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Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III in Streptococcus pyogenes
Umea Univ, UCMR, Dept Mol Biol, Lab Mol Infect Sweden MIMS, S-90187 Umea, Sweden.;Max Planck Inst Infect Biol, Dept Regulat Infect Biol, D-10117 Berlin, Germany.;Helmholtz Ctr Infect Res, Dept Regulat Infect Biol, D-38124 Braunschweig, Germany..
Umea Univ, UCMR, Dept Mol Biol, Lab Mol Infect Sweden MIMS, S-90187 Umea, Sweden.;Max Planck Inst Infect Biol, Dept Regulat Infect Biol, D-10117 Berlin, Germany..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Box 1031, SE-17121 Solna, Sweden..
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2017 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 45, no 5, 2329-2340 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
OXFORD UNIV PRESS , 2017. Vol. 45, no 5, 2329-2340 p.
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-320208DOI: 10.1093/nar/gkw1316ISI: 000397286600018PubMedID: 28082390OAI: oai:DiVA.org:uu-320208DiVA: diva2:1088927
Funder
Max Planck SocietyGöran Gustafsson Foundation for promotion of scientific research at Uppala University and Royal Institute of TechnologyScience for Life Laboratory - a national resource center for high-throughput molecular bioscience, b2013265The Kempe Foundations, K2010-57X-21436-01-3Swedish Research Council, K2013-57X-21436-04-3
Available from: 2017-04-18 Created: 2017-04-18 Last updated: 2017-04-18Bibliographically approved

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