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 59/39 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 59 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
