RNA - protein interactions in mrna decay A case study on TTP and HuR in AMD

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1 RNA - protein interactions in mrna decay A case study on TTP and HuR in AMD Jörg Fallmann Institute for Theoretical Biochemistry University of Vienna Research Platform Decoding mrna decay in inflammation Interdisciplinary project funded by the University of Vienna

2 ARE Mediated Decay (AMD) AU-rich element 5' UTR CDS 3' UTR poly-a tail J. Fallmann,TBI RNA - protein interactions in RNA decay 1/ 13

3 Open Questions How do ABPs choose their target(s)? Do RNA elements dictate function in AMD? What makes the difference (sequence and/or structure)? Different binding site == different decay rate? Do ABPs compete for RNA motifs? Exact mechanisms of AMD and ARE-ABP interaction remain unclear J. Fallmann,TBI RNA - protein interactions in RNA decay 2/ 13

4 Biological system Primary mouse macrophages LPS induces inflammatory response No overexpression needed TTP +/+ (WT) and TTP / (KO) mouse PAR-iCLIP based dataset RNA-Seq without crosslink (Vitaly Sedlyarov, Kovarik Lab) J. Fallmann,TBI RNA - protein interactions in RNA decay 3/ 13

5 Binding preferences TTP TTP binds predominantly to 3 UTR exons Surprisingly high read counts in CDS introns Function of intronic binding unclear (sponge?) HuR HuR binds predominantly to 3 UTR exons independently of TTPs presence J. Fallmann,TBI RNA - protein interactions in RNA decay 4/ 13

6 MEME J. Fallmann,TBI RNA - protein interactions in RNA decay 5/ 13

7 TTP/HuR 3 UTR target genes J. Fallmann,TBI RNA - protein interactions in RNA decay 6/ 13

8 Overlap sequence motif 2 bits 1 1U U 2A 3U AU C G 4 AU MEME (no SSC) :5 5 6AUU A 7 J. Fallmann,TBI RNA - protein interactions in RNA decay 7/ 13

9 Modeling binding cooperativity by constraint folding Calculation of cooperativity free energy via constraint folding A pair of binding sites is used as constraint ( G 1 = G 1 G c1 RT ln G 2 12 = G 12 G 2 RT ln K D,1 ( c1 K D,1 ) ) G = G 1 G 2 12 = G 1 +G 2 G 12 G Lin et al. 215, RNA structure generates natural cooperativity between single-stranded RNA binding proteins targeting 5 and 3 UTRs J. Fallmann,TBI RNA - protein interactions in RNA decay 8/ 13

10 Procedure Non-overlapping pairs of binding sites with minimal distance of 1nt Folding of 3 UTR with/without these bs as constraints Additionally Ago-CLIP derived mirna bs as constraints Lu et al. 214, ELAVL1 Modulates Transcriptome-wide mirna Binding in Murine Macrophages J. Fallmann,TBI RNA - protein interactions in RNA decay 9/ 13

11 Un/Cooperative binding HuR_KO_miRNA HuR_WT_miRNA count mirna TTP_miRNA 1 Sample HuR_KO_miRNA HuR_WT_miRNA mirna TTP_miRNA ddg J. Fallmann,TBI RNA - protein interactions in RNA decay 1/ 13

12 Un/Cooperative binding HuR_TTP_KO HuR_TTP_WT count TTP TTP_miRNA 4 Sample HuR_TTP_KO HuR_TTP_WT TTP TTP_miRNA ddg J. Fallmann,TBI RNA - protein interactions in RNA decay 11/ 13

13 Summary In general we see only a small effect ABPs bind ssrna, so this is not completely surprising Top targets among cooperative list TTP itself is one of the RNAs where mirna-27 binding has negative effect J. Fallmann,TBI RNA - protein interactions in RNA decay 12/ 13

14 Acknowledgments TBI Ivo Andrea Xtof Colleagues MFPL Pavel Kovarik Vitaly Sedlyarov Leipzig Peter Stadler Steve Hoffmann Christian Otto Stefan Bernhart Freiburg Rolf Backofen Daniel Maticzka Steffen Heyne Fabrizio Costa Research Platform Decoding mrna decay in inflammation Interdisciplinary project funded by the University of Vienna J. Fallmann,TBI RNA - protein interactions in RNA decay 13/ 13

Long non-coding RNAs

Long non-coding RNAs Dominic Rose Bioinformatics Group, University of Freiburg Bled, Feb. 2011 Outline De novo prediction of long non-coding RNAs (lncrnas) Genome-wide RNA gene-finding Intrinsic properties