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SRX20209094: GSM7290872: HA_parental_H4K91Q_Input; Mus musculus; ChIP-Seq
1 ILLUMINA (NextSeq 500) run: 38.2M spots, 2.9G bases, 950.6Mb downloads

External Id: GSM7290872_r1
Submitted by: Rockefeller University
Study: Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [ChIP-seq]
show Abstracthide Abstract
Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development. Overall design: Characterization of the genome-wide incorporation of H4WT and H4K91 mutants in mouse embryonic stem cells (mESCs) as well as in differentiated neural cells.
Sample: HA_parental_H4K91Q_Input
SAMN34568132 • SRS17533201 • All experiments • All runs
Organism: Mus musculus
Library:
Name: GSM7290872
Instrument: NextSeq 500
Strategy: ChIP-Seq
Source: GENOMIC
Selection: ChIP
Layout: SINGLE
Construction protocol: Cells were fixed with 1% paraformaldehyde for 5 minutes with gentle rotation and then quenched with 125 mM glycine for 5 minutes. After cell lysis, chromatin was sonicated using a Covaris E220. Genomic DNA was isolated after the immunoprecipitation of sonicated chromatin. Libraries were generated using NEBNext Ultra II kits.
Runs: 1 run, 38.2M spots, 2.9G bases, 950.6Mb
Run# of Spots# of BasesSizePublished
SRR2442130038,241,9192.9G950.6Mb2023-10-19

ID:
27629225

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