Histone Variants and H2A Ubiquitination
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PROVIDER: PRJNA1068018 | ENA |
REPOSITORIES: ENA
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Project description:Histone Variants and H2A Ubiquitination [Cut&Tag]
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Project description:Cut&Tag sequencing of mouse embryonic stem cell lines with knockin of tagged histone variants
2025-08-20 | GSE253967 | GEO
Project description:The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.
2024-12-06 | GSE281399 | GEO
Project description:The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.
2024-12-06 | GSE270449 | GEO
Project description:The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.
2024-12-06 | GSE270450 | GEO
Project description:Histone ubiquitination has been suggested to serve as a “tag” for nucleosome removal during histone-to-protamine exchange that is essential for chromatin packaging in round spermatids. Here, we screen for putative E3 ligase and identify that the PHF7, containing both RING finger and PHD domains, is critical for H2A ubiquitination and histone removal. Mechanistically, its PHD domain as a histone code reader can specifically bind H3K4me3/me2 and its RING domain as a histone writer can ubiquinate H2A. So we want to use ChIP-seq to see whether all PHF7-binding peaks overlapped with those of H3K4me3. We report the application of ChIP-seq for high-throughput profiling of histone modifications in spermatids. By obtaining over 240M of sequences from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps and PHF7 binding position of late spermatids. We find binding peaks of PHF7, H3K4me3 and ub-H2A were mainly enriched at gene-regulatory elements (-5kb to +5kb from transcriptional start site), including promoter and enhancers, indicative of important roles in gene regulations. More than 96% (n=15419) of all PHF7-binding peaks overlapped with those of H3K4me3, supporting a specific binding of PHF7 to H3k4me3. Moreover, the common binding sites between PHF7 and H3K4me3 were associated with ub-H2A. Taken together, these results demonstrate that PHF7 ubiquitinate H2A through binding with H3K4me3.
2019-07-05 | GSE112912 | GEO
Project description:The Arabidopsis H3K4me3-binding ALFIN-like proteins are components of the PRC1 complex and promote H2A ubiquitination, thereby establishing a connection between H3K4me3 and H2A ubiquitination across the genome. Additionally, the ALFIN-like proteins interact with various chromatin-related proteins involved in H2A.Z deposition, H3K27me3 demethylation, histone deacetylation, and chromatin accessibility. The ALFIN-like proteins play a crucial role in coordinating H3K4me3 with diverse other chromatin modifications.
2024-12-06 | GSE281398 | GEO
Project description:Polycomb repressive complex 1 (PRC1) catalyzes H2A monoubiquitination (uH2A) and regulates pluripotency in embryonic stem cells (ESCs). However the mechanisms controlling PRC1 recruitment and activity are largely unknown. Here we show that Fbxl10 interacts with Ring1B and Nspc1, forming a non-canonical PRC1. We demonstrate that Fbxl10-PRC1 is essential for H2A ubiquitination in mouse ESCs. Genome-wide analyses reveal that Fbxl10 preferentially binds to CpG islands and co-localizes with Ring1B on Polycomb target genes. Notably, Fbxl10 depletion causes modest dissociation of Ring1B but a major loss of uH2A on target genes. Furthermore rescue experiments for Fbxl10 reveal that its DNA binding capability and integration into PRC1 are required for proper H2A ubiquitination. ES cells lacking Fbxl10, like previously characterized Polycomb mutants, show a severely compromised capacity for successful differentiation. Our results shed light on a novel mechanism how CpG islands regulate chromatin function by affecting polycomb recruitment and activity. All ChIP-seq reactions were performed in either untransfected cells, cells expressing scrambled shRNA or Fbxl10 shRNA, Ring1b-/- or Suz12-/- mouse ES cells
2012-12-31 | E-GEOD-37930 | biostudies-arrayexpress
Project description:How histone intrinsic sequence variation or regulatory modifications regulate nucleosome interactions with transcription remain unclear. To clarify this question, we examined how histone variants and histone modifications assemble in the Arabidopsis thaliana genome, identifying a limited number of chromatin states that divide euchromatin and heterochromatin in biologically significant subdomains. We showed that histone variants were as significant as histone modifications to determine the composition of chromatin states. The loss of function of the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) prevented the exchange between the histone variants H2A.Z and H2A.W over transposons resulting in their enrichment in chromatin states found only on proteins coding genes in the wild type. Hence, the dynamics of histone H2A variants exchange impacted the definition and distribution of chromatin states. We propose that dynamics of histone variants control the organization of histone modifications into chromatin states to achieve landmarks that signify the ability for transcription. Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone H2A variants and histone modifications in seedlings .
2023-05-09 | GSE226469 | GEO
Project description:Two distinct Polycomb complexes, PRC1 and PRC2, collaborate to maintain epigenetic repression of key developmental loci in embryonic stem cells (ESCs). PRC1 and PRC2 have histone modifying activities, catalyzing mono-ubiquitination of histone H2A (H2AK119u1) and trimethylation of H3 lysine 27 (H3K27me3) respectively. Compared to H3K27me3, localization and role of H2AK119ub1 is not fully understood in ESCs. Here we present genome-wide H2AK119u1 maps in ESCs and identify a group of genes at which H2AK119u1 is deposited in a Ring1-dependent manner. These genes are a distinctive subset of genes with H3K27me3 enrichment and are the central targets of Polycomb silencing that are required to maintain ESC identity. We further show that the H2A ubiquitination activity of PRC1 is dispensable for its target binding and its activity to compact chromatin at Hox loci, but is indispensable for efficient repression of target genes and thereby ESC maintenance. These data demonstrate that multiple effector mechanisms including H2A ubiquitination and chromatin compaction combine to mediate PRC1-dependent repression of genes that are crucial for the maintenance of ESC identity. Utilization of these diverse effector mechanisms might provide a means to maintain a repressive state that is robust yet highly responsive to developmental cues during ES cell self-renewal and differentiation. This SuperSeries is composed of the following subset Series: GSE38224: Expression data from Ring1A(-/-);Ring1B(fl/fl);R26::CreERT2 ES cells expressing either of mock, WT or mutant Ring1B construct before or after OHT treatment GSE38504: ChIP-on-chip analysis of Ring1B, Ring1A, H2AK119u1 and H3K27me3 in mouse ES cells Total RNAs were extracted from the respective ES cells, and were subjected to microarray analysis using Affymetrix GeneChip Mouse Genome 430A 2.0 arrays. ChIP on chip analysis was carried out using the Mouse Promoter ChIP-on-chip Microarray Set (G4490A, Agilent, Palo Alto, Calif., USA). MEFs were subjected to ChIP assay using various antibodies. Purified immunoprecipitated and input DNA was subjected to T7 RNA polymerase-based amplification. Labeling, hybridization and washing were carried out according to the Agilent mammalian ChIP-on-chip protocol (ver.9.0). Scanned images were quantified with Agilent Feature Extraction software under standard conditions.
2012-06-11 | E-GEOD-38650 | biostudies-arrayexpress