Optimization of mESC ChIP-re-ChIP workflow
Ontology highlight
ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE242686 | GEO | 2024/02/26
REPOSITORIES: GEO
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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:The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-4. In plants, timely transition to a flowering state is crucial for successful reproduction5-7. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis8,9. Here, we revealed that bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules of EBS bind H3K27me3 and H3K4me3, respectively. A subset of EBS-associated genes was co-enriched with H3K4me3, H3K27me3, and the Polycomb repressor complex 2 (PRC2). Interestingly, EBS adopts an auto-inhibition mode to mediate its binding preference switch between H3K27me3 and H3K4me3. This binding balance is critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induces EBS-mediated early floral transition. This study identifies a single bivalent chromatin reader capable of recognizing two antagonistic histone marks and reveals a distinct mechanism of interplay between active and repressive chromatin states.v
2019-09-09 | PXD009794 | Pride
Project description:By mapping the genomic enrichments of H3K4me3 and H3K27me3 modifications in pure populations of hESCs during the G2, mitotic and G1 phases of the cell cycle, we characterize cell cycle-dependent variations in the epigenetic landscape of bivalent genes, altering the current view of mitotic inheritance in pluripotent cells. We identified novel classes of bivalent domains that are highly enriched with H3K4me3 during mitosis, depleted during G1 only, and ubiquitously bivalent. These bivalent domains are associated with specific genes and expression patterns during differentiation. These cell cycle-dependent epigenetic profiles are unique to hESCs and are not observed following initiation of phenotype commitment. Our results establish a new dimension in cell cycle-dependent chromatin regulation that advances understanding of contributions the pluripotent epigenetic landscape to hESC identity. Study of two histone modifications, H3K4me3 and H3K27me3, during three cell cycle phases in two cell types. Study of gene expression from these two cell types in asynchronous cells.
2015-12-23 | E-GEOD-55502 | biostudies-arrayexpress
Project description:Background: Bivalent chromatin refers to overlapping regions containing activating histone H3 Lys4 trimethylation (H3K4me3) and inactivating H3K27me3 marks. Existence of such bivalent marks on the same nucleosome has only recently been suggested. Previous genome-wide efforts to characterize bivalent chromatin have focused primarily on individual marks to define overlapping zones of bivalency rather than mapping positions of truly bivalent mononucleosomes. Results: Here, we developed an efficacious sequential ChIP technique for examining global positioning of individual bivalent nucleosomes. Using next generation sequencing approaches we show that although individual H3K4me3 and H3K27me3 marks overlap in broad zones, bivalent nucleosomes are focally enriched in the vicinity of the transcription start site (TSS). These seem to occupy the H2A.Z nucleosome positions previously described as salt-labile nucleosomes, and are correlated with low gene expression. Although the enrichment profiles of bivalent nucleosomes show a clear dependency on CpG island content, they demonstrate a stark anti-correlation with methylation status. Conclusions: We show that regional overlap of H3K4me3 and H3K27me3 chromatin tend to be upstream to the TSS, while bivalent nucleosomes with both marks are mainly promoter proximal near the TSS of CpG island-containing genes with poised/low expression. We discuss the implications of the focal enrichment of bivalent nucleosomes around the TSS on the poised chromatin state of promoters in stem cells.
2016-09-13 | GSE86838 | GEO
Project description:Bivalent histone modifications, including functionally opposite H3K4me3 and H3K27me3 marks simultaneously on the same nucleosome, control various cellular processes by fine-tuning the gene expression in eukaryotes. However, the role of bivalent histone modifications in fungal virulence remains elusive. Here, we report that bivalent chromatin modification of BCG1 (bivalent chromatin-marked gene1) is critical for Fusarium graminearum (Fg) successfully invading the host plant. By mapping the genome-wide landscape of H3K4me3 and H3K27me3 dynamic modifications in Fg during invasion, we identified the infection-related bivalent chromatin-marked genes (BCGs). BCG1, which encodes a xylanase containing a novel G/Q-rich motif, possessed the highest bivalent modification. We showed that the G/Q-rich motif of BCG1 is required for its xylanase activity and is essential for the full virulence of Fg. Intriguingly, this G/Q-rich motif can be recognized by pattern-recognition receptors (PRRs) to trigger plant immunity. Therefore, Fg tightly regulates BCG1 expression during different infection stages. During initial infection stages, Fg employs H3K4me3 modification to induce BCG1 expression required for host cell wall degradation. Upon breaching the cell wall barrier, this active chromatin state was reset to bivalency by co-modifying with H3K27me3, which enables epigenetic silencing of BCG1 to escape from host immune surveillance. Collectively, our study highlights how fungal pathogens deploy bivalent epigenetic modification to achieve temporally-coordinated activation and suppression of a critical fungal gene, thereby facilitating successful infection and host immunity evasion. This SuperSeries is composed of the SubSeries listed below.
