In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III

Efthimia Lioliou, Cynthia M. Sharma, Yaël Altuvia, Isabelle Caldelari, Cédric Romilly, Anne Catherine Helfer, Hanah Margalit, Pascale Romby*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

13 Scopus citations

Abstract

Ribonucleases play key roles in gene regulation and in the expression of virulence factors in Staphylococcus aureus. Among these enzymes, the double-strand specific endoribonuclease III (RNase III) is a key mediator of mRNA processing and degradation. Recently, we have defined, direct target sites for RNase III processing on a genome-wide scale in S. aureus. Our approach is based on deep sequencing of cDNA libraries obtained from RNAs isolated by in vivo co-immunoprecipitation with wild-type RNase III and two cleavage-defective mutants. The use of such catalytically inactivated enzymes, which still retain their RNA binding capacity, allows the identification of novel RNA substrates of RNase III. In this report, we will summarize the diversity of RNase III functions, discuss the advantages and the limitations of the approach, and how this strategy identifies novel mRNA targets of small non-coding RNAs in S. aureus.

Original languageAmerican English
Pages (from-to)135-143
Number of pages9
JournalMethods
Volume63
Issue number2
DOIs
StatePublished - 15 Sep 2013

Keywords

  • Antisense RNA regulation
  • Endoribonuclease
  • RNA-RNA interactions
  • RNA-protein interaction
  • Regulatory RNAs

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