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Analysis of gene expression and of H3.3 distribution and abundance in a ATRX loss-of-function line

ABSTRACT: Analysis of gene expression and of H3.3 distribution and abundance in a ATRX loss-of-function line

PROVIDER: PRJNA348185 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4420300.fastq.gz	Fastqsanger.gz
	SRR4420301.fastq.gz	Fastqsanger.gz
	SRR4420302.fastq.gz	Fastqsanger.gz
	SRR4420293_1.fastq.gz	Fastqsanger.gz
	SRR4420293_2.fastq.gz	Fastqsanger.gz

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Analysis of eH3.3 occupancy in a ATRX loss-of-function line [ChIP-seq]

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Genome-wide ChIP seq of H3.3 in WT and ATRX KO mouse ES cells

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DAXX-ATRX-H3.3 Regulation of p53 Chromatin Binding and DNA Damage Response [ChIP-Seq]

Project description:DAXX and ATRX are tumor suppressor proteins that form a complex with histone H3.3 chaperone and are frequently mutated in cancers with the alternative lengthening of telomeres (ALT), such as pediatric glioblastoma. Rapid loss of function of either DAXX or ATRX are not by themselves sufficient to induce the ALT phenotype. However, cells lacking DAXX or ATRX can be readily selected for ALT-like features. Here, we show that a key feature of ALT selected DAXX and ATRX null glioblastoma cells is the attenuation of p53 function. RNA-seq analysis of DAXX or ATRX null U87 glioblastoma cells with ALT-like features revealed that p53 pathway is among perturbed. ALT-selected DAXX and ATRX-null cells had aberrant response to DNA damaging agent etoposide. Both DAXX and ATRX-null ALT cells showed a loss of p53 binding at a subset of response elements. Complementation of DAXX null cells with wt DAXX rescued p53 binding and transcription, while the tumor associated mutation L130R, that disrupts ATRX binding, was incapable of rescuing p53 chromatin binding. We show that histone H3.3 binding is reduced in DAXX-null cells especially at subtelomeric p53 binding sites and telomere repeats. These findings indicate that DAXX and ATRX function to enable p53 chromatin binding through modulation of histone H3.3 binding, especially at sub-telomeric sites.

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PML protein organizes heterochromatin domains where it regulates histone H3.3 deposition by ATRX/DAXX

Project description:Maintenance of chromatin homeostasis involves proper delivery of histone variants to the genome. The interplay between different chaperones regulating the supply of histone variants to distinct chromatin domains remains largely undeciphered. We report a role of promyelocytic leukemia (PML) protein in the routing of histone variant H3.3 to chromatin and in the organization of megabase-size heterochromatic PML-associated domains that we call PADs. Loss of PML alters the heterochromatic state of PADs by shifting the histone H3 methylation balance from K9me3 to K27me3. Loss of PML impairs deposition of H3.3 by ATRX and DAXX in PADs but preserves the H3.3 loading function of HIRA in these regions. Our results unveil an unappreciated role of PML in the large-scale organization of chromatin and demonstrate a PML-dependent role of ATRX/DAXX in the deposition of H3.3 in PADs. Our data suggest that H3.3 loading by HIRA and ATRX-dependent H3K27 trimethylation constitute mechanisms ensuring maintenance of heterochromatin when the integrity of these domains is compromised.

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Analysis of gene expression and of H3.3 distribution and abundance in a ATRX loss-of-function line

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

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ATRX-mediated chromatin association of histone variant macroH2A1 regulates alpha globin gene expression

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