title: High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.
abstract: To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches: strand-specific RNA-seq, to survey the global transcriptome, and ChIP-seq, to monitor the genome-wide dynamics of RNA polymerase (RNAP) and the anti-terminator NusA. Although NusA does not bind directly to DNA, but rather to RNAP and/or to the nascent transcript, we demonstrate that NusA interacts with RNAP ubiquitously throughout the chromosome, and that its profile mirrors RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the data sets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align.
authors.affiliation: Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland.
authors.forename: Swapna
authors.initials: S
authors.lastname: Uplekar
authors.forename: Jacques
authors.initials: J
authors.lastname: Rougemont
authors.forename: Stewart T
authors.initials: ST
authors.lastname: Cole
authors.forename: Claudia
authors.initials: C
authors.lastname: Sala
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D003062:Codon; D012321:DNA-Directed RNA Polymerases / Q000378:metabolism*; D020869:Gene Expression Profiling; D016681:Genome, Fungal; D059014:High-Throughput Nucleotide Sequencing; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D016372:RNA, Antisense / Q000096:biosynthesis; D012343:RNA, Transfer / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D061805:Transcription Elongation, Genetic; D061785:Transcription Initiation, Genetic; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D016372:RNA, Antisense; D016601:RNA-Binding Proteins; C064872:antiterminator proteins, Bacteria; D012343:RNA, Transfer; D012321:DNA-Directed RNA Polymerases