Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA199926 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR835304.fastq.gz | Fastqsanger.gz | |||
| SRR835305.fastq.gz | Fastqsanger.gz | |||
| SRR835306.fastq.gz | Fastqsanger.gz | |||
| SRR835307.fastq.gz | Fastqsanger.gz | |||
| SRR835308.fastq.gz | Fastqsanger.gz |
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Project description:We developed a ChIP protocol for the analysis of histone marks using less than 10,000 cells per IP, and used it to investigate the chromatin state of E11.5 mouse primordial germ cells (PGCs). A genome-wide ChIP-Seq analysis of E11.5 PGCs revealed a distribution of H3K4me3/H3K27me3 bivalent domains highly enriched for developmental regulatory genes. H3K4me3 and H3K27me3 ChIP-Seq from mouse E11.5 primordial germ cells.
2013-05-30 | E-GEOD-46396 | biostudies-arrayexpress
Project description:Tissue homeostasis and regeneration require activation and subsequent lineage commitment of tissue-resident stem cells (SCs). These state changes are controlled by epigenetic barriers. Using hair follicle stem cells (HFSCs) as paradigm, we studied how aging impacts the chromatin landscape and function of mammalian SCs. Analyses of genome-wide chromatin accessibility revealed that aged HFSCs displayed widespread reduction of chromatin accessibility specifically at key SC self-renewal and differentiation genes that were characterized by bivalent promoters carrying both activating and repressive chromatin marks. Consistently, aged HFSCs showed reduced self-renewing capacity and attenuated ability to activate expression of these bivalent genes upon regeneration. These functional defects were niche-dependent as transplantation of aged HFSCs into young recipients or into ex vivo niches restored SC functions and transcription of poised genes. Mechanistically, aged HFSC niche displayed wide-spread alterations in extracellular matrix composition and mechanics, resulting in compressive forces on SCs and subsequent transcriptional repression, leading to loss of bivalent promoters. Tuning tissue mechanics both in vivo and in vitro recapitulated age-related SC changes, implicating niche mechanics as a central regulator of genome organization and function leading to age-dependent SC exhaustion.
2021-05-07 | PXD018352 | Pride
Project description:We developed a ChIP protocol for the analysis of histone marks using less than 10,000 cells per IP, and used it to investigate the chromatin state of E11.5 mouse primordial germ cells (PGCs). A genome-wide ChIP-Seq analysis of E11.5 PGCs revealed a distribution of H3K4me3/H3K27me3 bivalent domains highly enriched for developmental regulatory genes.
2013-05-30 | GSE46396 | GEO
Project description:Epigenetic priming factors establish a permissive epigenetic landscape which is not required until a later developmental or physiological time point, temporally uncoupling the presence of these factors with their phenotypic effects. One classic example of epigenetic priming is in the context of bivalent chromatin, found in pluripotent stem cells and early embryos at key developmental gene promoters marked by both activating-associated H3K4me3 and repressive-associated H3K27me3 histone modifications. It is currently unknown how these bivalent domains are targeted, or precisely how they impact on lineage commitment. Here we show that the small heterodimerising non-enzymatic DNA binding proteins Developmental Pluripotency Associated 2 (Dppa2) and 4 (Dppa4) act as epigenetic priming factors to establish bivalency at a subset of developmental genes. Dppa2/4 localise to the +1 nucleosome position of bivalent genes and while they are not required for pluripotency in embryonic stem cells (ESCs), double knockout cells fail to exit pluripotency and to differentiate efficiently, with delays in upregulating bivalently marked lineage genes. Proteomics reveal that Dppa2/4 interact on chromatin with members of the COMPASS and Polycomb complexes important for H3K4me3 and H3K27me3 deposition, respectively. Epigenetic profiling reveals a striking loss of H3K4me3, H3K27me3, and their associated enzymatic machinery at a significant subset of bivalent promoters in Dppa2/4 mutants, in addition to loss of H2A.Z and chromatin accessibility. In wild-type ESCs, these “Dppa2/4-dependent” bivalent promoters are characterised by low H3K4me3 enrichment and breadth, near-absent expression levels and initiating but not elongating RNA polymerase. Notably, Dppa2/4-dependent promoters are less evolutionarily conserved suggesting that they lack additional safeguard measures to maintain bivalency at these genes in the absence of Dppa2/4. Concomitantly with the loss of bivalency, Dppa2/4-dependent bivalent promoters gain DNA methylation and consequently are no longer able to be effectively activated upon ESC differentiation, leading to defects in cell fate acquisition. Our findings reveal a targeting principle for bivalency to developmental gene promoters poising them for future lineage specific gene activation.
