RNA-Seq analysis of Mycobacterium avium non-coding transcriptome

• Published in: PloS one Vol. 8; no. 9; p. e74209
• Main Authors: Ignatov, Dmitriy, Malakho, Sofia, Majorov, Konstantin, Skvortsov, Timofey, Apt, Alexander, Azhikina, Tatyana
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 16.09.2013; Public Library of Science (PLoS)
• Subjects: Analysis; Antisense RNA; Bacteria; Bioinformatics; Cloning; Disease; Gene expression; Gene Expression Regulation, Bacterial; Gene sequencing; Genes; Genetic aspects; Genomics; Infections; Metabolism; Metabolites; Mycobacterium avium; Mycobacterium avium - genetics; Mycobacterium tuberculosis; Pathogens; Proteins; Ribonucleic acid; Riboswitches; RNA; RNA sequencing; RNA, Antisense - genetics; RNA, Bacterial - genetics; RNA, Small Untranslated - genetics; Transcription; Transcription (Genetics); Transcriptome - genetics; Tuberculosis; Russia
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0074209

Deep sequencing was implemented to study the transcriptional landscape of Mycobacterium avium. High-resolution transcriptome analysis identified the transcription start points for 652 genes. One third of these genes represented leaderless transcripts, whereas the rest of the transcripts had 5' UTRs with the mean length of 83 nt. In addition, the 5' UTRs of 6 genes contained SAM-IV and Ykok types of riboswitches. 87 antisense RNAs and 10 intergenic small RNAs were mapped. 6 intergenic small RNAs, including 4.5S RNA and rnpB, were transcribed at extremely high levels. Although several intergenic sRNAs are conserved in M. avium and M. tuberculosis, both of these species have unique intergenic sRNAs. Moreover, we demonstrated that even conserved small RNAs are regulated differently in these species. Different sets of intergenic sRNAs may underlie differences in physiology between conditionally pathogenic M. avium and highly specialized pathogen M. tuberculosis.