Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes.

2.50
Hdl Handle:
http://hdl.handle.net/10033/621091
Title:
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes.
Authors:
Le Rhun, Anaïs; Lécrivain, Anne-Laure; Reimegård, Johan; Proux-Wéra, Estelle; Broglia, Laura; Della Beffa, Cristina; Charpentier, Emmanuelle
Abstract:
A better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.
Affiliation:
Helmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.
Citation:
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. 2017, 45 (5):2329-2340 Nucleic Acids Res.
Journal:
Nucleic acids research
Issue Date:
17-Mar-2017
URI:
http://hdl.handle.net/10033/621091
DOI:
10.1093/nar/gkw1316
PubMed ID:
28082390
Type:
Article
Language:
en
ISSN:
1362-4962
Appears in Collections:
publications of the department Regulation of infection

Full metadata record

DC FieldValue Language
dc.contributor.authorLe Rhun, Anaïsen
dc.contributor.authorLécrivain, Anne-Laureen
dc.contributor.authorReimegård, Johanen
dc.contributor.authorProux-Wéra, Estelleen
dc.contributor.authorBroglia, Lauraen
dc.contributor.authorDella Beffa, Cristinaen
dc.contributor.authorCharpentier, Emmanuelleen
dc.date.accessioned2017-09-05T11:36:06Z-
dc.date.available2017-09-05T11:36:06Z-
dc.date.issued2017-03-17-
dc.identifier.citationIdentification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes. 2017, 45 (5):2329-2340 Nucleic Acids Res.en
dc.identifier.issn1362-4962-
dc.identifier.pmid28082390-
dc.identifier.doi10.1093/nar/gkw1316-
dc.identifier.urihttp://hdl.handle.net/10033/621091-
dc.description.abstractA better understanding of transcriptional and post-transcriptional regulation of gene expression in bacteria relies on studying their transcriptome. RNA sequencing methods are used not only to assess RNA abundance but also the exact boundaries of primary and processed transcripts. Here, we developed a method, called identification of specific cleavage position (ISCP), which enables the identification of direct endoribonuclease targets in vivo by comparing the 5΄ and 3΄ ends of processed transcripts between wild type and RNase deficient strains. To demonstrate the ISCP method, we used as a model the double-stranded specific RNase III in the human pathogen Streptococcus pyogenes. We mapped 92 specific cleavage positions (SCPs) among which, 48 were previously described and 44 are new, with the characteristic 2 nucleotides 3΄ overhang of RNase III. Most SCPs were located in untranslated regions of RNAs. We screened for RNase III targets using transcriptomic differential expression analysis (DEA) and compared those with the RNase III targets identified using the ISCP method. Our study shows that in S. pyogenes, under standard growth conditions, RNase III has a limited impact both on antisense transcripts and on global gene expression with the expression of most of the affected genes being downregulated in an RNase III deletion mutant.en
dc.language.isoenen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-sa/4.0/*
dc.subject.meshBacterial Proteinsen
dc.subject.meshBase Pairingen
dc.subject.meshBase Sequenceen
dc.subject.meshGene Deletionen
dc.subject.meshGene Expression Regulation, Bacterialen
dc.subject.meshNucleic Acid Conformationen
dc.subject.meshRNA Cleavageen
dc.subject.meshRNA, Antisenseen
dc.subject.meshRNA, Bacterialen
dc.subject.meshRNA, Messengeren
dc.subject.meshRibonuclease IIIen
dc.subject.meshStreptococcus pyogenesen
dc.subject.meshTranscriptomeen
dc.subject.meshUntranslated Regionsen
dc.titleIdentification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes.en
dc.typeArticleen
dc.contributor.departmentHelmholtz Centre for infection research, Inhoffenstr. 7, 38124 Braunschweig, Germany.en
dc.identifier.journalNucleic acids researchen

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