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Surprising mechanisms and regulatory roles of yeast transcription factors [ChIP-seq]

ABSTRACT: Surprising mechanisms and regulatory roles of yeast transcription factors [ChIP-seq]

PROVIDER: PRJNA993169 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25220267_1.fastq.gz	Fastqsanger.gz
	SRR25220267_2.fastq.gz	Fastqsanger.gz
	SRR25220268_1.fastq.gz	Fastqsanger.gz
	SRR25220268_2.fastq.gz	Fastqsanger.gz
	SRR25220269_1.fastq.gz	Fastqsanger.gz

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Surprising mechanisms and regulatory roles of yeast transcription factors

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Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

Project description:DNA sequence-specific transcription factors (TFs) modulate transcription and chromatin architecture, acting from regulatory sites in enhancers and promoters of eukaryotic genes. How multiple TFs cooperate to regulate individual genes is still unclear. Most yeast TFs are thought to regulate transcription via binding to Upstream Activating Sequences, situated within a few hundred base pairs upstream of the regulated gene1. While this model has been validated for individual TFs and specific genes, it has not been tested in a systematic way. We integrated information on the binding and expression targets for the near-complete set of yeast TFs. Here we show that, contrary to expectations, there are few TFs with dedicated activator or repressor functions with most TFs having a dual role. While nearly all protein coding genes are regulated by one or more TFs, our analysis revealed limited overlap between TF binding and gene regulation. Rapid depletion of many TFs also revealed numerous regulatory targets distant from detectable TF binding sites, suggesting unexpected regulatory mechanisms. Our study provides a comprehensive survey of TF functions, offering insights into interactions between the set of TFs expressed in a single cell type and how they contribute to the complex program of gene regulation.

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Histone H3K36 trimethylation is essential for multiple silencing mechanisms in fission yeast.

Project description:In budding yeast, Set2 catalyzes di- and trimethylation of H3K36 (H3K36me2 and H3K36me3) via an interaction between its SRI domain and C-terminal repeats of RNA polymerase II (Pol2) phosphorylated at Ser2 and Ser5 (CTD-S2,5-P). H3K36me2 recruits the Rpd3S histone deacetylase complex to repress cryptic transcription from transcribed regions. In fission yeast, Set2 is also responsible for H3K36 methylation, which represses a subset of RNAs including heterochromatic and subtelomeric RNAs, at least in part via recruitment of Clr6 complex II, a homolog of Rpd3S. Here, we show that CTD-S2Pâdependent interaction of fission yeast Set2 with Pol2 via the SRI domain is required for formation of H3K36me3, but not H3K36me2. H3K36me3 silenced heterochromatic and subtelomeric transcripts through post-transcriptional and transcriptional mechanisms, respectively, whereas H3K36me2 did not. Clr6 complex II appeared not to be responsible for heterochromatic silencing. Our results demonstrate that H3K36 methylation has multiple outputs in fission yeast; these findings provide insight into the multiple roles of H3K36 methylation in metazoans, which have different enzymes for synthesis of H3K36me1/2 and H3K36me3. Gene expression profile at exponentially-growing phase.in the fission yeast deletion mutants of set2.

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