Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA224965 | ENA |
REPOSITORIES: ENA
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Project description:Arabidopsis EDM2 Promotes IBM1 Distal Polyadenylation and Regulates Genome DNA Methylation Patterns [BS-Seq]
| PRJNA224966 | ENA
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:We perform genome-wide profiling of H3K9me2 in the Arabidopsis thaliana edm3 mutant. By var-seq, we identified EDM3 as a nuclear-localized protein featuring a single RNA-recognition motif (RRM). Similar to PHD finger-containing histone binding protein EDM2, EDM3 promotes high levels of H3K9me2 at RPP7 and controls transcripts of this NLR gene by suppressing proximal polyadenylation and promoting the synthesis of full-length RPP7-coding mRNAs. Our results showed that EDM3 affects levels of this epigenetic mark at a set of genes and transposons, the vast majority of which also feature EDM2-dependent H3K9me2.
2020-01-29 | GSE108490 | GEO
Project description:Here we address that a mutation of EDM2 (Enhanced Downy Mildew 2), which is regarded as regulator of genome DNA methylation patterns, displays abnormal cotyledon number and shorted root length. Further, in early embryogenesis, edm2 shows embryonic developmental abnormalities, including the appearance of asymmetric embryos at the heart stage and unclear boundary between the spherical proembryo and suspensor cells. In addition, dysfunction of EDM2 alters the level of the auxin transporter PINs (PIN-FORMEDs), consistent with disordered distribution of auxin, which maybe the reason for developmental defect. Interestingly, analysis of high-throughput sequencing data show that the loss-of-function EDM2 exhibits the decreased expression of auxin polar transport-related gene PLT1 (PLETHORA 1), while methylation level and H3K9me2 enrichment in gene body are slightly higher than that in wide type. These results advance our understanding of EDM2 in establishment of auxin gradients through epigenetic modification and elucidate the roles of EDM2 in early embryogenesis.
2023-04-23 | GSE230021 | GEO
Project description:In diverse eukaryotes, constitutively silent sequences, such as transposons and repeats, are marked by methylation at histone H3 lysine 9 (H3K9me). Despites the conservation and importance in the genome integrity, mechanisms to exclude H3K9m from active genes remained largely unexplored. Here we show in Arabidopsis that the exclusion depends on a histone demethylase gene, IBM1 (increase in BONSAI methylation); loss-of-function ibm1 mutation caused ectopic H3K9me in thousands of genes, which accompanies genic DNA methylation at non-CG sites. The ibm1-induced genic H3K9me depended on both histone methylase KYP/SUVH4 and DNA methylase CMT3, suggesting interdependence of two epigenetic marks – H3K9me and non-CG methylation. Notably, IBM1 enhanced loss of H3K9m in transcriptionally de-repressed sequences. Furthermore, disruption of transcription in genes induced ectopic non-CG methylation, mimicking the loss of IBM1 function. We propose that active chromatin is stabilized by the autocatalytic loop of transcription and H3K9 demethylation. This process counteracts accumulation of silent epigenetic marks, H3K9me and non-CG methylation, which is also autocatalytic.
2010-09-21 | GSE22953 | GEO