Mol Biol. 2015 Sep 25;427(19):3086-95.
The Heptameric SmAP1 and SmAP2 Proteins of the Crenarchaeon Sulfolobus Solfataricus Bind to Common and Distinct RNA Targets.
Märtens B, Bezerra GA, Kreuter MJ, Grishkovskaya I, Manica A, Arkhipova V, Djinovic-Carugo K, Bläsi U.
Life (Basel). 2015 Apr 21;5(2):1264-81.
Development of giant bacteriophage ϕKZ is independent of the host transcription apparatus.
Ceyssens PJ, Minakhin L, Van den Bossche A, Yakunina M, Klimuk E, Blasdel B, De Smet J, Noben JP, Bläsi U, Severinov K, Lavigne R.
J Virol. 2014 Sep;88(18):10501-10
Regulation of Hfq by the RNA CrcZ in Pseudomonas aeruginosa carbon catabolite repression.
Sonnleitner E, Bläsi U.
PLoS Genet. 2014 Jun 19;10(6):e1004440.
Impact of Hfq on the Bacillus subtilis transcriptome.
Hämmerle H, Amman F, Večerek B, Stülke J, Hofacker I, Bläsi U.
PLoS One. 2014 Jun 16;9(6):e98661.
Back to translation: removal of aIF2 from the 5′-end of mRNAs by translation recovery factor in the crenarchaeon Sulfolobus solfataricus.
Märtens B, Manoharadas S, Hasenöhrl D, Zeichen L, Bläsi U.
Nucleic Acids Res. 2014 Feb;42(4):2505-11
Duplex formation between the sRNA DsrA and rpoS mRNA is not sufficient for efficient RpoS synthesis at low temperature.
Hämmerle H, Večerek B, Resch A, Bläsi U.
RNA Biol. 2013 Dec;10(12):1834-41.
Alterations of the transcriptome of Sulfolobus acidocaldarius by exoribonuclease aCPSF2.
Märtens B, Amman F, Manoharadas S, Zeichen L, Orell A, Albers SV, Hofacker I, Bläsi U.
PLoS One. 2013 Oct 7;8(10):e76569.
Bacterial helicases in post-transcriptional control.
Kaberdin VR, Bläsi U.
Biochim Biophys Acta. 2013 Aug;1829(8):878-83.
Antisense regulation by transposon-derived RNAs in the hyperthermophilic archaeon Sulfolobus solfataricus.
Märtens B, Manoharadas S, Hasenöhrl D, Manica A, Bläsi U.
EMBO Rep. 2013 Jun;14(6):527-33.
False positive RNA binding activities after Ni-affinity purification from Escherichia coli.
Milojevic T, Sonnleitner E, Romeo A, Djinović-Carugo K, Bläsi U.
RNA Biol. 2013 Jun;10(6):1066-9.
The Pseudomonas aeruginosa catabolite repression control protein Crc is devoid of RNA binding activity.
Milojevic T, Grishkovskaya I, Sonnleitner E, Djinovic-Carugo K, Bläsi U.
PLoS One. 2013 May 23;8(5):e64609.
Attack from both ends: mRNA degradation in the crenarchaeon Sulfolobus solfataricus.
Evguenieva-Hackenberg E, Bläsi U.
Biochem Soc Trans. 2013 Feb 1;41(1):379-83.
Translation initiation in the crenarchaeon Sulfolobus solfataricus: eukaryotic features but bacterial route.
La Teana A, Benelli D, Londei P, Bläsi U.
Biochem Soc Trans. 2013 Feb 1;41(1):350-5.
Structural flexibility of RNA as molecular basis for Hfq chaperone function.
Ribeiro Ede A Jr, Beich-Frandsen M, Konarev PV, Shang W, Vecerek B, Kontaxis G, Hämmerle H, Peterlik H, Svergun DI, Bläsi U, Djinović-Carugo K.
Nucleic Acids Res. 2012 Sep;40(16):8072-84.
