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RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription

ABSTRACT: RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription

PROVIDER: PRJNA743010 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15013952_1.fastq.gz	Fastqsanger.gz
	SRR15013952_2.fastq.gz	Fastqsanger.gz
	SRR15013953_1.fastq.gz	Fastqsanger.gz
	SRR15013953_2.fastq.gz	Fastqsanger.gz
	SRR15013954_1.fastq.gz	Fastqsanger.gz

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RSC mediated nucleosome positioning and GRFs form barriers in promoters to limit divergent noncoding transcription [RNA-Seq]

Project description:The directionality of gene promoters, the proportion of protein coding over divergent noncoding transcription, is highly variable and regulated. How promoter directionality is controlled remains poorly understood. We show that chromatin remodelling complex RSC, general regulatory factors (GRFs) including transcription factors (TFs) can facilitate promoter directionality by attenuating divergent noncoding transcription. Depletion of RSC increased divergent noncoding and decreased protein coding transcription of promoters with strong directionality. Consistent with RSC’s role in regulating chromatin, RSC depletion negatively impacts nucleosome positions upstream of the nucleosome depleted region where divergent transcription initiates, suggesting that nucleosome positioning upstream in promoters physically blocks the recruitment of transcription machinery. Likewise, divergent transcription can be suppressed by targeting GRFs and TFs or the bulky dCas9 protein to transcriptional initiation sites. We propose that RSC mediated nucleosome positioning, GRFs including TFs form the physical barriers in promoters for limiting of divergent transcription, thereby controlling promoter directionality.

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

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RSC Regulates Nucleosome Positioning at Pol II Genes and Density at Pol III Genes

Project description:Nucleosomes restrict the access of transcription factors to chromatin. RSC is a SWI/SNF-family chromatin-remodeling complex from yeast that repositions and ejects nucleosomes in vitro. Here, we examined these activities and their importance in vivo. We utilized array-based methods to examine nucleosome occupancy and positioning at more than 200 locations in the genome following the controlled destruction of the catalytic subunit of RSC, Sth1. Loss of RSC function caused pronounced and general reductions in transcription from Pol I, II, and III genes. At Pol III genes, Sth1 loss conferred a general gain in nucleosome density and an accompanying reduction in RNA Pol III occupancy. In contrast, we observed primarily single nucleosome changes, including movement, at Pol II promoters. Importantly, a greater number of changes were observed near the transcription start sites of RSC-occupied promoters than non-occupied promoters. These changes are distinct from those due to general loss of transcription. Thus, RSC action affects both nucleosome density and positioning in vivo, but applies these remodeling modes differently at Pol II and Pol III genes. Keywords: ChIP-chip, nucleosome, mononucleosome, RSC, transcription

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