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Pervasive promoter-proximal regulation in archaea: Permanganate ChIP-seq hydrogen-peroxide treated cells

ABSTRACT: Pervasive promoter-proximal regulation in archaea: Permanganate ChIP-seq hydrogen-peroxide treated cells

PROVIDER: PRJNA593549 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10587777.fastq.gz	Fastqsanger.gz
	SRR10587778.fastq.gz	Fastqsanger.gz
	SRR10587779.fastq.gz	Fastqsanger.gz
	SRR10587780.fastq.gz	Fastqsanger.gz

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Pervasive promoter-proximal regulation in archaea: ChIP-seq hydrogen peroxide-treated cells

Project description:Pervasive promoter-proximal regulation in archaea: ChIP-seq hydrogen peroxide-treated cells

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Pervasive promoter-proximal regulation in archaea: ChIP-exo hydrogen peroxide-treated cells

Project description:Pervasive promoter-proximal regulation in archaea: ChIP-exo hydrogen peroxide-treated cells

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Pervasive promoter-proximal regulation in archaea: ChIP-seq hydrogen peroxide-treated cells

Project description:Genome-wide occupancy of the basal transcription machinery in Saccharolobus solfataricus strain P2 (Sulfolobus solfataricus) after hydrogen peroxide treatment Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

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Pervasive promoter-proximal regulation in archaea: RNA-seq of hydrogen peroxide-treated cells and mock-treated control

Project description:Pervasive promoter-proximal regulation in archaea: RNA-seq of hydrogen peroxide-treated cells and mock-treated control

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Pervasive promoter-proximal regulation in archaea: Permanganate ChIP-seq exponential growth

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Response of Bacillus pumilus to hydrogen peroxide

Project description:Reactive oxygen species such as hydrogen peroxide occur in all aerobically living organisms. Oxidative stress during fermentation can impair the fitness of the production host and the quality of the product. B. pumilus has been described as highly resistant to hydrogen peroxide. The response of exponentially growing B. pumilus cells to hydrogen peroxide was studied.

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Adaptation to hydrogen peroxide

Project description:Adaptation to hydrogen peroxide in Saccharomyces cerevisiae is profiled with expression arrays. Adaptation describes the process in which a mild dose of toxin (in this case, hydrogen peroxide) is able to protect against a later acute dose. Here, we study two adaptive protocols (0.1 mM H2O2 and 0.1 + 0.4 mM H2O2) and one acute protocol (0.4 mM H2O2) to identify processes uniquely involved in adaptation. Predictions from these studies are validated in expression profiling of deletion mutants of the transcription factors Yap1, Mga2, and Rox1.

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Pervasive promoter-proximal regulation in archaea: ChIP-exo hydrogen peroxide-treated cells

Project description:Recruitment of RNA polymerase and initiation factors to the promoter is the only known mechanisms for transcription activation and repression in archaea. Whether any of the subsequent steps towards productive transcription elongation is involved in regulation is not known. We characterised how the basal transcription machinery is distributed along genes in the archaeon Sulfolobus solfataricus. We discovered a distinct early elongation phase where RNA polymerases sequentially recruit the elongation factors Spt4/5 and Elf1 to form the transcription elongation complex (TEC) before the TEC escapes into productive transcription. TEC escape is rate-limiting for transcription output during exponential growth. Oxidative stress causes changes in TEC escape that correlate with changes in the transcriptome. Our results thus establish that TEC escape contributes to the basal promoter strength and facilitates transcription regulation. Impaired TEC escape coincides with the accumulation of initiation factors at the promoter and recruitment of termination factor aCPSF1 to the early TEC. This suggests two possible mechanisms for how TEC escape limits transcription, physically blocking upstream RNA polymerases during transcription initiation and premature termination of early TECs.

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