2020-05-26 | PXD014981 | Pride
Project description:In mammals, many germline genes are repressed by epigenetic mechanisms to prevent their illegitimate expression in embryonic and somatic cells. To advance our understanding of the complete mechanisms restricting the expression of germline genes in mammals, we analyzed the chromatin signature of germline genes and performed a genome-wide CRISPR-Cas9 knock-out screen for genes involved in germline gene repression using a reporter system in which GFP is under the control of the epigenetically repressed Dazl germline promoter in mouse embryonic stem cells (ESCs). We showed that the repression of germline genes mainly depends on the polycomb complex PRC1.6 and DNA methylation, which function additively in mouse ESCs. Furthermore, we identified and validated several novel genes involved in the repression of germline genes, and characterized three of them: Usp7, Shfm1 (also known as Sem1) and Erh. Inactivation of Usp7, Shfm1 or Erh led to the upregulation of germline genes, as well as retrotransposons for Shfm1, in mouse ESCs. Functionally, Usp7 acts at two levels: firstly it associates with PRC1.6 components and represses germline genes independently of DNA methylation, and secondly it facilitates DNA methylation deposition at germline genes for long term repression. In summary, our study provides a global view of the epigenetic mechanisms and novel factors required for silencing germline genes in embryonic cells.
2023-02-03 | PXD030666 | Pride
Project description:Epigenetics helps define current cell states, yet also shapes how cells respond to external cues such as differentiation or stress. The epigenetic plasticity of a cell describes how flexible this regulation is. Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of the active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome was first described in mouse embryonic stem cells where it is found at promoters of key developmental genes. It has been postulated that bivalent chromatin poises these promoters, keeping them free from repressive DNAmethylation, enabling them to be transcriptionally upregulated upon differentiation. Bivalent chromatin has also been reported in other cell types including somatic cells and cancer cells, however we know little of the dynamics, resolution and regulation of this chromatin state. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from sample heterogeneity where some alleles have H3K4me3 and others H3K27me3. We developed a robust and sensitive reChIP method to accurately profile bivalent chromatin in as little as 2 million mouse embryonic stem cells. We validated the sensitivity of our method to detect changes in bivalent chromatin by profiling mouse ESCs lacking the epigenetic priming factors Dppa2 and Dppa4.
2024-02-26 | GSE242686 | GEO
Project description:Germ cell specification is accompanied by epigenetic remodeling, the scale and specificity of which are unclear. Here, we quantitatively delineate chromatin dynamics during induction of mouse embryonic stem cells (ESCs) to epiblast-like cells (EpiLCs) and from there into primordial germ cell-like cells (PGCLCs), revealing large-scale reorganization of chromatin signatures including H3K27me3 and H3K9me2 patterns. EpiLCs contain abundant bivalent gene promoters characterized by low H3K27me3, indicating a state primed for differentiation. PGCLCs initially lose H3K4me3 from many bivalent genes but subsequently regain this mark with concomitant upregulation of H3K27me3, particularly at developmental regulatory genes. PGCLCs progressively lose H3K9me2, including at lamina-associated perinuclear heterochromatin, resulting in changes in nuclear architecture. T recruits H3K27ac to activate BLIMP1 and early mesodermal programs during PGCLC specification, which is followed by BLIMP1-mediated repression of a broad range of targets, possibly through recruitment and spreading of H3K27me3. These findings provide a foundation for reconstructing regulatory networks of the germline epigenome.
2015-03-20 | GSE60204 | GEO
Project description:Histone modifications are associated with distinct transcriptional states, but it is unclear whether they instruct gene expression. To investigate this, we mutated histone H3.3 K9 and K27 residues in mouse embryonic stem cells (mESCs). Here, we find that H3.3K9 is essential for controlling specific distal intergenic regions and for proper H3K27me3 deposition at promoters. The H3.3K9A mutation resulted in decreased H3K9me3 at regions encompassing endogenous retroviruses and induced a gain of H3K27ac and nascent transcription. These changes in the chromatin environment unleashed cryptic enhancers, resulting in the activation of distinctive transcriptional programs and culminating in protein expression normally restricted to specialized immune cell types. The H3.3K27A mutant disrupted deposition and spreading of the repressive H3K27me3 mark, particularly impacting bivalent genes with higher basal level of H3.3 at promoters. Therefore, H3.3K9 and K27 crucially orchestrate repressive chromatin states at cis-regulatory elements and bivalent promoters, respectively, and instruct proper transcription in mESCs.
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Project description:Embryonic stem (ES) cells have the ability to differentiate into all the cell types of the adult organism. This unusual property has been proposed to emanate from a particular chromatin environment that simultaneously contains both H3K4 and H3K27 trimethylation marks at the regulatory regions of the developmental genes, which are thus poised for activation during differentiation following resolution of these “bivalent domains.” Our work identifies Lysine Specific Demethylase 1 (LSD1/AOF2/KDM1A) as a key histone modifier in the maintenance of pluripotency. We show that the knock-down of LSD1 causes the differentiation of human ES cells and the induction of key endo- and mesodermal genes marked with bivalent domains. This induction correlates with an increase in the levels of H3K4 methylation at the regulatory regions of these genes. ChIP on chip analysis reveals that in human ES cells LSD1 preferentially occupies the promoters of a subset of developmental genes that contain bivalent domains that are also occupied by OCT4 and NANOG. We conclude that LSD1 contributes to maintain a subset of developmental genes in human ES in a silenced state by maintaining the critical balance between H3K4 and H3K27 methylation at the regulatory regions of these genes.
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Project description:In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes, however the molecular mechanisms of this specificity remain unclear. Here we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in vivo, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long term epigenetic silencing during mammalian development.
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