Transcriptional regulation of nitrate assimilation in Pseudomonas aeruginosa occurs via transcriptional antitermination within the nirBD-PA1779-cobA operon.
Romeo A, Sonnleitner E, Sorger-Domenigg T, Nakano M, Eisenhaber B, Bläsi U.
Microbiology. 2012 Jun;158(Pt 6):1543-52.
Small regulatory RNAs in Pseudomonas aeruginosa.
Sonnleitner E, Romeo A, Bläsi U.
RNA Biol. 2012 Apr;9(4):364-71.
Structural and biochemical studies on ATP binding and hydrolysis by the Escherichia coli RNA chaperone Hfq.
Hämmerle H, Beich-Frandsen M, Večerek B, Rajkowitsch L, Carugo O, Djinović-Carugo K, Bläsi U.
PLoS One. 2012;7(11):e50892.
Structural insights into the dynamics and function of the C-terminus of the E. coli RNA chaperone Hfq.
Beich-Frandsen M, Vecerek B, Konarev PV, Sjöblom B, Kloiber K, Hämmerle H, Rajkowitsch L, Miles AJ, Kontaxis G, Wallace BA, Svergun DI, Konrat R, Bläsi U, Djinovic-Carugo K.
Nucleic Acids Res. 2011 Jun;39(11):4900-15.
Structural analysis of full-length Hfq from Escherichia coli.
Beich-Frandsen M, Večerek B, Sjöblom B, Bläsi U, Djinović-Carugo K.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 May 1;67(Pt 5):536-40.
The small RNA PhrS stimulates synthesis of the Pseudomonas aeruginosa quinolone signal.
Sonnleitner E, Gonzalez N, Sorger-Domenigg T, Heeb S, Richter AS, Backofen R, Williams P, Hüttenhofer A, Haas D, Bläsi U.
Mol Microbiol. 2011 May;80(4):868-85.
Identification of an RNase J ortholog in Sulfolobus solfataricus: implications for 5′-to-3′ directional decay and 5′-end protection of mRNA in Crenarchaeota.
Hasenöhrl D, Konrat R, Bläsi U.
RNA. 2011 Jan;17(1):99-107
Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA.
Resch A, Većerek B, Palavra K, Bläsi U.
RNA Biol. 2010 Nov-Dec;7(6):796-802.
Translational activation of rpoS mRNA by the non-coding RNA DsrA and Hfq does not require ribosome binding.
Vecerek B, Beich-Frandsen M, Resch A, Bläsi U.
Nucleic Acids Res. 2010 Mar;38(4):1284-93
Translation initiation complex formation in the crenarchaeon Sulfolobus solfataricus.
Hasenöhrl D, Fabbretti A, Londei P, Gualerzi CO, Bläsi U.
RNA. 2009 Dec;15(12):2288-98.
Antimicrobial activity of a chimeric enzybiotic towards Staphylococcus aureus.
Manoharadas S, Witte A, Bläsi U.
J Biotechnol. 2009 Jan 1;139(1):118-23
A single mutation in the IF3 N-terminal domain perturbs the fidelity of translation initiation at three levels.
Maar D, Liveris D, Sussman JK, Ringquist S, Moll I, Heredia N, Kil A, Bläsi U, Schwartz I, Simons RW.
J Mol Biol. 2008 Nov 28;383(5):937-44.
Crystal structure of the intact archaeal translation initiation factor 2 demonstrates very high conformational flexibility in the alpha- and beta-subunits.
Stolboushkina E, Nikonov S, Nikulin A, Bläsi U, Manstein DJ, Fedorov R, Garber M, Nikonov O.
J Mol Biol. 2008 Oct 10;382(3):680-91.
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.
Sonnleitner E, Sorger-Domenigg T, Madej MJ, Findeiss S, Hackermüller J, Hüttenhofer A, Stadler PF, Bläsi U, Moll I.
