Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparison of genome-wide distribution of histone modifications (H3K4me3, H3K9me2, H3K27me2, and H3K27me3) between wild-type and Kdm7a mutant embryos

ABSTRACT: Comparison of genome-wide distribution of histone modifications (H3K4me3, H3K9me2, H3K27me2, and H3K27me3) between wild-type and Kdm7a mutant embryos

PROVIDER: PRJNA550268 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Comparison of genome-wide distribution of histone modifications (H3K4me3, H3K9me2, H3K27me2, and H3K27me3) between wild-type and Kdm7a mutant embryos

Project description:Temporal and spatial colinear expression of Hox genes determines the specification of positional identities of the embryo. Post-translational modifications of histones contribute to transcriptional regulation, and are required for proper control of biological processes, including differentiation and development. Lysine demethylase 7A (Kdm7a) demethylates lysine 9 di-methylation of histone H3 (H3K9me2) and participates in transcriptional activation of developmental genes. However, the role of Kdm7a during mouse embryonic development remains to be elucidated. Here, we show that Kdm7a-/- mice exhibit anterior homeotic transformation of the axial skeleton (i.e. an increase in the number of presacral elements). Importantly, posterior Hox genes (caudally from Hox9) are specifically down-regulated in Kdm7a-/- embryos, which correlate with increased levels of H3K9me2. Taken together, these data suggest that Kdm7a is able to control transcription of posterior Hox genes, likely through its demethylating activity, and thereby regulating anterior-posterior development in mice.

2019-12-23 | GSE133188 | GEO

Genome-wide distribution of histone modification enzymes (KDM7A and UTX), histone modification (H3K9me2, H3K27me3, H3K4me3, H3K27ac), and transcription factor (p65) in TNF-alpha-stimulated human umbilical vein endothelial cell (HUVECs)

Project description:Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-κB) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-α. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and cooperatively activate NF-κB dependent inflammatory genes. Furthermore, using both in situ Hi-C and other 3C based technology, loops between super enhancers (SEs) are newly formed following TNF-α-stimuli at NF-κB-dependent inflammatory loci where KDM7A- and UTX-recruitment coincide. Collectively, these findings suggest that erasing of repressive histone marks by KDM7A and UTX within NF-κB-related elements might functionally associate with formation of SE-SE three-dimensional interactions and could be a cue signal during inflammatory responses in human endothelial cells.

2019-04-11 | GSE121890 | GEO

The lysine demethylase KDM7A regulates immediate early genes in neurons [CUT&Tag]

Project description:There are multiple post-translational modifications on amino acid residues at the N-terminus of histones that affect the structure of chromatin and alter the transcription of genes, thereby regulating a variety of biological processes. Lysine demethylase 7A (KDM7A) mainly removes histone modifications such as H3K9me1/2 and H3K27me1/2. Current research on KDM7A has focused on tumors, metabolism and development, while research on the function of the mammalian nervous system is still lacking. The functions and mechanisms of KDM7A in the regulation of neuronal cell differentiation and cell activity in the nervous system were investigated. Our study found that KDM7A regulates H3K9me2 and H3K27me2 but also affects other inhibitory or active histones, such as H3K9me3 and H3K27ac, thereby disturbing the transcription of some immediate early genes (IEGs) and consequently affecting the differentiation and activity of neuronal cells. IEGs are important for neuron cell proliferation, differentiation, formation of dendrites and neural circuit-related proteins, which are involved in maintaining the normal function of the nervous system. Imbalances in IEG expression have been found in some neurological disorders, such as depression and schizophrenia. Moreover, the changes in various histone modifications in neurodegenerative diseases and brain injury have recently received increasing attention. Therefore, our study provides a basis for revealing the epigenetic regulatory mechanisms of neurological disorders.

2023-08-21 | GSE236352 | GEO

Comparison of gene expression profiles between wild-type and Kdm7a mutan embryos

2019-12-23 | GSE133187 | GEO

Project description:Genome-wide distribution of histone modification enzymes (KDM7A and UTX), histone modification (H3K9me2, H3K27me3, H3K4me3, H3K27ac), and transcription factor (p65) in TNF-alpha-stimulated human umbilical vein endothelial cell (HUVECs)

| PRJNA498996 | ENA

Illumina Microarray of MRC5 cell with or without KDM7A-DT overexpression

Project description:KDM7A Divergent Transcript (KDM7A-DT) is a stress-induced lncRNAs. In our previous studies, KDM7A-DT showed the most robust cellular phenotype alteration and a significant TP53-dependency upon oxidative and oncogenic stress induction. To investigate the functional roles of KDM7A-DT, we first performed overexpression experiments using fibroblasts. We found that MRC5 cells overexpressing KDM7A-DT escaped cell cycle proliferation and long-term survival ability and were associated with a distinct stress-related morphology (enlarged and flattened cells) compared to cells expressing just the vehicle control. To examine the effects of KDM7A-DT overexpression on the transcriptome, we performed a differential expression gene (DEG) analysis comparing a group of four independent biological replicates of MRC5 overexpressing KDM7A-DT to a group of samples from control cells.

2023-05-01 | E-MTAB-11819 | biostudies-arrayexpress

ChIP-chip of H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, H3K9Me2, H3K27Me3, CTCF and HP1a in MCF7 breast cancer cells

Project description:We report the high-throughput profiling of histone modifications, CTCF and HP1a binding sites in MCF7 breast cancer cells. ChIP-chip experiments were performed using the Agilent Human Genome CGH Microarray 1x1M. Regulatory markers H3K4Me1, H3K4Me3, H3K4Ac, H3K9Ac, CTCF are known to be positively correlated with gene expression, and H3K9Me2, H3K27Me3 and HP1a are negative markers. Together with MCF7 methylation data, we showed hypomethylated promoters are significantly enriched with positive regulatory elements, and lacks repressive markers.

2015-02-25 | E-MTAB-1935 | biostudies-arrayexpress

Genome-wide distribution of two histone modifications, H3K4me3 and H3K27me3, in soybean embryos and seedlings

Project description:In this study, we examined the genome-wide deposition of two opposing histone modifications H3K4me3 and H3K27me3, in mid-maturation (stage B1) soybean embryos.

2018-08-03 | GSE114879 | GEO

The genomic distribution of G9a, H3K9me2 and H3K27me3 in cardiac hypertrophy.

Project description:The role of the histone methyltrasferase G9a (also known as Ehmt2) in the normal heart has not been studied extensively. To identify which genes were direct targets of G9a in hypertrophic cardiomyocytes, we performed ChIP-seq for G9a and H3K9me2 – the main histone methylation catalysed by the HMT – on cardiomyocytes isolated from normal mice (sham) and mice subject to transverse aortic constriction (TAC) for 1 wk, a surgical procedure that causes cardiac hypertrophy following the induction of pressure overload. We considered the best G9a-bound genomic regions as those in which G9a and H3K9me2 peaks overlapped. Since G9a contributes to trimethylation of H3K27 at a set of developmental genes through its interaction with PRC2, we also evaluated whether G9a had an effect on the distribution of this histone mark in hypertrophic cardiomyocytes. To this end, we performed ChIP-seq for H3K27me3 in CMs isolated from sham and TAC mice.

2017-08-30 | GSE93752 | 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