ChIP-seq for Polycomb and associated transcription factors in Arabidopsis
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE84483 | GEO | 2017/07/31
SECONDARY ACCESSION(S): PRJNA329443
REPOSITORIES: GEO
Similar Datasets
Project description:We performed ChIP-seq for the Polycomb protein FIE using anti-FIE antiserum in germinated wild-type and double class I BPC and C1-2iD transcruption factor family knockdown seedlings of Arabidopsis thaliana.
2017-07-31 | GSE95562 | GEO
Project description:Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However, RNA was extracted from intermediate phenotype siFIE plants, clf-7 swn-28 and Col using Qiagen Plant RNeasy mini kit. For each sample, three pools of 10-12 plants were used. The siFIE plants were analysed for FIE mRNA by RT-qPCR; the maximum level of FIE mRNA was found to be 10% of wildtype.
2013-09-01 | E-GEOD-48857 | biostudies-arrayexpress
Project description:Background. Polycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.Results. We used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).Conclusions. Our results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However,
2013-09-01 | GSE48857 | GEO
Project description:We report the mRNA profiles of the Arabidopsis thaliana seedlings germinated for 7days in the dark, then treated with light for 0h, 1h, 2h, 4h, 8h and 12h.
2022-10-05 | GSE189497 | GEO
Project description:Using Western blot, we found the level of H3K27me3, but not H3K4me3, H3K9me2 and H3K36me3, was specifically reduced in the tor-es mutant. To gain a genome-wide view of the effects of TOR activity on H3K27me3 distribution, we performed quantitative chromatin immunoprecipitation with an exogenous reference genome (ChIP-Rx) followed by deep-sequencing. We find a global reduction of H3K27me3 occupancy in tor-es, whereas the H3K9me2 level was largely unaffected. These results suggest that TOR may be a specific and direct regulator of global deposition of H3K27me3. To investigate the function of TOR phosphorylation of FIE, we complemented the heterozygous fie/+ plants with GFP-FIE or the phosphorylation site mutant (SSTS/AAAA) under the control of the FIE promoter. To provide a parallel comparison with SSTS/AAAA/fie, we generated estradiol-inducible fie-amiR-es transgenic lines, that eliminated FIE protein. Quantitative ChIP-seq analyses revealed greatly reduced H3K27me3 levels across the genome in SSTS/AAAA and fie-amiR-es mutants. And transcriptome profiling by RNA-Seq was conducted to globally identify thousands of genes coordinately dysregulated in the shoots of SSTS/AAAA and fie-amiR-es plants. Furthermore, gene Ontology analysis of 986 TOR-FIE-PRC2 target genes revealed significant enrichment for transcription factors/regulators controlling a broad spectrum of developmental programs.
2022-06-20 | GSE161807 | GEO
Project description:rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out
2010-12-01 | GSE19851 | GEO
Project description:rs09-08_fie - upregulation of transcripts in the absence of prc2 repressory complex - Role of PRC2 repressory complex for differentiation pathways in Arabidopsis thaliana? - Comparison of transcriptome between two biological replicates of fie mutants in comparison with two biological replicates of Col WT. Keywords: gene knock out 6 dye-swap - CATMA arrays
2010-12-01 | E-GEOD-19851 | biostudies-arrayexpress
Project description:Polycomb repression of gene expression is critical for development, with a pivotal role for trimethylation of lysine 27 of histone H3 (H3K27me3) deposited by Polycomb Repressive Complex 2 (PRC2). While the function and regulation of PRC2 have been extensively studied, the mechanism(s) by which it is recruited to specific genomic targets has remained largely elusive, in particular in vertebrates. Here we identify the PRC2-associated protein Mtf2 as a novel DNA methylation-sensitive PRC2 recruiter in mouse embryonic stem cells (mESCs). Mtf2 directly binds to DNA and is essential for recruitment of PRC2 both in vitro and in vivo. Genome-wide recruitment of the PRC2 catalytic subunit Ezh2 to genomic targets is drastically impaired in Mtf2 knock-out mESCs, resulting in largely reduced H3K27me3 deposition. Mtf2 selectively binds regions with high density of closely spaced unmethylated CpG-containing motifs with a locally unwound helical structure. This binding is dependent on one of the Mtf2 PHD domains, a protein domain shared among Pcl homologs, and an Mtf2-specific domain. The sequences bound by Mtf2 are enriched in PRC2-repressed CpG island-containing targets in zebrafish, Xenopus, mouse and human, suggesting that Mtf2-mediated PRC2 recruitment to unmethylated genomic regions is conserved among vertebrates.
2018-05-07 | PXD005821 | Pride
Project description:We generated a library of Brg variants with mutations in conserved regions of the N-terminal ATPase domain based on mutants observed in primary tumors and cancer cell lines. Heterozygous expression of ATPase mutants leads to increased occupancy of Polycomb Repressive Complex 1 (PRC1) at bivalent CpG-island promoters. Increased PRC1 binding was accompanied by increases in H3K27me3, the mark left by the Polycomb Repressive Complex 2 (PRC2) ~2 kbp away.
2016-10-21 | GSE77093 | GEO
Project description:Polycomb-group proteins play critical roles in gene silencing through the deposition of histone H3 lysine 27 trimethylation (H3K27me3) and chromatin compaction. This process is essential for embryonic stem cells (ESCs) pluripotency, differentiation, and development. Polycomb repressive complex 2 (PRC2) can both read and write H3K27me3, enabling processive spread of H3K27me3 on linear genome and epigenetic memory. Long-range Polycomb-associated DNA contacts have also been described, but their regulation and role in gene silencing remains unclear. Here, we develop H3K27me3 HiChIP and apply optical reconstruction of chromatin architecture to reveal long-range Polycomb-associated DNA loops that span tens to hundreds of megabases and across multiple topological associated domains in mouse ESCs and human induced pluripotent stem cells. H3K27me3 loop anchors are enriched for Polycomb nucleation points and coincide with key developmental genes, such as Hmx1, Wnt6 and Hoxa. Genetic deletion of H3K27me3 loop anchors causes spatially proximal partner chromosomal loci to break apart, and alters H3K27me3 deposition, both locally and megabases away on the same chromosome. A selective EZH2 mutant deficient in RNA binding but intact H3K27me3 enzymatic activity leads to global alteration in H3K27me3 loops, decreased spatial proximity, and failure to spread Polycomb from PRC2 nucleation points to partner loci at developmental genes. Together, these results suggest PRC2 acts as a “genomic wormhole”, using RNA binding to enhance long range chromosome folding and H3K27me3 spreading. Developmental gene loci have novel roles in Polycomb spreading, emerging as key architectural elements of the epigenome.
2022-05-13 | GSE150906 | GEO