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TranscriptomicsRpoE regulon in Rhodobacter sphaeroides
In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that con...
ORGANISM(S): Rhodobacter sphaeroides 2.4.1 
2010-06-30 | E-GEOD-22576 | biostudies-arrayexpress
ProteomicsGenome-scale transcription-translation mapping reveals features of Zymomonas mobilis transcription units and promoters
Limited functional annotation of the Z. mobilis genome is a current barrier to both basic studies of Z. mobilis and its development as a synthetic-biology chassis. To gain insight, we collected sample-matched multiomics data including RNA-seq, transcription start site sequencing (TSS-seq), terminati...
ORGANISM(S): Bacteria Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 
2020-07-10 | PXD016962 | Pride
Proteogenomics Multiomics Shotgun proteomics Zymomonas mobilis 
TranscriptomicsRho and NusG suppress pervasive antisense transcription in Escherichia coli [RNA-seq].
Despite the prevalence of antisense transcripts in bacterial transcriptomes, little is known about how their synthesis is controlled. We report that a major function of the Escherichia coli termination factor Rho and its co-factor NusG is suppression of ubiquitous antisense transcription genome-wide...
ORGANISM(S): Escherichia coli K-12 
2012-11-01 | E-GEOD-41939 | biostudies-arrayexpress
TranscriptomicsCorrecting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Ribosome_Profiling]
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains d...
ORGANISM(S): Escherichia coli 
2014-06-18 | E-GEOD-56372 | biostudies-arrayexpress
TranscriptomicsThe RPB2 flap loop of human RNA polymerase II is dispensable for transcription initiation and elongation.
Deletion of the flap loop in the Rp2 subunit of human RNAPII did not alter the ability of human RNAPII to initiate transcription or elongate the initiated transcripts in vivo and in vitro, and was also dispensable for elongation factor-mediated enhancement and inhibition of transcript elongation in ...
ORGANISM(S): Homo sapiens 
2011-06-24 | E-GEOD-29734 | biostudies-arrayexpress
UnknownRfaH Counter-Silences Inhibition of Transcript Elongation by H-NS-StpA Nucleoprotein Filaments in Pathogenic Escherichia coli.
Not available
S-EPMC9765446 | biostudies-literature
TranscriptomicsRegulator trafficking on bacterial transcription units in vivo
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 r...
ORGANISM(S): Escherichia coli 
2010-05-14 | E-GEOD-13938 | biostudies-arrayexpress
TranscriptomicsRho directs widespread termination of intragenic and stable RNA transcription
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 (...
ORGANISM(S): Escherichia coli 
2010-05-18 | E-GEOD-16562 | biostudies-arrayexpress
TranscriptomicsCorrecting Direct Effects of Ethanol on Translation and Transcription Machinery Confers Ethanol Tolerance in Bacteria [Terminator_Readthrough_RNAseq]
The molecular mechanisms of ethanol toxicity and tolerance in bacteria, while important for biotechnology and bioenergy applications, remain incompletely understood. Genetic studies have identified potential cellular targets for ethanol and revealed multiple mechanisms of tolerance, but it remains d...
ORGANISM(S): Escherichia coli 
2014-06-18 | E-GEOD-56407 | biostudies-arrayexpress
TranscriptomicsDksA Guards Elongating RNA Polymerase Against Ribosome-Stalling-Induced Arrest
In bacteria, translation-transcription coupling inhibits RNA polymerase (RNAP) stalling. We present evidence suggesting that, upon amino acid starvation, inactive ribosomes promote rather than inhibit RNAP stalling. We developed an algorithm to evaluate genome-wide polymerase progression independent...
ORGANISM(S): Escherichia coli 
2014-04-21 | E-GEOD-54669 | biostudies-arrayexpress
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