title: Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.
abstract: Deciphering physiological changes that mediate transition of Mycobacterium tuberculosis between replicating and nonreplicating states is essential to understanding how the pathogen can persist in an individual host for decades. We have combined RNA sequencing (RNA-seq) of 5' triphosphate-enriched libraries with regular RNA-seq to characterize the architecture and expression of M. tuberculosis promoters. We identified over 4,000 transcriptional start sites (TSSs). Strikingly, for 26% of the genes with a primary TSS, the site of transcriptional initiation overlapped with the annotated start codon, generating leaderless transcripts lacking a 5' UTR and, hence, the Shine-Dalgarno sequence commonly used to initiate ribosomal engagement in eubacteria. Genes encoding proteins with active growth functions were markedly depleted from the leaderless transcriptome, and there was a significant increase in the overall representation of leaderless mRNAs in a starvation model of growth arrest. The high percentage of leaderless genes may have particular importance in the physiology of nonreplicating M. tuberculosis.
authors.affiliation: Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK. Electronic address: tcortes@nimr.mrc.ac.uk.
authors.forename: Teresa
authors.initials: T
authors.lastname: Cortes
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Systems Biology Graduate School, 8057 Zurich, Switzerland.
authors.forename: Olga T
authors.initials: OT
authors.lastname: Schubert
authors.affiliation: Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
authors.forename: Graham
authors.initials: G
authors.lastname: Rose
authors.affiliation: Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK; Institute of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
authors.forename: Kristine B
authors.initials: KB
authors.lastname: Arnvig
authors.affiliation: Genomics and Health Unit, Centre for Public Health Research (FISABIO-CSISP), 46020 Valencia, Spain; CIBER in Epidemiology and Public Health, 28029 Madrid, Spain.
authors.forename: Iñaki
authors.initials: I
authors.lastname: Comas
authors.affiliation: Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8057 Zurich, Switzerland.
authors.forename: Ruedi
authors.initials: R
authors.lastname: Aebersold
authors.affiliation: Division of Mycobacterial Research, MRC National Institute for Medical Research, Mill Hill, London NW7 1AA, UK; Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK. Electronic address: dyoung@nimr.mrc.ac.uk.
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Young
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D002874:Chromosome Mapping; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D011401:Promoter Regions, Genetic; D017423:Sequence Analysis, RNA; D024363:Transcription Initiation Site; D014158:Transcription, Genetic; D059467:Transcriptome / Q000235:genetics
chemical_list: D020121:5' Untranslated Regions