Transcriptomics

Dataset Information

3

Regulator trafficking on bacterial transcription units in vivo


ABSTRACT: The in vivo trafficking patterns on DNA by the bacterial regulators of transcript elongation Sigma70, Rho, NusA, and NusG and the explanation for high promoter-proximal levels or peaks of RNA polymerase (RNAP) are unknown. Genome-wide ChIP-chip on E. coli revealed distinct association patterns of regulators as RNAP transcribes away from promoters (Rho first, then NusA, and then NusG). However, the interactions of elongating complexes with these regulators, including a weak interaction with Sigma70, did not differ significantly among most transcription units. A modest variation of NusG signal among genes reflected increased NusG interaction as transcription progresses, rather than functional specialization of elongating complexes. Promoter-proximal RNAP peaks were offset from Sigma70 peaks in the direction of transcription and co-occurred with NusA and Rho peaks, suggesting that the RNAP peaks reflected elongating, rather than initiating, complexes. However, inhibition of Rho did not increase RNAP levels within genes downstream of the RNAP peaks, suggesting the peaks are caused by a mechanism other than simple Rho-dependent attenuation. Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta' subunit), Sigma70, NusA, NusG, or Rho. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~24bp spacing across the entire genome. The series contains 17 total datasets.

ORGANISM(S): Escherichia coli  

SUBMITTER: Robert C Landick   Aseem Z Ansari  Rachel Anne Mooney  Jennifer L Rowland  Rachel A Mooney  Sarah E Davis  Jason M Peters 

PROVIDER: E-GEOD-13938 | ArrayExpress | 2010-05-14

SECONDARY ACCESSION(S): GSE13938PRJNA110275

REPOSITORIES: GEO, ArrayExpress

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Publications

Regulator trafficking on bacterial transcription units in vivo.

Mooney Rachel A RA   Davis Sarah E SE   Peters Jason M JM   Rowland Jennifer L JL   Ansari Aseem Z AZ   Landick Robert R  

Molecular cell 20090101 1


The trafficking patterns of the bacterial regulators of transcript elongation sigma(70), rho, NusA, and NusG on genes in vivo and the explanation for promoter-proximal peaks of RNA polymerase (RNAP) are unknown. Genome-wide, E. coli ChIP-chip revealed distinct association patterns of regulators as RNAP transcribes away from promoters (rho first, then NusA, then NusG). However, the interactions of elongating complexes with these regulators did not differ significantly among most transcription uni  ...[more]

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