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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation

ABSTRACT: Context dependent function of transcriptional regulator Rap1 in gene silencing and activation

PROVIDER: PRJNA946774 | ENA |

REPOSITORIES: ENA

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			Action	DRS
		Other
	SRR23919900_1.fastq.gz	Fastqsanger.gz
	SRR23919900_2.fastq.gz	Fastqsanger.gz
	SRR23920100_1.fastq.gz	Fastqsanger.gz
	SRR23920100_2.fastq.gz	Fastqsanger.gz

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIPseq I]

Project description:Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIPseq I]

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq III]

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq III]

Project description:As part of a study on the mechanism of Sir-based silencing at HML in S.cerevisiae, and the contribution of Rap1 to transcription of the locus, we performed ChIP-seq of multiple components of RNA Pol II machinery in different genetic backgrounds including: sir4∆, SIR+, and with or without a mutation that abbrogated Rap1 binding at the alpha promoter.

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIPseq I]

Project description:As part of a study on the role of Rap1 at the promoters of HML and MAT in S cerevisiae, we endogenously tagged Rap1 with a 3xV5 tag and performed ChIPseq in a variety of genetic backgrounds including: silenced (SIR); unsilenced (sir1∆/sir3∆/sir4∆); in strains witha wild type alpha2 promoter (wtpromoter); or with a point mutation at the promoter (mutpromoter).

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq II]

Project description:As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed ChIP-seq on myc-tagged Sir3 in cells with and without a Rap1 binding site mutation at the promoter.

2023-05-09 | GSE227759 | GEO

Context dependent function of transcriptional regulator Rap1 in gene silencing and activation [ChIP-seq timecourse]

Project description:As part of a study on the function of Rap1 at HML and MAT in Saccharomyces cerevisiae, we performed an Anchor Away experiment on Rap1, inducibly depleting it from the nucleus upon addition of Rapamycin, followed by a ChIP-seq time-course. This was done in a strain that had SNPs introduced to HMLalpha to make it distinguishable from MATalpha. Samples were spiked with a constant amount (5% by OD) of a S.paradoxus strain that also expressed 2xV5-Rap1. Reads from the S.paradoxus sample served as the normalization factor. Peaks were then fit to a non-linear regression model to extract the k(off) and apparent residence time in vivo.

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Context dependent function of transcriptional regulator Rap1 in gene silencing and activation

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

2023-05-09 | GSE227763 | GEO

Context-dependent function of the transcriptional regulator Rap1 in gene silencing and activation in <i>Saccharomyces cerevisiae</i>.

Project description:In Saccharomyces cerevisiae, heterochromatin is formed through interactions between site-specific DNA-binding factors, including the transcriptional activator Repressor Activator Protein (Rap1), and Sir proteins. Despite an understanding of the establishment and maintenance of Sir-silenced chromatin, the mechanism of gene silencing by Sir proteins has remained a mystery. Utilizing high-resolution chromatin immunoprecipitation, we found that Rap1, the native activator of the bidirectional HMLα promoter, bound its recognition sequence in silenced chromatin, and its binding was enhanced by the presence of Sir proteins. In contrast to prior results, various components of transcription machinery were not able to access HMLα in the silenced state. These findings disproved the long-standing model of indiscriminate steric occlusion by Sir proteins and led to investigation of the role of the transcriptional activator Rap1 in Sir-silenced chromatin. Using a highly sensitive assay that monitors loss-of-silencing events, we identified a role for promoter-bound Rap1 in the maintenance of silent chromatin through interactions with the Sir complex. We also found that promoter-bound Rap1 activated HMLα when in an expressed state, and aided in the transition from transcription initiation to elongation. Highlighting the importance of epigenetic context in transcription factor function, these results point toward a model in which the duality of Rap1 function was mediated by local chromatin environment rather than binding-site availability.

| S-EPMC10556627 | biostudies-literature

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