title: Genome-wide discovery of small RNAs in Mycobacterium tuberculosis.
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.
authors.affiliation: Emerging Bacterial Pathogens Unit, S. Raffaele Scientific Institute, Milan, Italy.
authors.forename: Paolo
authors.initials: P
authors.lastname: Miotto
authors.forename: Francesca
authors.initials: F
authors.lastname: Forti
authors.forename: Alessandro
authors.initials: A
authors.lastname: Ambrosi
authors.forename: Danilo
authors.initials: D
authors.lastname: Pellin
authors.forename: Diogo F
authors.initials: DF
authors.lastname: Veiga
authors.forename: Gabor
authors.initials: G
authors.lastname: Balazsi
authors.forename: Maria L
authors.initials: ML
authors.lastname: Gennaro
authors.forename: Clelia
authors.initials: C
authors.lastname: Di Serio
authors.forename: Daniela
authors.initials: D
authors.lastname: Ghisotti
authors.forename: Daniela M
authors.initials: DM
authors.lastname: Cirillo
mesh_terms: D020121:5' Untranslated Regions; D016000:Cluster Analysis; D016384:Consensus Sequence; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D058977:Molecular Sequence Annotation; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000378:metabolism; D059372:Nucleotide Motifs; D016372:RNA, Antisense / Q000235:genetics / Q000378:metabolism; D012329:RNA, Bacterial / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results; D015398:Signal Transduction; D013728:Terminator Regions, Genetic
chemical_list: D020121:5' Untranslated Regions; D016372:RNA, Antisense; D012329:RNA, Bacterial