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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ChIP-Seq]

ABSTRACT: We analyze ATRX enrichment in ATRX-GFP and FACT subunits KD mESC

ORGANISM(S): Mus musculus

PROVIDER: GSE151054 | GEO | 2021/05/17

REPOSITORIES: GEO

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ATAC-Seq]

Project description:We analyze the contribution of ATRX, DAXX and HIRA to the chromatin accessibility at G-quadruplex in mESC We analyze the contribution of ATRX and ESET to the chromatin accessibility at G-quadruplex in mESC

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [CUT&Tag]

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [EdU-seq]

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TERRA regulates DNA G-quadruplex formation and ATRX loading on chromatin

Project description:The genome consists of non-B-DNA structures such as G-quadruplexes (G4) that are involved in the regulation of genome stability and transcription. Telomeric-repeat containing RNA (TERRA) is capable of folding into G-quadruplex and interacting with chromatin remodeler ATRX. Here we show that TERRA modulates ATRX occupancy on repetitive sequences and over genes, and maintains DNA G-quadruplex structures at TERRA target and non-target sites in mouse embryonic stem cells. TERRA prevents ATRX from binding to subtelomeric regions and represses H3K9me3 formation. G4 ChIP-seq reveals that G4 abundance decreases at accessible chromatin regions, particularly at transcription start sites (TSS) after TERRA depletion; such G4 reduction at TSS is associated with elevated ATRX occupancy and differentially expressed genes. Loss of ATRX alleviates the effect of gene repression caused by TERRA depletion. Immunostaining analyses demonstrate that knockdown of TERRA diminishes DNA G4 signals, whereas silencing ATRX elevates G4 formation. Our results uncover an epigenetic regulation by TERRA that sequesters ATRX and preserves DNA G4 structures.

2022-11-09 | GSE194038 | GEO

ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

Project description:ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress

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

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ATRX - a chromatin remodelling protein interactome

Project description:ATRX is a chromatin remodelling protein of the SWI/SNF family, mutations in which cause alpha thalassemia X-linked (ATRX) intellectual disability syndrome and are highly associated with a number of cancers characterized by alternative lengthening of telomeres. ATRX functions with the histone chaperone DAXX to facilitate deposition of the histone variant H3.3 at heterochromatic regions such as telomere and pericentric repeats, resulting in a unique form of heterochromatin characterized by both trimethylation of histone H3 at lysine 9 (H3K9me3) and H3.3. How ATRX is recruited to these regions remain unclear.To better understand it, we therefore used immunoprecipitation-coupled to mass spectrometry (IP-MS) to identify potential factors that interact with ATRX and may promote its localization and function. Based on our proteomics results, we identified known ATRX-interacting proteins, DAXX and MRE11. We also identified a number of proteins that have been genetically linked to G-quadruplex structures. Interestingly, we identified members of DNA replcation machinery MCM complex (e.g. MCM2, MCM4, MCM6, and MCM7) and the faciliates chromatin transcription (FACT) comeplex as novel ATRX-interacting proteins. We then verified the interaction of ATRX to MCM proteins and FACT subunits by co-immunoprecipition/immunoblot and proximity ligation assay.

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ATAC-Seq]

Project description:ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ATAC-Seq]

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ATRX promotes heterochromatin formation to protect cells from G-quadruplex DNA-mediated stress [ChIP-Seq]

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