2023-12-04 | GSE213962 | GEO
Project description:TrxG and PcG complexes play key roles in the epigenetic regulation of development through H3K4me3 and H3K27me3 modification at specific sites throughout the human genome, but how these sites are selected is poorly understood. We find that in pluripotent cells, clustered CpG islands at genes predict occupancy of H3K4me3 and H3K27me3, and these "bivalent" chromatin domains precisely span the boundaries of CpG island clusters. Examination of two histone modifications (H3K4me3 and H3K27me3) in human induced pluripotent stem (hiPS) M23F cells.
2012-07-06 | E-GEOD-39137 | biostudies-arrayexpress
Project description:Bivalent chromatin modification containing opposing H3K4me3 and H3K27me3 marks controls various biological processes by fine-tuning gene expression in animals and plants, however how this bivalent modification regulates pathogenicity of fungal pathogen remains exclusive. Here, we provided a genome-wide landscape of H3K4me3 and H3K27me3 of wheat head blight fungus Fusarium graminearum (Fg), leading to the identification of infection-induced bivalent chromatin-marked genes (BCGs). Among those, BCG1, which encodes a novel xylanase with a G/Q rich motif, is required for the full virulence of Fg pathogenicity through degradation of host cell wall. However, the G/Q rich motif is recognized by pattern-recognition receptors and triggers plant innate immunity. Further data illustrates that Fg employs H3K4me3 modification to induce BCG1 expression rapidly during the early infection, and then switches to bivalent H3K4me3-H3K27me3 chromatin state that renders rapid epigenetic silencing of BCG1 for escaping from host immune monitor, therefore leading to the successful invasion. Collectively, our study highlights the molecular mechanism of how fungal pathogen employs bivalent epigenetic modification to facilitate the successful infection by escaping of host immunity, which provides conceptual insights into plant-microbe interaction.
2023-12-04 | GSE213961 | GEO
Project description:Bivalent chromatin modification containing opposing H3K4me3 and H3K27me3 marks controls various biological processes by fine-tuning gene expression in animals and plants, however how this bivalent modification regulates pathogenicity of fungal pathogen remains exclusive. Here, we provided a genome-wide landscape of H3K4me3 and H3K27me3 of wheat head blight fungus Fusarium graminearum (Fg), leading to the identification of infection-induced bivalent chromatin-marked genes (BCGs). Among those, BCG1, which encodes a novel xylanase with a G/Q rich motif, is required for the full virulence of Fg pathogenicity through degradation of host cell wall. However, the G/Q rich motif is recognized by pattern-recognition receptors and triggers plant innate immunity. Further data illustrates that Fg employs H3K4me3 modification to induce BCG1 expression rapidly during the early infection, and then switches to bivalent H3K4me3-H3K27me3 chromatin state that renders rapid epigenetic silencing of BCG1 for escaping from host immune monitor, therefore leading to the successful invasion. Collectively, our study highlights the molecular mechanism of how fungal pathogen employs bivalent epigenetic modification to facilitate the successful infection by escaping of host immunity, which provides conceptual insights into plant-microbe interaction.
2023-12-04 | GSE213960 | 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.
2020-06-23 | GSE135841 | GEO
Project description:We performed ChIP-Seq against histones H3K4me3, H3K27me3, and H3K79me2 in MCF10A cells to identify transcription factors with bivalent and pseudo-bivalent epigenetic modifications.
2018-02-01 | GSE109721 | GEO