Microbiology. 2008 Oct;154(Pt 10):3175-87.
Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5′-leader.
Resch A, Afonyushkin T, Lombo TB, McDowall KJ, Bläsi U, Kaberdin VR.
RNA. 2008 Mar;14(3):454-9.
Translation initiation factor a/eIF2(-gamma) counteracts 5′ to 3′ mRNA decay in the archaeon Sulfolobus solfataricus.
Hasenöhrl D, Lombo T, Kaberdin V, Londei P, Bläsi U.
Proc Natl Acad Sci U S A. 2008 Feb 12;105(6):2146-50.
The C-terminal domain of Escherichia coli Hfq is required for regulation.
Vecerek B, Rajkowitsch L, Sonnleitner E, Schroeder R, Bläsi U.
Nucleic Acids Res. 2008 Jan;36(1):133-43.
RNA chaperones, RNA annealers and RNA helicases.
Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, Jantsch MF, Konrat R, Bläsi U, Schroeder R.
RNA Biol. 2007 Nov;4(3):118-30. Review.
New insights into the interactions of the translation initiation factor 2 from archaea with guanine nucleotides and initiator tRNA.
Nikonov O, Stolboushkina E, Nikulin A, Hasenöhrl D, Bläsi U, Manstein DJ, Fedorov R, Garber M, Nikonov S.
J Mol Biol. 2007 Oct 19;373(2):328-36.
Bacteriophage-encoded toxins: the lambda-holin protein causes caspase-independent non-apoptotic cell death of eukaryotic cells.
Agu CA, Klein R, Lengler J, Schilcher F, Gregor W, Peterbauer T, Bläsi U, Salmons B, Günzburg WH, Hohenadl C.
Cell Microbiol. 2007 Jul;9(7):1753-65. Epub 2007 Mar 8.
Control of Fur synthesis by the non-coding RNA RyhB and iron-responsive decoding.
Vecerek B, Moll I, Bläsi U.
EMBO J. 2007 Feb 21;26(4):965-75. Epub 2007 Feb 1.
Distinct and overlapping binding sites of Pseudomonas aeruginosa Hfq and RsmA proteins on the non-coding RNA RsmY.
Sorger-Domenigg T, Sonnleitner E, Kaberdin VR, Bläsi U.
Biochem Biophys Res Commun. 2007 Jan 19;352(3):769-73.
E-mail: renee.schroeder(at)univie.ac.at
Phone: 0043 1 4277 54690
Research Group: www.mfpl.ac.at/schroeder
Institution: MFPL/UniWien
Full member of the DoktoratsKolleg RNA Biology from 2007 until 2016.
Full member of the Focus Regulatory RNA (SFB-RNA Reg) from 2007 until 2018.
PhD student associated to the DK:
Andrés Mágán Garcia
DK RNA Biology Alumni:
“in spe”: Ivana Bilusic: “Antisense RNAs in E. coli”
Max Radtke: “Exploring Intra-splicing and its regulatory potential”
Adam Weiss: “In search of cis-acting RNA regulators of RNA polymerase II”
Nadezda Tukhtubaeva: “Transcriptional regulation in bacteria: exploring the world of RNA aptamers”
Martina Dötsch: “RNA structural remodeling by RNA annealer proteins and RNA chaperones”
Bob Zimmermann: “Computational and Biochemical Analyses of Genomic Aptamers in Multiple Species”
Katarzyna Matylla Kulinska: “Function and expression of human alpha satellites”
Krzysztof Chylinski (PhD student with Emmanuelle Charpentier, Helmholtz Center for Infection Research, Braunschweig): “The bacterial immunity system CRISPR/Cas: evolution and mechanisms of action.”
For complete list of lab current lab members please visit the Schroeder group webpage.
