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Histone arginine demethylation by RDMe1

ABSTRACT: Histone arginine demethylation by RDMe1

PROVIDER: PRJNA514095 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8428513.fastq.gz	Fastqsanger.gz
	SRR8428514.fastq.gz	Fastqsanger.gz
	SRR8428515.fastq.gz	Fastqsanger.gz
	SRR8428516.fastq.gz	Fastqsanger.gz

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Histone arginine demethylation by RDMe1

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

Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression

Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression

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Mina53 demethylates histone 4 arginine 3 asymmetric di-methylation to regulate neural stem/progenitor cell identity

Project description:Arginine methylation of histones plays a critical role in regulating gene expression. The writers (methyltransferases) and readers of methylarginine marks are well-known, but the erasers－arginine demethylases－remain mysterious. Here we identify Myc-induced nuclear antigen 53 (Mina53), a jumonji C domain containing protein, as an arginine demethylase for removing asymmetric di-methylation at arginine 3 of histone H4 (H4R3me2a). Using photoaffinity capture method, we first identified Mina53 as an interactor of H4R3me2a. Biochemical assays in vitro and in cells characterized the arginine demethylation activity of Mina53. Molecular dynamics simulations provide further atomic-level evidence that Mina53 acts on H4R3me2a. In a transgenic mouse model, specific Mina53 deletion in neural stem/progenitor cells prevented H4R3me2a demethylation at distinct genes clusters, dysregulating genes important for neural stem/progenitor cell proliferation and differentiation, and consequently impairing the cognitive function of mice. Collectively, we identify Mina53 as a bona fide H4R3me2a eraser, expanding the understanding of epigenetic gene regulation.

2024-10-22 | PXD045247 | Pride

Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (NUGC3 cell line)

Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (NUGC3 cell line)

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Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (AGS cell line)

Project description:Asymmetric demethylation at histone H3 arginine 2 by PRMT6 in gastric cancer progression (AGS cell line)

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Gene expression changes in a histone sprocket arginine mutant in histone H2A R78A

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

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Define roles of JMJD1B in mediating histone demethylation and gene expression

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.

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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

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Metabolic control of histone demethylation

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

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