Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder

ABSTRACT: ChIP experiment was performed with antibody against H3K36me3 (active motif; 61101). we generated genome-wide characterization of H3K36me3 occupancy in E13 H2A.Z cKO forebrain. We found H3K36me3 is decreased throughout the whole genome in E13 H2A.Z cKO forebrain.

ORGANISM(S): Mus musculus

PROVIDER: GSE106679 | GEO | 2017/11/09

SECONDARY ACCESSION(S): PRJNA417668

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder.

Project description:Defects in neurogenesis alter brain circuit formations and may lead to neurodevelopmental disorders such as autism and schizophrenia. Histone H2A.z, a variant of histone H2A, plays critical roles in chromatin structure and epigenetic regulation, but its function and mechanism in brain development remain largely unknown. Here, we find that the deletion of H2A.z results in enhanced proliferation of neural progenitors but reduced neuronal differentiation. In addition, neurons in H2A.z knockout mice exhibit abnormal dendrites during brain development. Furthermore, H2A.zcKO mice exhibit serial behavioral deficits, such as decreased exploratory activity and impaired learning and memory. Mechanistically, H2A.z regulates embryonic neurogenesis by targeting Nkx2-4 through interaction with Setd2, thereby promoting H3K36me3 modification to activate the transcription of Nkx2-4. Furthermore, enforced expression of Nkx2-4 can rescue the defective neurogenesis in the H2A.z-knockdown embryonic brain. Together, our findings implicate the epigenetic regulation by H2A.z in embryonic neurogenesis and provide a framework for understanding how disruption in the H2A.z gene may contribute to neurological disorders.

| S-EPMC5861433 | biostudies-literature

Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder

Project description:Brain-specific deletion of histone variant H2A.z results in cortical neurogenesis defects and neurodevelopmental disorder

| PRJNA417668 | ENA

Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

Project description:The histone variant H2A.Z is evolutionarily conserved from yeast to vertebrates. H2A.Z regulates gene expression when localized to promoter region. Recently, we identified two genes encoding H2A.Z, H2A.Z-1 and H2A.Z-2 in vertebrate genome. However, it is not clear that both H2A.Z-1 and H2A.Z-2 were required for the function of H2A.Z in gene regulation. To address this issue, we generated the H2A.Z-1 and H2A.Z-2 double knock out (KO) cells in chicken DT40 cells. The expression pattern of H2A.Z-1 and H2A.Z-2 double KO cells was compared with WT cells to characterize the genes regulated by H2A.Z-1 and H2A.Z-2. We used microarrays to analysis the alternation of gene expression between WT and H2A.Z double KO cells and identify classes of up or down regulated gene by H2A.Z-1 and H2A.Z-2. In H2A.Z-1 and H2A.Z-2 double KO cells, H2A.Z-2 is knocked out constitutively, but H2A.Z-1 conditionally by tetracycline. The expression of H2A.Z-1 transgene is suppressed completely when H2A.Z-1 and H2A.Z-2 double KO cells culture with tetracycline for three days. For this reason, we prepared the total RNA of WT cells and H2A.Z-1and H2A.Z-2 double KO cells treated with tetracycline for three days and hybridization on Affymetrix microarrays.

2015-11-04 | E-GEOD-35430 | biostudies-arrayexpress

H2A.Z regulates zygotic genome activation

Project description:Affinity Purification Mass Spectrometry (AP-MS) of Drosophila ovaries expressing an H2A.Z-FlagHA transgene to identify interacting partners of H2A.Z to elucidate potential maternally supplied histone chaperones that deposit H2A.Z on the transcription start site (TSS).

2022-02-15 | PXD029061 | Pride

Expression data from H2A.Z-1 and H2A.Z-2 double KO cells

2015-11-04 | GSE35430 | GEO

Identification of PWWP2A interactors using label-free quantitative affinity enrichment mass spectrometry

Project description:Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified PWWP2A, which tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays we show that distinct domains of PWWP2A moreover mediate binding to free linker DNA as well as H3K36me3 nucleosomes. In vivo, PWWP2A strongly recognizes H2A.Z-containing regulatory regions and weakly H3K36me3-containing gene bodies. Additionally, PWWP2A bind to an MTA1-specific core NuRD (M1HR) complex solely consisting of MTA1, HDAC1 and RBBP4/7, excluding CHD and MBD proteins. Depletion of PWWP2A leads to an increase of acetylation levels on H3K27 as well as H2A.Z, presumably by impaired chromatin recruitment of M1HR. Thus, this study identifies PWWP2A as an ever more complex chromatin binding protein serving as adapter for M1HR to H2A.Z-containing chromatin, thereby promoting changes in histone acetylation levels and likely fine-tuning the transcriptional balance.

