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Histone H3.3 is required for endogenous retroviral element silencing and genome stability [ChIP-Seq]

ABSTRACT: Endogenous retroviruses (ERVs) have provided an evolutionary advantage in the diversification of transcript regulation and are thought to be involved in the establishment of extraembryonic tissues during development. However, silencing of these elements remains critical for the maintenance of genome stability. Here, we define a new chromatin state that is uniquely characterized by the combination of the histone variant H3.3 and H3K9me3, two chromatin ‘marks’ that have previously been considered to belong to fundamentally opposing chromatin states. H3.3/H3K9me3 heterochromatin is fundamentally distinct from ‘canonical’ H3K9me3 heterochromatin that has been under study for decades and this unique functional interplay of a histone variant and a repressive histone mark is crucial for silencing ERVs in ESCs. Our study solidifies the emerging notion that H3.3 is not a histone variant associated exclusively with “active” chromatin and further suggests that its incorporation at unique heterochromatic regions may be central to its function during development and the maintenance of genome stability.

ORGANISM(S): Mus musculus

PROVIDER: GSE59188 | GEO | 2015/05/05

SECONDARY ACCESSION(S): PRJNA254708

REPOSITORIES: GEO

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Histone H3.3 is required for endogenous retroviral element silencing and genome stability [RNA-Seq]

Project description:Endogenous retroviruses (ERVs) have provided an evolutionary advantage in the diversification of transcript regulation and are thought to be involved in the establishment of extraembryonic tissues during development. However, silencing of these elements remains critical for the maintenance of genome stability. Here, we define a new chromatin state that is uniquely characterized by the combination of the histone variant H3.3 and H3K9me3, two chromatin ‘marks’ that have previously been considered to belong to fundamentally opposing chromatin states. H3.3/H3K9me3 heterochromatin is fundamentally distinct from ‘canonical’ H3K9me3 heterochromatin that has been under study for decades and this unique functional interplay of a histone variant and a repressive histone mark is crucial for silencing ERVs in ESCs. Our study solidifies the emerging notion that H3.3 is not a histone variant associated exclusively with “active” chromatin and further suggests that its incorporation at unique heterochromatic regions may be central to its function during development and the maintenance of genome stability. RNA-seq analysis of three embryonic stem cell lines WT, H3.3 KO1, and H3.3 KO2)

2015-05-05 | E-GEOD-59104 | biostudies-arrayexpress

Histone H3.3 is required for endogenous retroviral element silencing and genome stability [RNA-Seq]

2015-05-05 | GSE59104 | GEO

Profiling of H3.3

Project description:Histone variants can effect nucleosome stability or affect histone of DNA modifications. H3.3 is a major H3 histone variant that is incorporated into chromatin outside of S-phase in various eukaryotes. In animals, H3.3 is associated with active transcription and possibly maintenance of transcriptional memory. Plant H3.3, which evolved independently of animal H3.3, is much less well understood. We performed ChIP-chip using chromatin from rosette leaves of 35S:H3.3-YFP plants.

2014-03-10 | E-MTAB-1685 | biostudies-arrayexpress

Histone H3.3 fills gaps in heterochromatin generated by Smarcad1 in mouse embryonic stem cells (ESC)

Project description:Nucleosome turnover concomitant with incorporation of the replication-independent histone variant H3.3 is a hallmark of regulatory regions in the animal genome. In our current understanding, nucleosome turnover is universally linked to DNA accessibility and histone acetylation. In mouse embryonic stem cells, H3.3 is also highly enriched at interstitial heterochromatin, most prominently intracisternal-A particle endogenous retroviral elements. Interstitial heterochromatin is established over confined domains by the TRIM28/SETDB1 corepressor complex and has stereotypical features of repressive chromatin, such as H3K9me3 and recruitment of all HP1 isoforms. Here, we demonstrate that fast histone turnover and H3.3 incorporation is compatible with these hallmarks of heterochromatin. We identify Smarcad1 to be a chromatin remodeler that generates nucleosome-free regions which are subsequently filled with histone H3.3, generating a surprisingly dynamic heterochromatin state. Loss of histone H3.3 elicits a highly specific opening of interstitial heterochromatin demonstrating that in the wake of Smarcad1 remodeling, H3.3 is required to maintain minimal DNA accessibility by reassembling nucleosomes.

2020-08-28 | GSE149080 | GEO

RNA-seq analysis about Hira/Ubn1/Ubn2 knocked down samples

Project description:Histone chaperones are responsible for the deposition and removal of histones in chromatin and critical to prevent the abnormal activation of retrotransposable elements, which can be harmful to genome stability. One of the important histone chaperones is HIRA complex, which consists of Hira, Ubn1/Ubn2, and Cabin1 and mediates the installment of H3.3-H4 to nucleosome. We studied the function of members of HIRA complex in suppressing ERVs and found that histone H3.3 are enriched on all three classes of ERVs. Different HIRA members act distinctly in silencing ERVs. Ubn2 represses Class III ERVs including MERVL and Hira mainly silences Class I and Class II ERVs. Hira is enriched on Class I and II ERVs whereas its depletion affects the recruitment of H3.3. In contrast, Ubn2 is enriched on Class III ERVs, while its depletion influences H3.3 deposition and H3K9 methylation. This study extends our understandings of the mechanism by novel factors regulates ERVs.

2021-12-12 | GSE177026 | GEO

Suv39h-dependent H3K9me3 represses intact retrotransposons in mouse embryonic stem cells

Project description:Heterochromatin is required to restrict aberrant expression of retrotransposons, but it remains poorly defined due to the underlying repeat-rich sequences. We dissected Suv39h-dependent histone H3 lysine 9 trimethylation (H3K9me3) by genome-wide ChIP-sequencing in mouse embryonic stem cells (ESCs). Refined bioinformatic analyses of repeat subfamilies indicated selective accumulation of Suv39h-dependent H3K9me3 at interspersed repetitive elements that cover ~ 5% of the ESC epigenome. The majority of the ~ 8,150 intact long interspersed nuclear elements (LINEs) and endogenous retroviruses (ERVs), but only a minor fraction of the > 1.8 million degenerate and truncated LINEs/ERVs, are enriched for Suv39h-dependent H3K9me3. Transcriptional repression of these intact LINEs and ERVs is differentially regulated by Suv39h and other chromatin modifiers in ESCs but governed by DNA methylation in committed cells. These data provide a novel function for Suv39h-dependent H3K9me3 chromatin to specifically repress intact retrotransposon elements in the ESC epigenome. ChIP-seq and RNA-seq in mouse ES cells, Neural precursors and MEFs wild type and Suv39h double KO. The input for ES cells is accessioned as GSM1251941. A link to this sample can be found below.

2014-06-26 | E-GEOD-57092 | biostudies-arrayexpress

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network (part 1)

Project description:A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between histone H3–H4 chaperones in the histone chaperone network. We identify several novel histone dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3–H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.

2023-03-02 | PXD034888 | Pride

DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network (part 2)

2023-03-02 | PXD038263 | Pride

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.

2020-06-03 | MSV000085543 | MassIVE

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.

2017-03-06 | GSE66364 | GEO

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