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SRX3462001: GSM2883924: 18776_WTBM-H4R3_S4_L999_R1_001; Mus musculus; ChIP-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 40.9M spots, 2.1G bases, 710.3Mb downloads

Submitted by: NCBI (GEO)
Study: Define roles of JMJD1B in mediating histone demethylation and gene expression
show Abstracthide Abstract
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. Overall design: For each genetic background, a pool of HSPCs and BMCs from four biological replicates are collected and analyzed by ChIP-seq. HSPCs from two biological replicates are analyzed by RNA-seq. For ChIP-seq, the input and/or ChIP histone H4 is used as control.
Sample: 18776_WTBM-H4R3_S4_L999_R1_001
SAMN08161506 • SRS2750157 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: ChIP on native chromatin from hematopoitic stem/progenitor cells was performed following previously published protocols (M. Girardot et al., 2014. Nucleic acids research 42, 235-248) with the following modifications using ChIP-grade Magna protein A/G beads (Cat#: 16-663, EMB Millipore). The isolated nuclei were incubated for 15 min at 37°C with 4 units/uL of Micrococcal nuclease (M0247, New England Biolabs) to produce mono/di-nucleosomes as verified by agarose gel electrophoresis. Nucleosomes were precipitated with control IgG, ChIP-grade anti-H4R3me2s (Cat#: Ab5823, Abcam) or anti-H3K9me2s (Cat#: 39375, Active motif). ChIP or input DNA was purified with Ampure XP beads (Cat#: A63880, Beckman Coulter). ChIP libraries were repard according to standard Illumina protocols. Transcriptome libraries were constructed with TruSeq RNA Sample Preparation Kit V2 (Illumia) with minor modifications.
Experiment attributes:
GEO Accession: GSM2883924
Links:
Runs: 1 run, 40.9M spots, 2.1G bases, 710.3Mb
Run# of Spots# of BasesSizePublished
SRR636650340,909,9332.1G710.3Mb2018-03-15

ID:
4822015

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