Genome-wide profiling of EDM3 dependent H3K9me2 in Arabidopsis thaliana
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE108490 | GEO | 2020/01/29
REPOSITORIES: GEO
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Project description:EDM2 is a PHD finger-containing histone binding protein in Arabidopsis thaliana (Arabidopsis) that affects levels of the transposon silencing mark H3K9me2. Here we report on genome-wide profiling by ChIP-seq and RNA-seq of EDM2-mediated effects on H3K9me2 and rRNA-depleted transcripts, respectively. EDM2 affects H3K9me2 and/or transcript levels at hundreds transposons and over 3000 gene loci including 60 NLR genes. In addition, EDM2 also binds to several NLR genes and transposons.
2020-08-03 | GSE108487 | GEO
Project description:A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin. Col-0 and edm2-4 total genomic DNAs are extracted from leaves and then subjected to bisulfite convertion and sequencing in accordance with standard protocol.
2013-10-29 | E-GEOD-51762 | biostudies-arrayexpress
Project description:A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin. Col-0 and edm2-4 total RNA are extracted from leaves and then polyA mRNAs are isolated for mRNA-seq.
2013-10-29 | E-GEOD-51763 | biostudies-arrayexpress
Project description:A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.
2013-10-29 | GSE51763 | GEO
Project description:A forward genetics screen led to the identification of the putative chromatin regulator EDM2 as a cellular anti-silencing factor and regulator of genome DNA methylation patterns. EDM2 contains a composite PHD finger domain that recognizes both active H3K4 and repressive H3K9 methylation marks at the intronic repeat elements in genes such as the histone H3K9 demethylase gene IBM1, and is necessary for maintaining the expression of these genes by promoting mRNA distal polyadenylation. Because of its role in maintaining IBM1 expression, EDM2 is required for preventing CHG methylation in the bodies of thousands of genes.Our results thus increase the understanding of anti-silencing, genome methylation patterns, and regulation of alternative RNA processing by intronic heterochromatin.
2013-10-29 | GSE51762 | GEO
Project description:In several eukaryotic organisms, heterochromatin (HC) in the introns of genes can regulate RNA processing, including polyadenylation, but the mechanism underlying this regulation is poorly understood. By promoting distal polyadenylation, the bromo-adjacent homology (BAH) domain-containing and RNA recognition motif-containing protein ASI1 and the H3K9me2-binding protein EDM2 are required for the expression of functional full-length transcripts of intronic HC-containing genes in Arabidopsis. Here we report that ASI1 and EDM2 form a protein complex in vivo via a bridge protein, ASI1-Immunoprecipitated Protein 1 (AIPP1), which is another RNA recognition motif-containing protein. The complex also may contain the Pol II CTD phosphatase CPL2, the plant homeodomain-containing protein AIPP2, and another BAH domain protein, AIPP3. As is the case with dysfunction of ASI1 and EDM2, dysfunction of AIPP1 impedes the use of distal polyadenylation sites at tested intronic HC-containing genes, such as the histone demethylase gene IBM1, resulting in a lack of functional full-length transcripts. A mutation in AIPP1 causes silencing of the 35S-SUC2 transgene and genome-wide CHG hypermethylation at gene body regions, consistent with the lack of full-length functional IBM1 transcripts in the mutant. Interestingly, compared with asi1, edm2, and aipp1 mutations, mutations in CPL2, AIPP2, and AIPP3 cause the opposite effects on the expression of intronic HC-containing genes and other genes, suggesting that CPL2, AIPP2, and AIPP3 may form a distinct subcomplex. These results advance our understanding of the interplay between heterochromatic epigenetic modifications and RNA processing in higher eukaryotes.
2017-08-17 | GSE98655 | GEO
Project description:modENCODE_submission_3695 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var)3-9 mutant Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9 [6]/Su(var)3-9 [6]; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var)3-9 mutant Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44471 | biostudies-arrayexpress
Project description:modENCODE_submission_3889 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)3-9^06/Su(var)3-9^17; Transgene: n/a; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain Su(var) 3-9 06 17 mutant(official name : Su(var)3-9^06/Su(var)3-9^17 genotype : Su(var)3-9^06/Su(var)3-9^17 outcross : n/a transgene : n/a tags : X-ray tag : GFP description : Stocks with the Su(var)3-9^06 and Su(var)3-9^17 alleles were maintained as heterozygous stocks over a third chromosome balancer. To generate the transheterozygotes description : individuals from the heterozygous stocks were crossed together. The F1 individuals lacking the balancer chromosome were used for these experiments. made_by : Stocks were obtained from Gary Karpen ); Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44502 | biostudies-arrayexpress
Project description:modENCODE_submission_3771 This submission comes from a modENCODE project of Gary Karpen. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We aim to determine the locations of the major histone modifications across the Drosophila melanogaster genome. The modifications under study are involved in basic chromosomal functions such as DNA replication, gene expression, gene silencing, and inheritance. We will perform Chromatin ImmunoPrecipitation (ChIP) using genomic tiling arrays. We will initially assay localizations using chromatin from three cell lines and two embryonic stages, and will then extend the analysis of a subset of proteins to four additional animal tissues/stages. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-chip. BIOLOGICAL SOURCE: Strain: HP1a mutant Developmental Stage: 3rd Instar Larvae; Genotype: Su(var)205 [4]/Su(var)205 [5]; Transgene: none; NUMBER OF REPLICATES: 4; EXPERIMENTAL FACTORS: Strain HP1a mutant Antibody H3K9me2-Ab2 (new lot) (target is H3K9me2); Developmental Stage 3rd Instar Larvae
2013-02-22 | E-GEOD-44487 | biostudies-arrayexpress
Project description:Genome-wide profilings of EDM2-mediated effects on H3K9me2 and transcripts in Arabidopsis thaliana
| PRJNA427432 | ENA