Genome-wide antisense transcription drives mRNA processing in bacteria

Lasa, I., Toledo-Arana, A., Dobin, A., Villanueva, M., de los Mozos, I. R., Vergara-Irigaray, M., Segura, V., Fagegaltier, D., Penades, J. R., Valle, J., Solano, C., Gingeras, T. R. (December 2011) Genome-wide antisense transcription drives mRNA processing in bacteria. Proceedings of the National Academy of Sciences of the United States of America, 108 (50). pp. 20172-20177. ISSN 0027-8424

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URL: http://www.ncbi.nlm.nih.gov/pubmed/22123973
DOI: 10.1073/pnas.1113521108

Abstract

RNA deep sequencing technologies are revealing unexpected levels of complexity in bacterial transcriptomes with the discovery of abundant noncoding RNAs, antisense RNAs, long 5' and 3' untranslated regions, and alternative operon structures. Here, by applying deep RNA sequencing to both the long and short RNA fractions (<50 nucleotides) obtained from the major human pathogen Staphylococcus aureus, we have detected a collection of short RNAs that is generated genome-wide through the digestion of overlapping sense/antisense transcripts by RNase III endoribonuclease. At least 75% of sense RNAs from annotated genes are subject to this mechanism of antisense processing. Removal of RNase III activity reduces the amount of short RNAs and is accompanied by the accumulation of discrete antisense transcripts. These results suggest the production of pervasive but hidden antisense transcription used to process sense transcripts by means of creating double-stranded substrates. This process of RNase III-mediated digestion of overlapping transcripts can be observed in several evolutionarily diverse Gram-positive bacteria and is capable of providing a unique genome-wide posttranscriptional mechanism to adjust mRNA levels.

Item Type: Paper
Uncontrolled Keywords: antisense RNA overlapping transcription RNA processing posttranscriptional regulation microRNA staphylococcus-aureus reveals escherichia-coli genome experimental discovery virulence factors noncoding rnas start sites expression complexity search genes
Subjects: bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL Post Doctoral Fellows
CSHL labs > Gingeras lab
CSHL labs > Hannon lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: CSHL Librarian
Date: December 2011
Date Deposited: 07 Mar 2012 21:57
Last Modified: 02 Jan 2018 20:07
PMCID: PMC3250193
Related URLs:
URI: http://repository.cshl.edu/id/eprint/25349

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