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Homo sapiens

ABSTRACT: Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells

PROVIDER: PRJNA133145 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR065790.fastq.gz	Fastqsanger.gz
	SRR065791.fastq.gz	Fastqsanger.gz
	SRR065792.fastq.gz	Fastqsanger.gz

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An integrative analysis of the SOX2 response program in glioblastoma

Project description:This SuperSeries is composed of the following subset Series: GSE23795: Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells GSE23838: Genes regulated by Sox2 in glioma cancer cell line Refer to individual Series

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Chip-Seq analysis of Sox2 protein genome-wide DNA binding sites in glioma cancer cells

Project description:We report here our results of the genome wide target identification of SOX2 in GBM cells by ChIP-seq analysis. Identification of Sox2 DNA binding site in glioma cancer cells

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Project description:Genome-wide transcriptional activity involves the binding of many transcription factors to thousands of sites in the genome. Determining which sites are directly driving transcription remains a challenge. Here we use acute protein depletion of the pioneer transcription factor SOX2 to establish its functionality in maintaining chromatin accessibility. We show that thousands of accessible sites are lost within an hour of protein depletion, indicating rapid turnover of these sites in the absence of pioneer factors. To understand the relationship with transcription we performed nascent transcription analysis and found that open chromatin sites that are maintained by SOX2 are highly predictive of gene expression, in contrast to all other SOX2 binding sites. We use CRISPR-Cas9 genome editing in the Klf2 locus to functionally validate a predicted regulatory element. We conclude that the regulatory activity of SOX2 is exerted largely at sites where it maintains accessibility and that other binding sites are largely dispensable for gene regulation.

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Project description:To understand the mechanism underlying the versatility in transcriptional regulation by Sox2 and Esrrb, we compared genome-wide binding sites of Sox2 and Esrrb in embryonic stem (ES) cells and trophoblast stem (TS) cells by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq).

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Project description:Genome-wide mapping of protein–DNA interactions is essential for a full understanding of transcriptional regulation. A precise map of binding sites for transcription factors, core transcriptional machinery is vital for deciphering the gene regulatory networks that underlie various biological processes. Chromatin immunoprecipitation followed by sequencing (ChIP–seq) is a technique for genome-wide profiling of DNA-binding proteins. However, our conventional ChIP–seq occasionally gives wider peaks which might be due to overlapping binding sites of two or more transcription factors. Therefore, to improve the resolution of our conventional ChIP–seq which have DNA-protein footprint of ~100 bp, we decreased the size of DNA-protein footprint to ~ 50 bp by DNaseI digestion of whole cell extract (WCE).

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Project description:High-resolution Sox2 DNA-binding sites mapping by ChIP-exo in TSA-treated ES cells

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