RNA Biology

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.