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Phylogenetic signatures of RNA-RNA contacts in bacteria. Daniel Gautheret Institut de Génétique et Microbiologie CNRS-Université Paris-Sud. RNA-based gene regulation. In eukaryotes: RNAi, microRNA (1990’s). RNAi and miRNA function. ds RNA. Dicer. Ago. Regulatory RNA. Target mRNA.
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Phylogenetic signatures of RNA-RNA contacts in bacteria Daniel Gautheret Institut de Génétique et Microbiologie CNRS-Université Paris-Sud
RNA-based gene regulation • In eukaryotes: RNAi, microRNA (1990’s)
RNAi and miRNA function ds RNA Dicer Ago Regulatory RNA Target mRNA Degradation or Translation stop
RNA: the ideal information-based regulator Universal G C C A G U U G A U C C A G Regulatorysequencesdictatetargets
RNA absent from regulation networks KEGG regulation network for actin biosyntesis, modified by Clement & Zucker
Target prediction Mixed results, lots of False Positives
Taking accessibility into account Hofacker 2007
sRNA tend to bind via accessible regions ryhB oxyS dsrA Bind to targets
Target prediction with accessibility Improvedresults, but far fromperfect
Javascript is required to show this page properly. • Drag image to reposition. Double click to magnify further. • Javascript is required to show this page properly. • Drag image to reposition. Double click to magnify further. Obstacles to correct target prediction The Hfqchaperone Chevalier et al. 2010
Using sRNA conservation Pairwise Blast vs. all completegenomes Escherichia coli k12 MG1655 ACGAGUGCGGCACG Escherichia coli O157H7 EDL933 AACGGAGCGGCACC Shigella flexneri 2a -ACGAAGCTGCACC Yersinia pestis Antiqua AACGAAG--GCACC reference 1 x 0,01 0 x 0,2 1 x 0,6 Weighted by evolutionary distance conservation dsrA Sequence
dsrA rpoS Accessibilité hns Conservation Résultante
arcZ Accessibilité STM3216 tpx Conservation sdaC Résultante
micC ompC Accessibilité Conservation Résultante
ryhB sdhC Accessibilité Conservation Résultante
oxyS fhlA Hfq binding site fhlA Accessibilité Conservation Résultante
Constraints on sRNA vs. mRNA sRNA Target 1 Target 2 Target 3 Target 4
sRNA vs. Target conservation 142 140 120 110 100 99 # species with homology 80 69 60 40 24 20 14 13 11 9 ryhB oxyS dsrA ompC hns rpoS fhlA sdhC micC
mRNA conservation AveragetargettedmRNAs Average E. coli mRNAs -1
Profile clustering: 5’ regions of mRNAs 4/50 vs 35/2097 Pvalue : 0.014 3/45 vs 35/2097 Pvalue : 0.049 2/63 vs 35/2097 Pvalue : 0.030
Next developments sRNA mRNA1 mRNA2 Covariation
Combine with phylogenetic profiling 1070 bacterialgenomes Genes and RNA elements Cluster of co-evolvingRNAs and genes
Acknowledgements Alban Ott Antonin Marchais RNA sequence, structure & function lab