Transcriptomics,Multiomics

Dataset Information

4

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)


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 and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring 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 datasets 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. RNA-Seq in exponential and stationary phase cultures

OTHER RELATED OMICS DATASETS IN: PRJNA175134PRJNA175136GSE40862PRJNA175135

ORGANISM(S): Mycobacterium Tuberculosis

SUBMITTER: Stewart T Cole   Jacques Rougemont  Swapna Uplekar  Claudia Sala 

PROVIDER: E-GEOD-40846 | ArrayExpress | 2012-12-01

SECONDARY ACCESSION(S): SRP015746GSE40846PRJNA175135

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

Uplekar Swapna S   Rougemont Jacques J   Cole Stewart T ST   Sala Claudia C  

Nucleic acids research 20121207 2


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,  ...[more]

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