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Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [RNA-Seq]

ABSTRACT: Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [RNA-Seq]

PROVIDER: PRJNA635918 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11878400_1.fastq.gz	Fastqsanger.gz
	SRR11878400_2.fastq.gz	Fastqsanger.gz
	SRR11878401_1.fastq.gz	Fastqsanger.gz
	SRR11878401_2.fastq.gz	Fastqsanger.gz
	SRR11878402_1.fastq.gz	Fastqsanger.gz

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Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

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Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function [ChIP-Seq]

Project description:Protein-DNA interactions are dynamic and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide-range, varying between 4.5 and 37 minutes. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.

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Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

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Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function.

Project description:Protein-DNA interactions are dynamic, and these dynamics are an important aspect of chromatin-associated processes such as transcription or replication. Due to a lack of methods to study on- and off-rates across entire genomes, protein-DNA interaction dynamics have not been studied extensively. Here, we determine in vivo off-rates for the Saccharomyces cerevisiae chromatin organizing factor Abf1, at 191 sites simultaneously across the yeast genome. Average Abf1 residence times span a wide range, varying between 4.2 and 33 min. Sites with different off-rates are associated with different functional characteristics. This includes their transcriptional dependency on Abf1, nucleosome positioning and the size of the nucleosome-free region, as well as the ability to roadblock RNA polymerase II for termination. The results show how off-rates contribute to transcription factor function and that DIVORSEQ (Determining In Vivo Off-Rates by SEQuencing) is a meaningful way of investigating protein-DNA binding dynamics genome-wide.

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