Our research:
RNA is at the center of all steps of gene expression. Cells can be defined by their transcriptomes, not by their genomes. We are interested in discovering many regulatory elements that are part of the RNA regulon and in identifying their interacting partners and their targets. To achieve this goal we adapted the classical SELEX procedure to be used in combination with genome sequences and deep sequencing. Genomic systematic evolution of ligands by exponential enrichment (SELEX) allows the isolation of protein binding RNAs independently of computational predictions and expression conditions. We used genomic SELEX with an E. coli library to isolate RNA aptamers against RNA polymerase and the regulator protein Hfq. We further selected RNA polymerase II binding aptamers from the yeast and human genomes. These experiments delivered thousands of genomic RNA aptamers that regulate gene expression. We are currently analyzing the mode of action of these aptamers.
Another focus in our laboratory deals with proteins that promote RNA folding: RNA chaperones. As model examples we are analyzing the mode of action of the E. coli protein StpA and the HIV-1 Tat peptide. While StpA promotes RNA annealing and strand exchange, HIV-1 Tat only promotes RNA annealing. Using biochemical and biophysical methods (NMR) we study the structural dynamics of both RNA and protein.
Publications: (since 2007)
Nascent RNA signaling to yeast RNA Pol II during transcription elongation.
Klopf E, Moes M, Amman F, Zimmermann B, von Pelchrzim F, Wagner C, Schroeder R.
PLoS One. 2018 Mar 23;13(3):e0194438.
Natural RNA Polymerase Aptamers Regulate Transcription in E. coli.
Sedlyarova N, Rescheneder P, Magán A, Popitsch N, Rziha N, Bilusic I, Epshtein V, Zimmermann B, Lybecker M, Sedlyarov V, Schroeder R, Nudler E.
Mol Cell. 2017 Jul 6;67(1):30-43.e6.
In vivo expression technology and 5′ end mapping of the Borrelia burgdorferi transcriptome identify novel RNAs expressed during mammalian infection.
Adams PP, Flores Avile C, Popitsch N, Bilusic I, Schroeder R, Lybecker M, Jewett MW.
Nucleic Acids Res. 2017 Jan 25;45(2):775-792.
Temperature-dependent sRNA transcriptome of the Lyme disease spirochete.
Popitsch N, Bilusic I, Rescheneder P, Schroeder R, Lybecker M.
BMC Genomics. 2017 Jan 5;18(1):28.
sRNA-Mediated Control of Transcription Termination in E. coli.
Sedlyarova N, Shamovsky I, Bharati BK, Epshtein V, Chen J, Gottesman S, Schroeder R, Nudler E.
Cell. 2016 Sep 22;167(1):111-121.e13.
The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.
Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC.
Nucleic Acids Res. 2016 Feb 29;44(4):1703-17.
RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E.
RNA Biol. 2016;13(2):177-95.
Soups & SELEX for the origin of life.
Schroeder R.
RNA. 2015 Apr;21(4):729-32
Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs.
Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R.
Wiley Interdiscip Rev RNA. 2014 Sep-Oct;5(5):591-600.
The double-stranded transcriptome of Escherichia coli.
Lybecker M, Zimmermann B, Bilusic I, Tukhtubaeva N, Schroeder R.
Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):3134-9.
Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation.
Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M.
RNA Biol. 2014;11(5):641-54.
Study of E. coli Hfq’s RNA annealing acceleration and duplex destabilization activities using substrates with different GC-contents.
Doetsch M, Stampfl S, Fürtig B, Beich-Frandsen M, Saxena K, Lybecker M, Schroeder R.
Nucleic Acids Res. 2013 Jan 7;41(1):487-97.
Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA.
Stampfl S, Doetsch M, Beich-Frandsen M, Schroeder R.
RNA Biol. 2013 Jan;10(1):149-56.
Finding aptamers and small ribozymes in unexpected places.
Matylla-Kulinska K, Boots JL, Zimmermann B, Schroeder R.
Wiley Interdiscip Rev RNA. 2012 Jan-Feb;3(1):73-91.
Transient RNA-protein interactions in RNA folding.
