H3 ChIP-chip
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE7062 | GEO | 2007/04/17
SECONDARY ACCESSION(S): PRJNA104149
REPOSITORIES: GEO
Similar Datasets
Project description:Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. Here we identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways such as DNA methylation or RNAi. Unlike in animals where H3K27m3 occupies large genomic regions, we found that H3K27m3 domains in Arabidopsis were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals. Keywords: ChIP-chip
2007-04-17 | GSE7064 | GEO
Project description:Trimethylation of histone H3 lysine27 (H3K27me3) plays critical roles in regulating animal development, and in several cases, H3K27me3 is also required for the proper expression of developmentally important genes in plants. However, the extent to which H3K27me3 regulates plant genes on a genome-wide scale remains unknown. In addition, it is not clear whether the establishment and spreading of H3K27me3 occur through the same mechanisms in plants and animals. Here we identified regions containing H3K27me3 in the genome of the flowering plant Arabidopsis thaliana using a high-density whole-genome tiling microarray. The results suggest that H3K27me3 is a major silencing mechanism in plants that regulates an unexpectedly large number of genes in Arabidopsis (~4,400), and that the maintenance of H3K27me3 is largely independent of other epigenetic pathways such as DNA methylation or RNAi. Unlike in animals where H3K27m3 occupies large genomic regions, we found that H3K27m3 domains in Arabidopsis were largely restricted to the transcribed regions of single genes. Furthermore, unlike in animals systems, H3K27m3 domains were not preferentially associated with low nucleosome density regions. The results suggest that different mechanisms may underlie the establishment and spreading of H3K27me3 in plants and animals. Keywords: genomic
2007-04-17 | GSE7063 | GEO
Project description:Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants.
2016-11-01 | GSE83801 | GEO
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3. We used the met1-3 allele (Saze et al. 2003) and the salk_006042 line for isolating ibm1 mutants. met1-1st generation homozygous mutants and ibm1-1st generation homozygous mutants were isolated from a segragating population by genotyping. met1-2nd generation second mutants are the progeny of a single met1-1st generation homozygous mutant that was partially fertile. The entire shoots of 3 weeks old Arabidopsis plants (Col-0 ecotype), grown for 3 weeks under continuous light, were harvested, cross-linked as described in (Bernatavichute et al., 2007), frozen under liquid nitrogen and grown to powder (2g). Arabidopsis chromatin enriched for H3K9m2 and H3K27m3 was immunoprecipitated using an antibody that specifically recognizes H3K9m2 (Abcam 1220) and an antibody that specifically recognizes H3K27m3 (Upstate 07-449) respectively. Unmodified H3 was immunoprecipitated using Abcam 1791-100. Nucleosomal DNA and Input DNA were used as controls. ChIP, DNA purification and amplification were performed as in (Bernatavichute et al., 2007); Roche Nimblegen performed labelling and hybridization of the samples, washing and scanning resolution. All ChIP signals were normalized with either H3 ChIP or input genomic DNA by taking the log2 ratio and adjusted so that the average log2 ratio score across the genome was zero. 6 samples
2013-03-02 | E-GEOD-37075 | biostudies-arrayexpress
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3.
2016-06-22 | GSE83607 | GEO
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3. Keywords: Genome binding/occupancy profiling by genome tiling array
2016-06-22 | GSE83606 | GEO
Project description:Dimethylation of histone H3 lysine 9 (H3K9m2) and trimethylation of histone H3 lysine 27 (H3K27m3) are two hallmarks of transcriptional repression in many organisms. In Arabidopsis thaliana, H3K27m3 is targeted by Polycomb Group (PcG) proteins and is associated with silent protein coding genes, while H3K9m2 is correlated with DNA methylation and is associated with transposons and repetitive sequences. Recently, ectopic genic DNA methylation in the CHG context (where H is any base except G) has been observed in globally DNA hypomethylated mutants such as met1, but neither the nature of the hypermethylated loci nor the biological significance of this epigenetic phenomenon have been investigated. Here, we generated high-resolution genome-wide maps of both H3K9m2 and H3K27m3 in wild type and met1 plants, which we integrated with transcriptional data, to explore the relationships between these two marks. We found that most of the ectopic H3K9m2 observed in met1 is not due to defects in IBM1-mediated H3K9m2 demethylation, but instead targets H3K27m3-marked genes suggesting an interplay between these two silencing marks. Furthermore, H3K9m2/DNA-hypermethylation at these PcG targets in met1 is coupled with a decrease in H3K27m3 marks, whearas H3K9m2 hypomethylated transposons become ectopically H3K27me3 hypermethylated. Our results bear interesting similarities with cancer cells, which show global losses of DNA methylation, but ectopic hypermethylation of genes previously marked by H3K27m3. RNA-seq: 3 week old tissue was ground in Trizol. Total RNA were treated with DNaseI (Roche), and cleaned up with phenol-chlorophorm and precipitated with ethanol. Libraries were generated and sequenced following manufacturer instructions (Illumina).
