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ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

ABSTRACT: To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

ORGANISM(S): Oryza sativa Japonica Group

PROVIDER: GSE225484 | GEO | 2024/04/10

REPOSITORIES: GEO

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ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

Project description:ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

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Project description:To investigate the effect of the OsINO80, we analysed DNA methylation of osino80 mutant compared to WT.

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RNAseq for WT and osino80

Project description:To investigate the effect of the OsINO80, we analysed differentially expressed genes of osino80 mutant compared to WT. We then performed gene expression profiling analysis using data obtained from RNA-seq of WT and osino80 mutant.

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Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

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Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [anti-H2A.Z & H3 ChIP-seq]

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Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

Project description:Chromatin-remodeling factor OsINO80 regulate H2A.Z incorporation [OsINO80 ChIP-seq]

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Role of remodeling and spacing factor 1 in histone H2A ubiquitination mediated gene silencing

Project description:Posttranslational modification of histones plays important roles in regulating chromatin-based nuclear processes. Histone H2A ubiquitination (H2Aub) is a prevalent modification and has been primarily linked to gene silencing; however, the mechanism by which H2Aub represses gene expression remains largely unclear. Here we report the identification of RSF1 (remodeling and spacing factor 1), a subunit of the RSF (remodeling and spacing factor) complex, as a novel H2Aub binding protein which mediates the repressive function of H2Aub on gene expression. RSF1 preferentially associates with H2Aub nucleosomes through a previously uncharacterized region designated as the ubiquitinated H2A binding (UAB) motif. RSF1 interacts with H2Aub nucleosomes specifically and the UAB motif is required for RSF1 to interact with H2Aub nucleosomes in vitro and in vivo. Genes regulated by RSF1 overlap significantly with genes regulated by RNF2 or Ring1B, the catalytic subunit of Polycomb repressive complex 1, in both human and mouse cells. RSF1 binds to gene promoter regions, and over 92% of H2Aub enriched genes, including the classic PRC1 target Hox genes, are co-bound by RSF1. Reduction of H2Aub levels by Ring1B knockout results in a significant reduction of RSF1 binding. RSF1 knockout does not affect RNF2/Ring1B or H2Aub levels but results in re-expression of H2Aub target genes, accompanied by a reduction in the spacing and stability of H2Aub nucleosomes. The direct role of RSF1 in repressing H2Aub target gene expression is further demonstrated by chromatin based in vitro transcription assay. Finally, RSF1 regulates Xenopus early embryonic development and gene expression in a fashion similar to that of PRC1 subunit Ring1A. Therefore, this study identifies RSF1 as a novel H2Aub binding protein and reveals that RSF1 contributes to H2Aub mediated gene silencing by maintaining a regular spaced, stable nucleosome array at promoter regions.

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H2A ubiquitination is essential for Polycomb Repressive Complex 1-mediated gene regulation in Marchantia polymorpha

Project description:Polycomb repressive complex 1 (PRC1) and PRC2 are chromatin regulators maintaining transcriptional repression by depositing H2A mono-ubiquitination (H2Aub) or H3 lysine 27 tri-methylation (H3K27me3), respectively. While PRC1 is known to be required for transcriptional repression, the contribution of H2Aub in the Polycomb repressive system remains unclear in plants. Here, we directly test the requirement of H2Aub for gene repression in Marchantia polymorpha by generating point mutants in H2A that fail to be ubiquitinated by PRC1. These mutants show reduced H3K27me3 levels on the same target sites as mutants in PRC1 subunits MpBMI1 and the homolog MpBMI1L, revealing that PRC1-catalyzed H2Aub is essential for Polycomb system function. Furthermore, we demonstrate that H2Aub contributes to the PRC1-mediated silencing of genes and transposable elements. Together, our data provide evidence that H2Aub plays indispensable roles in the PRC1-initiated repressive system in Marchantia.

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