Doetsch M, Schroeder R, Fürtig B.
FEBS J. 2011 May;278(10):1634-42.
The RNA annealing mechanism of the HIV-1 Tat peptide: conversion of the RNA into an annealing-competent conformation.
Doetsch M, Fürtig B, Gstrein T, Stampfl S, Schroeder R.
Nucleic Acids Res. 2011 May;39(10):4405-18.
Mechanisms of StpA-mediated RNA remodeling.
Doetsch M, Gstrein T, Schroeder R, Fürtig B.
RNA Biol. 2010 Nov-Dec;7(6):735-43.
Genomic SELEX: a discovery tool for genomic aptamers.
Zimmermann B, Bilusic I, Lorenz C, Schroeder R.
Methods. 2010 Oct;52(2):125-32.
Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts.
Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R.
Nucleic Acids Res. 2010 Jun;38(11):3794-808.
Monitoring genomic sequences during SELEX using high-throughput sequencing: neutral SELEX.
Zimmermann B, Gesell T, Chen D, Lorenz C, Schroeder R.
PLoS One. 2010 Feb 11;5(2):e9169.
In vitro selection of RNA aptamers derived from a genomic human library against the TAR RNA element of HIV-1.
Watrin M, Von Pelchrzim F, Dausse E, Schroeder R, Toulmé JJ.
Biochemistry. 2009 Jul 7;48(26):6278-84.
Janus chaperones: assistance of both RNA- and protein-folding by ribosomal proteins.
Kovacs D, Rakacs M, Agoston B, Lenkey K, Semrad K, Schroeder R, Tompa P.
FEBS Lett. 2009 Jan 5;583(1):88-92.
The impact of target site accessibility on the design of effective siRNAs.
Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, Martinez J, Hofacker IL.
Nat Biotechnol. 2008 May;26(5):578-83.
The C-terminal domain of Escherichia coli Hfq is required for regulation.
Vecerek B, Rajkowitsch L, Sonnleitner E, Schroeder R, Bläsi U.
Nucleic Acids Res. 2008 Jan;36(1):133-43.
Screening for engineered neomycin riboswitches that control translation initiation.
Weigand JE, Sanchez M, Gunnesch EB, Zeiher S, Schroeder R, Suess B.
RNA. 2008 Jan;14(1):89-97.
Isolation of small RNA-binding proteins from E. coli: evidence for frequent interaction of RNAs with RNA polymerase.
Windbichler N, von Pelchrzim F, Mayer O, Csaszar E, Schroeder R.
RNA Biol. 2008 Jan-Mar;5(1):30-40.
Dissecting RNA chaperone activity.
Rajkowitsch L, Schroeder R.
RNA. 2007 Dec;13(12):2053-60.
RNA chaperones, RNA annealers and RNA helicases.
Rajkowitsch L, Chen D, Stampfl S, Semrad K, Waldsich C, Mayer O, Jantsch MF, Konrat R, Bläsi U, Schroeder R.
RNA Biol. 2007 Nov;4(3):118-30. Review.
Coupling RNA annealing and strand displacement: a FRET-based microplate reader assay for RNA chaperone activity.
Rajkowitsch L, Schroeder R.
Biotechniques. 2007 Sep;43(3):304, 306, 308 passim. Erratum in: Biotechniques. 2007 Nov;43(5):573.
Molecular basis for target RNA recognition and cleavage by human RISC.
Ameres SL, Martinez J, Schroeder R.
Cell. 2007 Jul 13;130(1):101-12.
Monovalent ion dependence of neomycin B binding to an RNA aptamer characterized by spectroscopic methods.
Stampfl S, Lempradl A, Koehler G, Schroeder R.
Chembiochem. 2007 Jul 9;8(10):1137-45.
RNA techniques for bacteria.
Charpentier E, Schroeder R.
Curr Opin Microbiol. 2007 Jun;10(3):254-6.
Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA.
