Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis

Paolo Miotto, Francesca Forti, Alessandro Ambrosi, Danilo Pellin, Diogo F. Veiga, Gabor Balazsi, Maria L. Gennaro, Clelia Di Serio, Daniela Ghisotti, Daniela M. Cirillo

Research output: Contribution to journalArticle

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Abstract

Only few small RNAs (sRNAs) have been characterized in Mycobacterium tuberculosis and their role in regulatory networks is still poorly understood. Here we report a genome-wide characterization of sRNAs in M. tuberculosis integrating experimental and computational analyses. Global RNA-seq analysis of exponentially growing cultures of M. tuberculosis H37Rv had previously identified 1373 sRNA species. In the present report we show that 258 (19%) of these were also identified by microarray expression. This set included 22 intergenic sRNAs, 84 sRNAs mapping within 5′/3′ UTRs, and 152 antisense sRNAs. Analysis of promoter and terminator consensus sequences identified sigma A promoter consensus sequences for 121 sRNAs (47%), terminator consensus motifs for 22 sRNAs (8.5%), and both motifs for 35 sRNAs (14%). Additionally, 20/23 candidates were visualized by Northern blot analysis and 5′ end mapping by primer extension confirmed the RNA-seq data. We also used a computational approach utilizing functional enrichment to identify the pathways targeted by sRNA regulation. We found that antisense sRNAs preferentially regulated transcription of membrane-bound proteins. Genes putatively regulated by novel cis-encoded sRNAs were enriched for two-component systems and for functional pathways involved in hydrogen transport on the membrane.

Original languageEnglish (US)
Article numbere51950
JournalPloS one
Volume7
Issue number12
DOIs
StatePublished - Dec 19 2012

Fingerprint

Mycobacterium tuberculosis
Genes
Genome
RNA
genome
Antisense RNA
Consensus Sequence
consensus sequence
Genetic Terminator Regions
promoter regions
Membranes
5' Untranslated Regions
3' Untranslated Regions
Northern Blotting
3' untranslated regions
Transcription
Microarrays
Hydrogen
Northern blotting
Membrane Proteins

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Miotto, P., Forti, F., Ambrosi, A., Pellin, D., Veiga, D. F., Balazsi, G., ... Cirillo, D. M. (2012). Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. PloS one, 7(12), [e51950]. https://doi.org/10.1371/journal.pone.0051950
Miotto, Paolo ; Forti, Francesca ; Ambrosi, Alessandro ; Pellin, Danilo ; Veiga, Diogo F. ; Balazsi, Gabor ; Gennaro, Maria L. ; Di Serio, Clelia ; Ghisotti, Daniela ; Cirillo, Daniela M. / Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. In: PloS one. 2012 ; Vol. 7, No. 12.
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Miotto, P, Forti, F, Ambrosi, A, Pellin, D, Veiga, DF, Balazsi, G, Gennaro, ML, Di Serio, C, Ghisotti, D & Cirillo, DM 2012, 'Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis', PloS one, vol. 7, no. 12, e51950. https://doi.org/10.1371/journal.pone.0051950

Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. / Miotto, Paolo; Forti, Francesca; Ambrosi, Alessandro; Pellin, Danilo; Veiga, Diogo F.; Balazsi, Gabor; Gennaro, Maria L.; Di Serio, Clelia; Ghisotti, Daniela; Cirillo, Daniela M.

In: PloS one, Vol. 7, No. 12, e51950, 19.12.2012.

Research output: Contribution to journalArticle

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Miotto P, Forti F, Ambrosi A, Pellin D, Veiga DF, Balazsi G et al. Genome-Wide Discovery of Small RNAs in Mycobacterium tuberculosis. PloS one. 2012 Dec 19;7(12). e51950. https://doi.org/10.1371/journal.pone.0051950