Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c.

ABSTRACT: We conducted ChIP-Seq of KDM5c in neurons isolated from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

ORGANISM(S): Mus musculus

PROVIDER: GSE75866 | GEO | 2016/01/27

SECONDARY ACCESSION(S): PRJNA305550

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-01-27 | E-GEOD-61036 | biostudies-arrayexpress

Aggression, cognitive and neurodevelopmental abnormalities associated with disruption of the intellectual disability and histone demethylase gene Kdm5c

Project description:This SuperSeries is composed of the SubSeries listed below.

2016-01-27 | GSE61036 | GEO

Activation of Xist by An Evolutionarily Conserved Function of the KDM5C Demethylase

Project description:We performed Kdm5c (Smcx) ChIP-Seq in del_Tsix XY mouse epiblast cells with two genotypes: Smcx-WT and Smcx-KO

2022-04-14 | GSE96740 | GEO

DNA methylation fingerprint of a KDM5C loss-of-function mutation in patients with intellectual disability

Project description:Characterization of methylation changes related do KDM5C c.807delC (p.V271X) Mutations in KDM5C (lysine (K)-specific demethylase 5C) were associated to up to 3% of the X-linked ID cases. Males carrying KDM5C mutations present reduced activity of the KDM5C protein, increasing H3K4 tri-methylation, which ultimately leads to up-regulation of KDM5C target genes. Whole-exome sequencingi n one of three brothers with intellectual disability followed by confirmation by Sanger sequencing in the family identified a frameshift mutation in the KDM5C exon 7 that devoid of the JmjC catalytic domain from the protein. Two other brothers also presenting intellectual disability as well as in their clinically normal mother, who had completely skewed X-inactivation also had the mutation. An empirical Bayesian analysis of methylation levels between cases and controls identified 399 differentially methylated positions, 288 hypomethylated and 111 hypermethylated.Among the genes associated with the hypomethylated CpGs were FBXL5 and CACYBP, both involved in the ubiquitination pathway.

2018-11-30 | GSE108423 | GEO

The Kdm5c histone demethylase controls enhancer and promoter function.

Project description:Here, we show that the Kdm5c/Smcx member of the Jarid1 family of H3K4 demethylases is recruited to both enhancer and core promoter elements in ES and neuronal progenitor cells (NPC). Knockdown of Kdm5c deregulates transcription via a local increase in H3K4me3. While at core promoters the function of Kdm5c is to restrict transcription, loss of Kdm5c impairs enhancer function. Remarkably, an impaired enhancer function activates promoter activity from Kdm5c-bound intergenic regions. Our results demonstrate that the Kdm5c demethylase plays a crucial role in the functional identity and discrimination of enhancers and core promoters. We speculate that this is related to recruitment of H3K4me3 binders like the TFIID and NURF complexes6-8. Providing functional identity to genomic regions through balancing enzymes that deposit and remove histone modifications may prove to be a general epigenetic mechanism for the functional indexing of eukaryotic genomes. Examination of the KDM5C binding sites in mouse embryonic stem cells and in neuronal progenitor cells. Effect of KDM5C knock down on H3K4me3 and H3K4me1 levels and gene expression.

2013-04-01 | E-GEOD-34975 | biostudies-arrayexpress

NO001: Kdm5c controls promoter and enhancer activities

Project description:The functional organization of eukaryotic genomes correlates with specific patterns of histone methylations. Regulatory regions in genomes like enhancers and promoters differ in their extent of methylation of histone H3 at lysine-4 (H3K4), but it is largely unknown how the different methylation states are specified and controlled. Here, we show that the Kdm5c/Jarid1c/SMCX member of the Kdm5 family of H3K4 demethylases can be recruited to both enhancer and promoter elements in embryonic stem cells and neuronal progenitor cells via gene-specific transcription factors. Knockdown of Kdm5c deregulates transcription via local increases in H3K4me3. Our data show that restricting H3K4me3 modification at core promoters dampens transcription, but Kdm5c is required at enhancers for their full activity. Remarkably, an impaired enhancer function activates the intrinsic promoter activity of Kdm5c-bound distal elements. Our results demonstrate that the Kdm5c demethylase plays a crucial and dynamic role in the functional discrimination between enhancers and core promoters. RNA from four independent cultures from each sh Kdm5c #1, sh Kdm5c #2 and non-targeting shRNA polyclonal cell lines were hybridized in dye-swap against a common reference of RNA from IB10 ES cells.

2013-04-05 | E-GEOD-38862 | biostudies-arrayexpress

Altered gene-regulatory function of KDM5C by a novel mutation associated with autism and intellectual disability

Project description:We describe a new variant in histone demethylase KDM5C in a male with autism and intellectual disability

2018-04-18 | GSE104319 | GEO

ChIP-Seq of H3K4 methylation in neurons isolated from E16.5 mouse embryonic cortices from WT and SMCX KO mice

Project description:We conducted ChIP-Seq of H3K4 methylation in neurons isolated from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

2016-01-27 | GSE61023 | GEO

RNA-Seq in neurons from E16.5 mouse embryonic cortices from WT and SMCX KO mice

Project description:We conducted RNA-Seq (using Direct Ligation of Adapters to first strand cDNA) in neurons from E16.5 mouse embryonic cortices from WT and SMCX KO mice and harvested after 10 days in vitro culture.

2016-01-27 | GSE61024 | GEO

The Kdm5c histone demethylase controls enhancer and promoter function.

2013-04-01 | GSE34975 | GEO