RNA Biology

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.

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.

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.

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.

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.

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: 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:

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: 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.