Global Mapping of Small RNA-Target Interactions in Bacteria

Sahar Melamed; Asaf Peer; Raya Faigenbaum-Romm; Yair E. Gatt; Niv Reiss; Amir Bar; Yael Altuvia; Liron Argaman; Hanah Margalit

doi:10.1016/j.molcel.2016.07.026

Global Mapping of Small RNA-Target Interactions in Bacteria

Sahar Melamed, Asaf Peer, Raya Faigenbaum-Romm, Yair E. Gatt, Niv Reiss, Amir Bar, Yael Altuvia^*, Liron Argaman, Hanah Margalit

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

284 Scopus citations

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.

Original language	English
Pages (from-to)	884-897
Number of pages	14
Journal	Molecular Cell
Volume	63
Issue number	5
DOIs	https://doi.org/10.1016/j.molcel.2016.07.026
State	Published - 1 Sep 2016

Bibliographical note

Funding Information:
This study was supported by the European Research Council Advanced Grant #322920, I-CORE Programs of the Planning and Budgeting Committee and The Israel Science Foundation (grants 1796/12 and 41/1), and the Israel Science Foundation administered by the Israeli Academy for Sciences and Humanities (grant 1411/13). We thank T. Kaplan for his helpful advice, R. Rehani for her contribution to the experiments, H. Aiba for the hfq-Flag strain, O. Pines for the Saccharomyces cerevisiae strain, S. Pearl-Mizrahi, O. Shechter, and M. Nitzan for technical assistance, G. Storz for work conducted by S.M. in her lab and for very helpful advice, S. Altuvia, E. Holmqvist, I. Rosenshine, and S. Ben-Yehuda for their very useful comments, and K. McDowall and J. Wade for data sharing.

Publisher Copyright:
© 2016 Elsevier Inc.

Access to Document

10.1016/j.molcel.2016.07.026

Cite this

@article{ff3648b1885243ae9c972d9a20744e3a,

title = "Global Mapping of Small RNA-Target Interactions in Bacteria",

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.",

author = "Sahar Melamed and Asaf Peer and Raya Faigenbaum-Romm and Gatt, {Yair E.} and Niv Reiss and Amir Bar and Yael Altuvia and Liron Argaman and Hanah Margalit",

note = "Publisher Copyright: {\textcopyright} 2016 Elsevier Inc.",

year = "2016",

month = sep,

day = "1",

doi = "10.1016/j.molcel.2016.07.026",

language = "אנגלית",

volume = "63",

pages = "884--897",

journal = "Molecular Cell",

issn = "1097-2765",

publisher = "Cell Press",

number = "5",

}

TY - JOUR

T1 - Global Mapping of Small RNA-Target Interactions in Bacteria

AU - Melamed, Sahar

AU - Peer, Asaf

AU - Faigenbaum-Romm, Raya

AU - Gatt, Yair E.

AU - Reiss, Niv

AU - Bar, Amir

AU - Altuvia, Yael

AU - Argaman, Liron

AU - Margalit, Hanah

PY - 2016/9/1

Y1 - 2016/9/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84992459016&partnerID=8YFLogxK

U2 - 10.1016/j.molcel.2016.07.026

DO - 10.1016/j.molcel.2016.07.026

M3 - ???researchoutput.researchoutputtypes.contributiontojournal.article???

C2 - 27588604

AN - SCOPUS:84992459016

SN - 1097-2765

VL - 63

SP - 884

EP - 897

JO - Molecular Cell

JF - Molecular Cell

IS - 5

ER -

Global Mapping of Small RNA-Target Interactions in Bacteria

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this