Histone arginine demethylation by RDMe1
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ABSTRACT:
PROVIDER: PRJNA514095 | ENA |
REPOSITORIES: ENA
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Project description:Histone methylation mainly occurs on lysine and arginine residues. While lysine methylation can be removed by LSD1 and JmjC domain-containing demethylases, the existence of histone arginine demethylases is highly controversial. Here, we performed a high-content cell-based screening of a cDNA library containing 2,500 nuclear proteins and identified RDMe1 as a histone arginine demethylase. Overexpression of RDMe1 in HEK293T cells reduces H3R2me1/2a and H4R3me1/2a levels. In vitro, RDMe1 specifically demethylates H3R2me1/2a and H4R3me1/2a, and generates formaldehyde and succinate. The enzymatic activity requires Fe(II) and α-ketoglutarate as cofactors. RDMe1 is mainly located in the nucleolar and regulates rRNA transcription by demethylating H3R2me2a. ChIP-seq reveals that RDMe1 demethylates H4R3me2a in the promoter in a genome-wide scale. NMR reveals that RDMe1 binds iron and substrate peptides with N and C termini, respectively. Mutation of the iron binding residues abolished the binding and the demethylase activity. Thus, we identify a histone arginine demethylase and reveal the reversibility of arginine methylation.
2022-01-09 | GSE124890 | GEO
Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression
| PRJNA450398 | ENA
Project description:Examined gene expression changes in a histone H2A R78A mutant in Saccharomyces cerevisiae relative to wild-type cells. THe overall goal of this study was to determine the functions of histone 'sprocket' arginine residues, which insert into the DNA minor groove in the nucleosome. We examined the roles of sprocket arginine mutants in gene expression, histone incorporation, and DNA repair. Three wild-type control replicate samples and three experimental (H2A R78A) replicates
2015-08-05 | E-GEOD-68159 | biostudies-arrayexpress
Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (AGS cell line)
| PRJNA450399 | ENA
Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (NUGC3 cell line)
| PRJNA450400 | ENA
Project description:The arginine or lysine methylation status of histones dynamically changes during many essential cellular processes, particularly during embryonic and hematopoietic stem cell development. The enzymes demethylate methyllysine residues have been well defined, but the enzymes demethylate the methylarginine residues during different cellular processes are unknown. In current study, we demonstrate that JMJD1B is a lysine demethylase for H3K9me2 and an arginine demethylase for H4R3me2s. To reveal the biological significance of JMJD1B as an arginine demethylase, we isolate hematopoietic stem/progenitor cells (HSPC) from wild-type and JMJD1B knockout (JKO) bone marrow. We then conduct ChIP-seq on H4R3me2s and H3K9me2 histone markers and perform RNA-seq to determine the global gene expression profiles. We have observed global demethylation of H4R3me2s at the gene body but not the intergenic regions in hematopoietic stem/progenitor cells. H4R3me2s demethylation at the gene body region is directly correlated with gene expression in these cells. Furthermore, knockout of JMJD1B causes defects in removing the H4R3me2s epigenetic marker, leading to down-regulation of genes important for blood cells differentiation and development. Altogether, our current study demonstrates that arginine demethylases exist in cellular systems and that JMJD1B demethylates H4R3me2s for proper epigenetic programming during development.
2018-03-14 | GSE94966 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE22477: PHF8 mediates histone demethylation events in cell cycle progression [expression] GSE22478: PHF8 mediates histone demethylation events in cell cycle progression [ChIP-Seq] Refer to individual Series
2010-08-31 | E-GEOD-22400 | biostudies-arrayexpress
Project description:To analyze whether metabolites regulate histone methylation in plants, we examined genome-wide histone 3 lysine-27 trimethylation (H3K27me3) in an Arabidopsis dehydrogenase mutant (ogdh1/2) by ChIP-seq. We found that the levels of H3K27me3 were reduced at various loci in ogdh1/2 relative to wild type, indicating that metabolites control histone demethylation in Arabidopsis.
2023-07-14 | GSE182411 | GEO
Project description:Examined gene expression changes in a histone H2A R78A mutant in Saccharomyces cerevisiae relative to wild-type cells. THe overall goal of this study was to determine the functions of histone 'sprocket' arginine residues, which insert into the DNA minor groove in the nucleosome. We examined the roles of sprocket arginine mutants in gene expression, histone incorporation, and DNA repair.
2015-08-05 | GSE68159 | GEO
Project description:Dimethylation of histone H3 arginine 2 (H3R2me2) maintains transcriptional silencing by inhibiting Set-1 mediated trimethylation of H3K4. Here we demonstrate that arginine 2 is also monomethylated (H3R2me1) in yeast but that its functional characteristics are distinct from H3R2me2: (a) H3R2me1 does not inhibit H3K4 methylation, (b) it is present throughout the coding region of genes and (c) it correlates with active transcription. Collectively, these results indicate that different H3R2 methylated states have defined roles in gene expression. hIP-chip analysis was performed to determine the genomic distribution of histone modifications H3R2me1, H3R2me2a, H3K4me3, H3K36me3, and H3K79me3 in the BY4741 yeast strain. ChIP samples were amplified, labelled, and hybridized to 50-mer tiling arrays covering the entire yeast genome at a 64 bp resolution.
2010-05-06 | E-GEOD-14453 | biostudies-arrayexpress