2018-08-27 | PXD010424 | Pride

Replacement of Arabidopsis H2A.Z with human H2A.Z orthologs reveals extensive functional conservation and limited importance of the N-terminal tail sequence for Arabidopsis development (WT, h2a.z, h2a.z + AtHTA11 RNA-Seq)

Project description:To investigate the functional conservation of H2A.Z histones during eukaryotic evolution we transformed h2a.z deficient plants with three human H2A.Z proteins to assess their ability to rescue the mutant defects. We discovered that human H2A.Z.1 and H2A.Z.2.1 fully complement the phenotypic abnormalities of h2a.z plants even though Arabidopsis and human H2A.Z N-terminal tail sequences are divergent, while the brain-specific splice variant H2A.Z.2.2 has a dominant-negative effect in wild-type plants. Furthermore, H2A.Z.1 almost completely re-establishes normal H2A.Z chromatin occupancy in h2a.z plants and restores the expression of more than 84 % of misexpressed genes. Finally, our hypothesis that the N-terminal tail of Arabidopsis H2A.Z is not crucial for its overall function was supported by the ability of N-terminal end truncations of Arabidopsis HTA11 to largely rescue the defects of h2a.z mutants.

2024-05-13 | GSE263310 | GEO

H2A.Z acetylation fine-tunes gene expression dynamics by regulating H2A.Z degradation

Project description:H2A.Z acetylation has been suggested to regulate genes but effects on gene expression globally have not been reported. We find that the H2A.Z acetylation sites are required for normal growth in the presence of caffeine and therefore examined the gene expression response to caffeine when H2A.Z can’t be acetylated. Surprisingly we found little or no change in gene induction but a marked failure to remove H2A.Z from activated promoters. Caffeine causes a proteasome-dependent degradation of H2A.Z that is impaired in the absence of the H2A.Z acetylation sites. The proteasomal regulator Blm10 that has previously been implicated in acetylation-dependent histone degradation is required for H2A.Z degradation, revealing a novel role for acetylation in regulating H2A.Z protein levels. When H2A.Z levels are raised, either through loss of the acetylation sites or overexpression of the protein, a shared set of genes aberrantly retains H2A.Z at their 5’ ends during the caffeine response. As a result, expression of these genes fails to return to normal levels. H2A.Z is therefore subject to post-translational proteasomal regulation that controls protein levels, and the fine-tuning of gene expression during a stress response requires the normal function of this pathway. This regulation of H2A.Z degradation by acetylation is a previously unrecognised aspect of gene regulation.

2018-04-05 | GSE97822 | GEO

H2A.Z Regulates Astrocyte Proliferation and Differentiation via H3K56ac Modification

Project description:Purpose:To gain a deeper insight into how H2A.Z regulates astrocytogenesis, RNA-sequencing (RNA-seq) was performed to analyze the genome-wide changes by H2AZ deletion at E16. Methods: Total RNA was extracted from E16 telencephalic tissue of H2A.ZcKO and H2A.Zfl/fl mice. Then total RNA was quality controlled and quantified using an Agilent 2100 Bioanalyzer. After converting to cDNA and building library, high-throughput sequencing was performed using the Illumina HiSeq 2500 platform in Annoroad Genomics. Results: Approximately approximately one thousand transcripts showed differential expression between the H2A.Zfl/fl and H2A.ZcKO brain, with a fold change ≥1.5 and p value <0.05. Gene ontology (GO) analysis showed that the down-regulated genes were enriched in the terms related to regulation of glial cell differentiation and forebrain development, and cerebellum development. Up-regulated genes showed a significant enrichment of terms involved in negative regulation of cell differentiation. These results reflected the importance of H2A.Z in cortical development. Conclusions: We conclude that RNA-seq based transcriptome characterization would provide a framework for understanding how H2A.Z gene contribute to cortical development.

2017-07-28 | GSE101939 | GEO

ChIP-seq for OsINO80 location using YFP antibody, and ChIP-seq for WT and osino80 using H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 antibodies

Project description:To investigate the effect of the OsINO80, we analysed OsINO80 binding regions and analysed genome-wide H3, H2A, H2A.Z, H2Aub, H3K9me2, H3K4me2, H3K4me3, H3K27me3, and H3K36me3 in the mutant and WT by ChIP-seq.

2024-04-10 | GSE225484 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data