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DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast)

ABSTRACT: DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast)

PROVIDER: PRJNA475777 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7296730_1.fastq.gz	Fastqsanger.gz
	SRR7296730_2.fastq.gz	Fastqsanger.gz
	SRR7296740_1.fastq.gz	Fastqsanger.gz
	SRR7296740_2.fastq.gz	Fastqsanger.gz
	SRR7296750_1.fastq.gz	Fastqsanger.gz

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DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast II)

Project description:DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast II)

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DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast III)

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DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast)

Project description:DNA accessibility is thought to be of major importance in regulating gene expression. Here we test this hypothesis, using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes. Remarkably, AluI sites in inactive mouse promoters are accessible in some cells. Furthermore, heterochromatin and euchromatin have very similar accessibilities. Cell-to-cell heterogeneity in DNA accessibility has implications for chromatin models of gene regulation: a transcription factor binding site is blocked in some cells, but not in all cells, guaranteeing neither activation nor repression.

2019-08-27 | GSE115692 | GEO

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast III)

Project description:DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that DNA accessibility is primarily determined by nucleosome spacing. Remarkably, AluI sites in inactive mouse promoters are accessible in some cells. Furthermore, euchromatin and heterochromatin have very similar accessibilities. Cell-to-cell heterogeneity in DNA accessibility has implications for chromatin models of gene regulation: a transcription factor binding site is blocked in some cells, but not in all cells, guaranteeing neither activation nor repression.

2019-08-27 | GSE120956 | GEO

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (yeast II)

2019-08-27 | GSE120955 | GEO

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation

Project description:DNA accessibility is not the primary determinant of chromatin-mediated gene regulation

| PRJNA475773 | ENA

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (mouse)

Project description:DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (mouse)

| PRJNA475776 | ENA

DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (mouse)

2019-08-27 | GSE115691 | GEO

Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation.

Project description:DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at almost all genomic AluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, suggesting that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell. AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.

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Intrinsic histone-DNA interactions and low nucleosome density are important for accessibility of promoters in yeast

Project description:In yeast cells, preferential accessibility of the HIS3-PET56 promoter region is determined by a general property of the DNA sequence, not by defined sequence elements. In vivo, this region is largely devoid of nucleosomes, and accessibility is directly related to reduced histone density. The HIS3-PET56 and DED1 promoter regions associate poorly with histones in vitro, indicating that intrinsic nucleosome positioning and stability is a major determinant of preferential accessibility. Specific and genome-wide analyses indicate that low nucleosome density is a very common feature of yeast promoter regions that correlates poorly with transcriptional activation. Thus, the yeast genome is organized into structurally distinct promoter and non-promoter regions, whose DNA sequences inherently differ with respect to nucleosome formation. This organization ensures that transcription factors bind preferentially to appropriate sites in promoters, rather than to the excess of irrelevant sites in non-promoter regions. Keywords: other

2005-06-15 | GSE2659 | GEO

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