Dataset Information

Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells.

ABSTRACT: Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that Escherichia coli Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in E. coli. Although Gre factors are conserved in general bacteria, limited functional studies have been performed in bacteria other than E. coli. In this investigation, ChAP-chip analysis (chromatin affinity precipitation coupled with DNA microarray) was conducted to visualize the distribution of Bacillus subtilis GreA on the chromosome and to determine the effects of GreA inactivation on core RNAP trafficking. Our data show that GreA is uniformly distributed in the transcribed region from the promoter to coding region with core RNAP, and its inactivation induces RNAP accumulation at many promoter or promoter-proximal regions. Based on these findings, we propose that GreA would constantly associate with core RNAP during transcriptional initiation and elongation and resolves its stalling at promoter or promoter-proximal regions, thus contributing to the even distribution of RNAP along the promoter and coding regions in B. subtilis cells.

SUBMITTER: Kusuya Y

PROVIDER: S-EPMC3133182 | biostudies-literature | 2011 Jun

REPOSITORIES: biostudies-literature

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Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells.

Kusuya Yoko Y Kurokawa Ken K Ishikawa Shu S Ogasawara Naotake N Oshima Taku T

Journal of bacteriology 20110422 12

Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that Escherichia coli Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in E. coli. Although G ...[more]

PMID: 21515770

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Project description:Herpes simplex virus 1 (HSV-1) genes are transcribed by cellular RNA polymerase II (Pol II). Expression of viral immediate early (?) genes is followed sequentially by early (?), late (?1), and true late (?2) genes. We used precision nuclear run-on with deep sequencing to map and to quantify Pol II on the HSV-1(F) genome with single-nucleotide resolution. Approximately 30% of total Pol II relocated to viral genomes within 3?h postinfection (hpi), when it occupied genes of all temporal classes. At that time, Pol II on ? genes accumulated most heavily at promoter-proximal pause (PPP) sites located ?60?nucleotides downstream of the transcriptional start site, while ? genes bore Pol II more evenly across gene bodies. At 6 hpi, Pol II increased on ?1 and ?2 genes while Pol II pausing remained prominent on ? genes. At that time, average cytoplasmic mRNA expression from ? and ? genes decreased, relative to levels at 3 hpi, while ?1 relative expression increased slightly and ?2 expression increased more substantially. Cycloheximide treatment during the first 3?h reduced the amount of Pol II associated with the viral genome and confined most of the remaining Pol II to ? gene PPP sites. Inhibition of both cyclin-dependent kinase 9 activity and viral DNA replication reduced Pol II on the viral genome and restricted much of the remaining Pol II to PPP sites.IMPORTANCE These data suggest that viral transcription is regulated not only by Pol II recruitment to viral genes but also by control of elongation into viral gene bodies. We provide a detailed map of Pol II occupancy on the HSV-1 genome that clarifies features of the viral transcriptome, including the first identification of Pol II PPP sites. The data indicate that Pol II is recruited to late genes early in infection. Comparing ? and ? gene occupancy at PPP sites and gene bodies suggests that Pol II is released more efficiently into the bodies of ? genes than ? genes at 3 hpi and that repression of ? gene expression late in infection is mediated by prolonged promoter-proximal pausing. In addition, DNA replication is required to maintain full Pol II occupancy on viral DNA and to promote elongation on late genes later in infection.

Dataset Information

Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells.

Publications

Transcription factor GreA contributes to resolving promoter-proximal pausing of RNA polymerase in Bacillus subtilis cells.

Similar Datasets

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