title: In vivo mapping of RNA-RNA interactions in Staphylococcus aureus using the endoribonuclease III.
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.
authors.affiliation: Architecture et Réactivité de l'ARN, Université de Strasbourg, CNRS, IBMC, 15 rue René Descartes, F-67084 Strasbourg, France.
authors.forename: Efthimia
authors.initials: E
authors.lastname: Lioliou
authors.forename: Cynthia M
authors.initials: CM
authors.lastname: Sharma
authors.forename: Yaël
authors.initials: Y
authors.lastname: Altuvia
authors.forename: Isabelle
authors.initials: I
authors.lastname: Caldelari
authors.forename: Cédric
authors.initials: C
authors.lastname: Romilly
authors.forename: Anne-Catherine
authors.initials: AC
authors.lastname: Helfer
authors.forename: Hanah
authors.initials: H
authors.lastname: Margalit
authors.forename: Pascale
authors.initials: P
authors.lastname: Romby
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002874:Chromosome Mapping / Q000379:methods*; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D047468:Immunoprecipitation; D055029:Inverted Repeat Sequences; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics; D043244:Ribonuclease III / Q000302:isolation & purification / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D013211:Staphylococcus aureus / Q000201:enzymology / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D043244:Ribonuclease III
keywords: Antisense RNA regulation; Endoribonuclease; RNA–RNA interactions; RNA–protein interaction; Regulatory RNAs