Panzitt K, Tschernatsch MM, Guelly C, Moustafa T, Stradner M, Strohmaier HM, Buck CR, Denk H, Schroeder R, Trauner M, Zatloukal K.
Gastroenterology. 2007 Jan;132(1):330-42.
RNA chaperone activity of L1 ribosomal proteins: phylogenetic conservation and splicing inhibition.
Ameres SL, Shcherbakov D, Nikonova E, Piendl W, Schroeder R, Semrad K.
Nucleic Acids Res. 2007;35(11):3752-63.
RNA chaperone activity and RNA-binding properties of the E. coli protein StpA.
Mayer O, Rajkowitsch L, Lorenz C, Konrat R, Schroeder R.
Nucleic Acids Res. 2007;35(4):1257-69.
Annual SFB & DK RNA Retreat: 10th – 12th May 2012 in Aflenz (Steiermark).
E-mail: andrea.barta(at)meduniwien.ac.at
Phone: 0043 1 4277 61640
Research website: www.maxperutzlabs.ac.at/education/lecturers/barta
Institution: May Perutz Labs/MedUniWien
Speaker of the DoktoratsKolleg (DK) RNA Biology since 2007 and member of the Focus Regulatory RNA (SFB RNA Reg) from 2011 to 2015.
PhD students within/associated to the DK:
Manali MISHRA
Katarina RADISAVLJEVIC (co-supervised by Alwin Köhler)
DK RNA Biology alumni & their PhD theses:
Olga BANNIKOVA: “Finding RNA targets for the multidomain cyclophilin AtCyp59 by Genomic SELEX in Arabidopsis thaliana”
Janett GÖHRING: “Imaging of Endogenous mRNA Splice Variants in Living Plant Cells”
Yamile MARQUEZ ORTIZ: “Identification of Alternative Splicing Events in Arabidopsis thaliana: Regulation by abiotic stress and plant specific SR proteins”
Armin FUCHS: “Unraveling the role of the plant-specific Ser/Arg-rich proteins RS31 and RS31a in alternative splicing and the DNA damage response in Arabidopsis thaliana”
Our research:
What determines the complexity of higher organisms? No correlation has been found to DNA content and gene number and therefore studies in the field are now focusing on post-transcriptional processes and the impact of the dynamic transcriptome on gene expression.
Alternative splicing is one of the posttranscriptional events to expand the repertoire of genes and it has been exploited for various differentiation processes. In plants, the significance of alternative splicing was long underestimated, but we and others have shown that it greatly impacts on development and response to the environment. As alternative splicing in Arabidopsis is not well defined we are using RNAseq to define the rules and targets of alternative splicing.
SR (Ser/Arg) proteins are important splicing factors and to date we have isolated and partially characterized several Arabidopsis SR proteins, which are important for splice site selection and spliceosome assembly. In addition, we have isolated several regulatory proteins which seem to be essential to drive the splicing process, like SRPK kinases, helicases and cyclophilins. To elucidate their mechanisms of action some of the plant SR proteins and cyclophilins are currently characterized in greater detail in terms of their RNA targets, interacting proteins and their impact on flowering and UV-stress response. Interestingly, some of these factors seem to connect splicing to transcription and are therefore currently investigated in greater detail.
Furthermore, a project has been started to investigate the influence of chromatin and DNA modifications on alternative splicing in plants. In another line of research, we are developing a genomic method to select for riboswitches (these are regulatory RNA elements which can bind metabolites) in plants, as they are implicated in regulating alternative splicing and gene expression.
Publications: (since 2011)
The Cyclin Dependent Kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.
Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan JH.
Plant J. 2018 Mar 30.
RNA in Disease and development.
Barta A, Jantsch MF.
RNA Biol. 2017 May 4;14(5):457-459.
doi: 10.1080/15476286.2017.
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
Zhang R, Calixto CP, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W, Spensley M, Entizne JC, Lewandowska D, Ten Have S, Frei Dit Frey N, Hirt H, James AB, Nimmo HG, Barta A, Kalyna M, Brown JW.