2016-06-22 | E-GEOD-83607 | biostudies-arrayexpress
Project description:Maintenance of gene expression programs requires cell-type specific barcoding of genomes through euchromatin interspaced with facultative heterochromatin domains where PRC1/2 hinder chromatin accessibility thereby repressing genes inside such domains. At heterochromatin-euchromatin borders, regulation of heterochromatin spreading may depend on transcriptional activity, histone modifiers, and chromatin barrier insulators or the borders of topological associated domain (TADs). Here we show that depletion of H3K36 di- or tri-methyl histone methyl transferases dMes-4/NSD or Hypb/dSet2 induces H3K27me3 spreading at H3K27me3 borders, accounting for the repression of hundreds of genes upon depletion of these enzymes. dMes-4/NSD influences genes within active chromatin hubs and flanked by H3K27me3 borders demarcated by a TAD border, unlike dHypb/dSet2 that protects genes near H3K27me3 borders in absence of a TAD border. Insulator mutants that disrupt 3D chromatin hubs recapitulate only the H3K27me3 spreading observed upon depletion of dMes-4/NSD, and not of Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD directly block the propagation of the long-range interactions marking the inactive TADs, onto neighbor active regions, unlike Hypb/dSet2. Our data thus show a division of labor between dMes-4/NSD and Hypb/dSet2 to protect genes against H3K27me3 silencing, highlighting a direct influence of H3K36me marks on the demarcation of H3K27me3 domains within repressive TADs.
2023-07-01 | GSE146993 | GEO
Project description:Maintenance of gene expression programs requires cell-type specific barcoding of genomes through euchromatin interspaced with facultative heterochromatin domains where PRC1/2 hinder chromatin accessibility thereby repressing genes inside such domains. At heterochromatin-euchromatin borders, regulation of heterochromatin spreading may depend on transcriptional activity, histone modifiers, and chromatin barrier insulators or the borders of topological associated domain (TADs). Here we show that depletion of H3K36 di- or tri-methyl histone methyl transferases dMes-4/NSD or Hypb/dSet2 induces H3K27me3 spreading at H3K27me3 borders, accounting for the repression of hundreds of genes upon depletion of these enzymes. dMes-4/NSD influences genes within active chromatin hubs and flanked by H3K27me3 borders demarcated by a TAD border, unlike dHypb/dSet2 that protects genes near H3K27me3 borders in absence of a TAD border. Insulator mutants that disrupt 3D chromatin hubs recapitulate only the H3K27me3 spreading observed upon depletion of dMes-4/NSD, and not of Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD directly block the propagation of the long-range interactions marking the inactive TADs, onto neighbor active regions, unlike Hypb/dSet2. Our data thus show a division of labor between dMes-4/NSD and Hypb/dSet2 to protect genes against H3K27me3 silencing, highlighting a direct influence of H3K36me marks on the demarcation of H3K27me3 domains within repressive TADs.
2023-07-01 | GSE209956 | GEO
Project description:Maintenance of gene expression programs requires cell-type specific barcoding of genomes through euchromatin interspaced with facultative heterochromatin domains where PRC1/2 hinder chromatin accessibility thereby repressing genes inside such domains. At heterochromatin-euchromatin borders, regulation of heterochromatin spreading may depend on transcriptional activity, histone modifiers, and chromatin barrier insulators or the borders of topological associated domain (TADs). Here we show that depletion of H3K36 di- or tri-methyl histone methyl transferases dMes-4/NSD or Hypb/dSet2 induces H3K27me3 spreading at H3K27me3 borders, accounting for the repression of hundreds of genes upon depletion of these enzymes. dMes-4/NSD influences genes within active chromatin hubs and flanked by H3K27me3 borders demarcated by a TAD border, unlike dHypb/dSet2 that protects genes near H3K27me3 borders in absence of a TAD border. Insulator mutants that disrupt 3D chromatin hubs recapitulate only the H3K27me3 spreading observed upon depletion of dMes-4/NSD, and not of Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD directly block the propagation of the long-range interactions marking the inactive TADs, onto neighbor active regions, unlike Hypb/dSet2. Our data thus show a division of labor between dMes-4/NSD and Hypb/dSet2 to protect genes against H3K27me3 silencing, highlighting a direct influence of H3K36me marks on the demarcation of H3K27me3 domains within repressive TADs.
2023-07-01 | GSE146992 | GEO