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Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

ABSTRACT: This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus.

ORGANISM(S): Staphylococcus aureus Staphylococcus aureus subsp. aureus NCTC 8325

PROVIDER: GSE70041 | GEO | 2016/03/08

SECONDARY ACCESSION(S): PRJNA287530

REPOSITORIES: GEO

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Transcriptome analysis of a Staphylococcus aureus mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different biological conditions. The data revealed a relatively low abundance of antisense RNAs in S. aureus, overlapping only 6% of the coding genes. Transcriptome analysis of the rho deletion mutant revealed a remarkable overall increase in antisense transcription in S. aureus. delta rho and wild type

2016-03-08 | E-GEOD-70041 | biostudies-arrayexpress

Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (Mäder, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift.

2016-03-08 | GSE70042 | GEO

Tiling array hybridizations of genomic DNA from Staphylococcus aureus HG001.

Project description:This analysis is part of the study Whole-transcriptome analysis of Staphylococcus aureus under laboratory and infection-mimicking conditions (MÃ¤der, Nicolas et al., to be submitted) where the S. aureus HG001 transcriptome was analyzed under more than 40 different bilogical conditions. Genomic DNA was prepared from four independent cultures of S. aureus HG001 cells; after sonication, DNA was labeled with Cy3 and hybridized to tiling arrays. The data are used in transcriptome studies to compute expression intensities from raw intensity data using a model of shift and drift. genomic DNA from wild type

2016-03-08 | E-GEOD-70042 | biostudies-arrayexpress

A link between transcription termination, antibiotic action and virulence: Inhibition of Rho activity increases expression of SaeRS-dependent virulence factor genes in Staphylococcus aureus

Project description:Comparative proteome analysis of cells and supernatant from S. aureus HG001 and its isogenic rho deletion mutant in exponential and stationary growth phase in RPMI and TSB medium. Proteome analysis of supernatant from S. aureus HG001 and its isogenic rho deletion mutant in RPMI medium after treatment with Bicyclomycin (BCM).

2018-04-12 | MSV000082270 | MassIVE

Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

Project description:This analysis is part of the study GSE27219, The condition-dependent transcriptome of Bacillus subtilis 168. In this study, 120 transcription units where identified for which transcription did not terminate at any specific site, leading to mRNA extension over long distances with slowly decreasing signal intensity. In most cases, lack of termination and read-through generated antisense transcripts. These findings together with the lack of intrinsic terminators suggested that transcription termination of the 120 transcription units could be mediated by the transcription termination factor Rho. In order to investigate the impact of Rho-mediated termination, tiling array hybridizations using RNA samples of a B. subtilis rho-null mutant and its parental strain were performed. B. subtilis 1012 wild-type and rho-mutant cells were grown in LB medium. Samples for tiling array analysis were taken during exponential growth phase. Hybridizations were performed in triplicate using RNA isolated from independent cultures.

2012-03-07 | E-GEOD-27303 | biostudies-arrayexpress

Transcriptome analysis of a Bacillus subtilis mutant defective in the transcription termination factor Rho.

2012-03-07 | GSE27303 | GEO

Trancriptional profiling of Bacillus subtilis BsB1 and NCIB3610 rho-deletion mutant

Project description:With these experiments we investigate the impact of the deletion of the gene encoding transcription termination Rho on the transcriptomes of two different Bacillus subtilis strains, BsB1 and NCIB3610. The results confirm massive increase of antisense transcription initially observed with tiling arrays in B. subtilis strain 1012 (Nicolas et al. 2012; PMID:22383849; GSE27303).

2017-07-10 | GSE94303 | GEO

Termination factor Rho mediates transcriptional reprogramming of Bacillus subtilis stationary phase

Project description:Here, we described comparative transcriptomic analysis of B. subtilis strain stably expressing rho with the wild type and rho-deficient strains. We show that maintaining a stable Rho level caused global changes of B. subtilis transcriptome including both strong down-regulation of the antisense transcription and considerable modifications of the sense transcription. The observed changes were more noticeable upon entering the stationary phase and comprised majority of genes controlled by global transcription regulators AbrB and CodY, competence transcription factor ComK, and stringent response. Constitutively expressed rho reprograms stationary phase-specific cellular physiology, affects adaptation of cells to nutrient limitations by attenuating the stringent response and alters cell-fate decision-making to such an extent that it blocks competence development and sporulation.

2022-02-10 | GSE195579 | GEO

Rho directs widespread termination of intragenic and stable RNA transcription

Project description:The transcription termination factor Rho is a global regulator of RNA polymerase (RNAP). Although individual Rho-dependent terminators have been studied extensively, less is known about the sites of RNAP regulation by Rho on a genome-wide scale. Using chromatin immunoprecipitation and microarrays (ChIP-chip), we examined changes in the distribution of Escherichia coli RNAP in response to the Rho-specific inhibitor bicyclomycin (BCM). We found ~200 Rho-terminated loci that were divided evenly into two classes: intergenic (at the ends of genes) and intragenic (within genes). The intergenic class contained noncoding RNAs such as small RNAs (sRNAs) and transfer RNAs (tRNAs), establishing a previously unappreciated role of Rho in termination of stable RNA synthesis. The intragenic class of terminators included a novel set of short antisense transcripts, as judged by a shift in the distribution of RNAP in BCM-treated cells that was opposite to the direction of the corresponding gene. These Rho-terminated antisense transcripts point to a novel role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation. Chromatin immunoprecipitation (ChIP) experiments were performed using antibodies against RNA polymerase (Beta or Beta' subunit) in cells treated with 20ug/ml bicyclomycin or untreated cells. Differentially labeled ChIP DNA and genomic DNA were competitively hybridized to an E. coli K-12 MG1655 tiling array with overlapping probes at ~12bp spacing across the entire genome. The series contains 4 datasets.

2010-05-18 | E-GEOD-16562 | biostudies-arrayexpress

Rho directs widespread termination of intragenic and stable RNA transcription

2009-06-23 | GSE16562 | GEO

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