Nucleic Acids Res. 2017 Apr 11.
The spliceosome-associated protein Nrl1 suppresses homologous recombination-dependent R-loop formation in fission yeast.
Aronica L, Kasparek T, Ruchman D, Marquez Y, Cipak L, Cipakova I, Anrather D, Mikolaskova B, Radtke M, Sarkar S, Pai CC, Blaikley E, Walker C, Shen KF, Schroeder R, Barta A, Forsburg SL, Humphrey TC.
Nucleic Acids Res. 2016 Feb 29;44(4):1703-17.
Lost in Translation: Pitfalls in Deciphering Plant Alternative Splicing Transcripts.
Brown JW, Simpson CG, Marquez Y, Gadd GM, Barta A, and Kalyna M
Plant Cell. 2015 Aug;27(8):2083-7.
Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity.
Marquez Y, Höpfler M, Ayatollahi Z, Barta A, Kalyna M.
Genome Res. 2015 Jul;25(7):995-1007.
AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W, Marquez Y, Kalyna M, Patro R, Eyras E, Barta A, Nimmo HG, Brown JW.
New Phytol. 2015 Jun 25.
Suitable transfection methods for single particle tracing in plant suspension cells.
Göhring J, Fulcher N, Schilcher K, Barta A, Jacak J.
Plant Methods. 2014 May 31;10:15.
A chloroplast retrograde signal regulates nuclear alternative splicing.
Petrillo E, Godoy Herz MA, Fuchs A, Reifer D, Fuller J, Yanovsky MJ, Simpson C, Brown JWS, Barta A, Kalyna M, Kornblihtt AR
Science. 2014 Apr 25;344(6182):427-30.
Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis.
Göhring J, Jacak J, Barta A.
Plant Cell. 2014 Feb;26(2):754-64.
Suitable transfection methods for single particle tracing in plant suspension cells.
Göhring J, Fulcher N, Schilcher K, Barta A, Jacak J.
Plant Methods. 2014 May 31;10:15.
Shedding light on the chloroplast as a remote control of nuclear gene expression.
Godoy Herz MA, Kornblihtt AR, Barta A, Kalyna M, Petrillo E.
Plant Signal Behav. 2014;9(11):e976150.
Let there be light: regulation of gene expression in plants.
Petrillo E, Godoy Herz MA, Barta A, Kalyna M, Kornblihtt AR.
RNA Biol. 2014;11(10):1215-20
Complexity of the alternative splicing landscape in plants.
Reddy AS, Marquez Y, Kalyna M, Barta A.
Plant Cell. 2013 Oct;25(10):3657-83.
Introns of plant pri-miRNAs enhance miRNA biogenesis.
Bielewicz D, Kalak M, Kalyna M, Windels D, Barta A, Vazquez F, Szweykowska-Kulinska Z, Jarmolowski A.
EMBO Rep. 2013 Jul;14(7):622-8.
Identification of RNA targets for the nuclear multidomain cyclophilin atCyp59 and their effect on PPIase activity.
Bannikova O, Zywicki M, Marquez Y, Skrahina T, Kalyna M, Barta A.
Nucleic Acids Res. 2013 Feb 1;41(3):1783-96.
Alternative splicing in plants–coming of age.
Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW.
Trends Plant Sci. 2012 Oct;17(10):616-23.
Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis.
Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M.
Genome Res. 2012 Jun;22(6):1184-95.
Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis.
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 JW.
Nucleic Acids Res. 2012 Mar;40(6):2454-69.
Localization and dynamics of nuclear speckles in plants.
Reddy AS, Day IS, Göhring J, Barta A.
Plant Physiol. 2012 Jan;158(1):67-77.
Bianca M. Mladek, VIPS Postdoc at MFPL since one year, has been awarded a prestigious Marie Curie Career Integration Grant. ((more…))