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Nucleosomes gate cofactor access to the transcription factor p53 [CUT&Run]

ABSTRACT: Nucleosomes gate cofactor access to the transcription factor p53 [CUT&Run]

PROVIDER: PRJNA1272474 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR33839389_1.fastq.gz	Fastqsanger.gz
	SRR33839389_2.fastq.gz	Fastqsanger.gz
	SRR33839390_1.fastq.gz	Fastqsanger.gz
	SRR33839390_2.fastq.gz	Fastqsanger.gz
	SRR33839391_1.fastq.gz	Fastqsanger.gz

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Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

Project description:Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

| PRJNA1272473 | ENA

Nucleosomes gate cofactor access to the transcription factor p53 [CUT&Run]

Project description:The transcription factor p53 regulates cell cycle progression, apoptosis, and the DNA damage response. A large fraction of p53 resides in inaccessible chromatin, where it is unclear how nucleosomes impact p53’s ability to engage cofactors. We examined the interaction of p53 with the members of the ubiquitin proteasome system (UPS) on chromatin. At two distinct motif locations (SHL-5.7, +5.9), the viral E3 ubiquitin ligase E6-E6AP was unable to bind nucleosome-engaged p53. The deubiquitinase USP7, on the other hand, readily engages nucleosome-bound p53 in vitro and in cells. The corresponding cryo-EM structure finds USP7 intricately engaged with p53 and nucleosomes, with the TRAF domain contacting the nucleosome at SHL-5.7 sandwiched between the p53 tetramerisation and DNA-binding domains. The structures of p53 bound to USP7/nucleosomes and E6AP illustrate how chromatin imposes a barrier for some, albeit not all p53 interactors. Our work suggests a conceptual framework for how nucleosomes govern TF/cofactor interactions.

2025-06-15 | GSE299057 | GEO

Nucleosomes gate cofactor access to the transcription factor p53 [ChIP-seq]

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Nucleosomes gate cofactor access to the transcription factor p53 P53_USP7TRAF_FL_NCP

Project description:In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

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Nucleosomes gate cofactor access to the transcription factor p53 P53-pos8-NCP

Project description:In solution crosslinking mass spectrometry of transcription factor p53 with the members of the ubiquitin proteasome system (UPS) on chromatin.

2025-07-31 | PXD054140 | Pride

The Mi-2 homolog, Mit1, actively positions nucleosomes within heterochromatic domains to suppress transcription

Project description:Nucleosome positioning is both active and passive and regulates access to the genome for replication, transcription and repair. Here we report that Mit1, a subunit of the fission yeast SHREC complex similar to Mi-2/NuRD, regulates transcription at regions of heterochromatin by positioning nucleosomes to preclude access to RNA Polymerase II. Purified Mit1 is a nucleosome remodeling factor capable of mobilizing histone octamers on short DNA fragments and requires ATP hydrolysis and chromatin tethering domains to remodel nucleosomes and silence transcription. We propose that SHREC is recruited to heterochromatin to mobilize nucleosomes onto unfavorable positions to prevent spurious transcription within heterochromatin.

2014-04-08 | GSE46649 | GEO

The Mi-2 homolog, Mit1, actively positions nucleosomes within heterochromatic domains to suppress transcription

2014-04-08 | E-GEOD-46649 | biostudies-arrayexpress

Genome access is transcription factor specific and defined by nucleosome position [ChIP-Seq]

Project description:Mammalian gene expression is controlled by transcription factors (TFs) that engage sequence motifs in a chromatinized genome, where nucleosomes can restrict DNA access. Yet, how nucleosomes affect individual TFs remains unclear. Here, we measure the ability of over one hundred TF motifs to recruit TFs in a defined chromosomal locus in mouse embryonic stem cells. This identifies a set sufficient to enable binding of TFs with diverse tissue specificities, functions, and DNA binding domains. These chromatin-competent factors are further classified when challenged to engage motifs within a highly-phased nucleosome. The pluripotency factors OCT4- SOX2 preferentially engage non-nucleosomal and entry-exit motifs, but not nucleosome internal sites, a preference that also guides binding genome-wide. By contrast, factors such as BANP, REST, or CTCF, engage throughout causing nucleosomal displacement.This reveals that TFs vary widely in their sensitivity to nucleosomes and that genome access is TF-specific and influenced by nucleosome position in the cell.

2024-08-13 | GSE240647 | GEO

Genome access is transcription factor specific and defined by nucleosome position [NOMe-seq]

2024-08-13 | GSE242066 | GEO

DDM1/Lsh remodelers allow methylation of DNA wrapped in nucleosomes

Project description:Eukaryotic DNA is wrapped around histone octamers to form nucleosomes, which are separated by linker DNA bound by histone H1. In many species, the DNA exhibits methylation of CG dinucleotides, which is epigenetically inherited via a semiconservative mechanism. How methyltransferases access DNA within nucleosomes remains mysterious. Here we show that methylation of nucleosomes requires DDM1/Lsh nucleosome remodelers in Arabidopsis thaliana and mouse. We also show that removal of histone H1, which partially restores methylation in ddm1 mutants, does so primarily in the linker DNA between nucleosomes. In h1ddm1 compound mutants, substantial portions of the genome exhibit dramatically periodic methylation that approaches wild-type levels in linker DNA but is virtually absent in nucleosomes. We also present evidence that de novo methylation supplements semiconservative maintenance of CG methylation across generations. Overall, our results demonstrate that nucleosomes and H1 are barriers to DNA methylation, which are overcome by DDM1/Lsh nucleosome remodelers.

2017-11-15 | GSE96994 | GEO

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