Global Mapping of Small RNA-Target Interactions in Bacteria

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2016 Sep 3

PMID 27588604

Citations 200

Authors

Sahar Melamed

Asaf Peer

Raya Faigenbaum-Romm

Yair E Gatt

Niv Reiss

Amir Bar

Yael Altuvia

Liron Argaman

Hanah Margalit

Affiliations

Soon will be listed here.

Abstract

Small RNAs (sRNAs) associated with the RNA chaperon protein Hfq are key posttranscriptional regulators of gene expression in bacteria. Deciphering the sRNA-target interactome is an essential step toward understanding the roles of sRNAs in the cellular networks. We developed a broadly applicable methodology termed RIL-seq (RNA interaction by ligation and sequencing), which integrates experimental and computational tools for in vivo transcriptome-wide identification of interactions involving Hfq-associated sRNAs. By applying this methodology to Escherichia coli we discovered an extensive network of interactions involving RNA pairs showing sequence complementarity. We expand the ensemble of targets for known sRNAs, uncover additional Hfq-bound sRNAs encoded in various genomic regions along with their trans encoded targets, and provide insights into binding and possible cycling of RNAs on Hfq. Comparison of the sRNA interactome under various conditions has revealed changes in the sRNA repertoire as well as substantial re-wiring of the network between conditions.

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References

Miyakoshi M, Chao Y, Vogel J . Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge of the GcvB small RNA. EMBO J. 2015; 34(11):1478-92. PMC: 4474525. DOI: 10.15252/embj.201490546. View

Helwak A, Kudla G, Dudnakova T, Tollervey D . Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell. 2013; 153(3):654-65. PMC: 3650559. DOI: 10.1016/j.cell.2013.03.043. View

Morita T, Ueda M, Kubo K, Aiba H . Insights into transcription termination of Hfq-binding sRNAs of Escherichia coli and characterization of readthrough products. RNA. 2015; 21(8):1490-501. PMC: 4509938. DOI: 10.1261/rna.051870.115. View

Bilusic I, Popitsch N, Rescheneder P, Schroeder R, Lybecker M . Revisiting the coding potential of the E. coli genome through Hfq co-immunoprecipitation. RNA Biol. 2014; 11(5):641-54. PMC: 4152368. DOI: 10.4161/rna.29299. View

Fender A, Elf J, Hampel K, Zimmermann B, Wagner E . RNAs actively cycle on the Sm-like protein Hfq. Genes Dev. 2010; 24(23):2621-6. PMC: 2994036. DOI: 10.1101/gad.591310. View

Jager D, Pernitzsch S, Richter A, Backofen R, Sharma C, Schmitz R . An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res. 2012; 40(21):10964-79. PMC: 3510493. DOI: 10.1093/nar/gks847. View

Chao Y, Vogel J . A 3' UTR-Derived Small RNA Provides the Regulatory Noncoding Arm of the Inner Membrane Stress Response. Mol Cell. 2016; 61(3):352-363. DOI: 10.1016/j.molcel.2015.12.023. View

Mandin P, Gottesman S . Integrating anaerobic/aerobic sensing and the general stress response through the ArcZ small RNA. EMBO J. 2010; 29(18):3094-107. PMC: 2944060. DOI: 10.1038/emboj.2010.179. View

Muckstein U, Tafer H, Hackermuller J, Bernhart S, Stadler P, Hofacker I . Thermodynamics of RNA-RNA binding. Bioinformatics. 2006; 22(10):1177-82. DOI: 10.1093/bioinformatics/btl024. View

10.

Thomason M, Bischler T, Eisenbart S, Forstner K, Zhang A, Herbig A . Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli. J Bacteriol. 2014; 197(1):18-28. PMC: 4288677. DOI: 10.1128/JB.02096-14. View

11.

Romero D, Hasan A, Lin Y, Kime L, Ruiz-Larrabeiti O, Urem M . A comparison of key aspects of gene regulation in Streptomyces coelicolor and Escherichia coli using nucleotide-resolution transcription maps produced in parallel by global and differential RNA sequencing. Mol Microbiol. 2014; . PMC: 4681348. DOI: 10.1111/mmi.12810. View

12.

Fei J, Singh D, Zhang Q, Park S, Balasubramanian D, Golding I . RNA biochemistry. Determination of in vivo target search kinetics of regulatory noncoding RNA. Science. 2015; 347(6228):1371-4. PMC: 4410144. DOI: 10.1126/science.1258849. View

13.

Storz G, Vogel J, Wassarman K . Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell. 2011; 43(6):880-91. PMC: 3176440. DOI: 10.1016/j.molcel.2011.08.022. View

14.

Sayed N, Jousselin A, Felden B . A cis-antisense RNA acts in trans in Staphylococcus aureus to control translation of a human cytolytic peptide. Nat Struct Mol Biol. 2011; 19(1):105-12. DOI: 10.1038/nsmb.2193. View

15.

Kent W, Sugnet C, Furey T, Roskin K, Pringle T, Zahler A . The human genome browser at UCSC. Genome Res. 2002; 12(6):996-1006. PMC: 186604. DOI: 10.1101/gr.229102. View

16.

Keseler I, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C . EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 2012; 41(Database issue):D605-12. PMC: 3531154. DOI: 10.1093/nar/gks1027. View

17.

Morita T, Maki K, Aiba H . RNase E-based ribonucleoprotein complexes: mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 2005; 19(18):2176-86. PMC: 1221888. DOI: 10.1101/gad.1330405. View

18.

Peer A, Margalit H . Evolutionary patterns of Escherichia coli small RNAs and their regulatory interactions. RNA. 2014; 20(7):994-1003. PMC: 4114697. DOI: 10.1261/rna.043133.113. View

19.

Wang J, Rennie W, Liu C, Carmack C, Prevost K, Caron M . Identification of bacterial sRNA regulatory targets using ribosome profiling. Nucleic Acids Res. 2015; 43(21):10308-20. PMC: 4666370. DOI: 10.1093/nar/gkv1158. View

20.

Grosswendt S, Filipchyk A, Manzano M, Klironomos F, Schilling M, Herzog M . Unambiguous identification of miRNA:target site interactions by different types of ligation reactions. Mol Cell. 2014; 54(6):1042-1054. PMC: 4181535. DOI: 10.1016/j.molcel.2014.03.049. View