Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

KDM3A and KDM3B maintain naïve pluripotency through regulation of alternative splicing

ABSTRACT: Histone modifying enzymes play a central role in maintaining cell identity by establishing a conducive chromatin environment for lineage specific transcription factor activity. Pluripotent embryonic stem cells (ESCs) identity is characterized by lower abundance of gene repression associated histone modifications that enables rapid response to differentiation cues. The KDM3 histone demethylase family remove the repressive histone H3 lysine 9 dimethylation (H3K9me2). Here we uncover a surprising role for the KDM3 proteins in the maintenance of the pluripotent state through post-transcriptional regulation. We find through immunoaffinity purification of the KDM3A or KDM3B interactome and proximity ligation assays that KDM3A and KDM3B interact with the RNA processing factors such as EFTUD2 and PRMT5. By generating double “degron” ESCs to degrade KDM3A and KDM3B in the rapid timescale of splicing, we find altered splicing independent of H3K9me2 status. These splicing changes partially resemble the splicing pattern of the more blastocyst like ground state of pluripotency and occurred in important chromatin and transcription factors such as Dnmt3b, Tbx3 and Tcf12. Our findings reveal non-canonical roles of histone modifying enzymes in splicing to regulate cell identity. Cells were plated, allowed to adhere overnight, then treated for four hours with dTAG-13.

ORGANISM(S): Mus musculus

PROVIDER: GSE230341 | GEO | 2024/01/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Vitamin C Induces Specific Demethylation of H3K9me2 in Mouse Embryonic Stem Cells via Kdm3a/b

Project description:Histone methylation patterns regulate gene expression and are highly dynamic during development. The erasure of histone methylation is carried out by histone demethylase enzymes. We had previously shown that vitamin C enhances the activity of Tet enzymes in embryonic stem (ES) cells, leading to DNA demethylation and activation of germline genes. We report here that vitamin C induces a remarkably specific demethylation of histone H3 lysine 9 dimethylation (H3K9me2) in ES cells. Vitamin C treatment reduces global levels of H3K9me2, but not other histone methylation marks analyzed, as measured by Western blot, immunofluorescence and mass spectrometry. Vitamin C leads to widespread loss of H3K9me2 at large chromosomal domains as well as gene promoters and repeat elements. Vitamin C-induced loss of H3K9me2 occurs rapidly within 24 hours and is reversible. Importantly, we found that the histone demethylases Kdm3a and Kdm3b are required for vitamin C-induced demethylation of H3K9me2. Moreover, we show that vitamin C-induced Kdm3a/b-mediated H3K9me2 demethylation and Tet-mediated DNA demethylation are independent processes. Lastly, we document Kdm3a/b are partially required for the up-regulation of germline genes by vitamin C. These results reveal a specific role for vitamin C in histone demethylation in ES cells, and document that DNA methylation and H3K9me2 cooperate to silence germline genes in pluripotent cells.

2017-06-30 | GSE84009 | GEO

m6A directs the demethylation of histone H3K9me2 co-transcriptionall

Project description:Here we show the repressive H3K9me2 mark is specifically removed by the induction of m6A-modified transcripts. We demonstrate that the methyltransferase METTL3/METTL14 regulates H3K9me2 modification. We observed a genome-wide correlation between m6A and occupancy by the H3K9me2 demethylase KDM3B, and we found m6A reader YTHDC1 physically interacts and recruits KDM3B to m6A-associated chromatin regions, promoting H3K9me2 demethylation and gene expression. This study establishes a direct link between m6A and dynamic chromatin modification and provides mechanistic insight into the co-transcriptional interplay between RNA modification and histone modifications.

2020-07-01 | GSE153651 | GEO

Specific phosphorylation of histone demethylase KDM3A determines target gene expression in response to heat shock

Project description:Histone lysine (K) residues, which are modified by methyl- and acetyl-transferases, diversely regulate RNA synthesis. Unlike the ubiquitously activating effect of histone K acetylation, the effects of histone K methylation vary with the number of methyl groups added and with the position of these groups in the histone tails. Histone K demethylases (KDMs) counteract the activity of methyl-transferases and remove methyl group(s) from specific K residues in histones.KDM3A (also known as JHDM2A or JMJD1A) is an H3K9me2/1 demethylase. KDM3Aperforms diverse functions via the regulation of its associated genes, which are involved in spermatogenesis, metabolism, and cell differentiation. However, the mechanism by which the activity of KDM3A is regulated is largely unknown. First, we demonstrated that mitogen- and stress-activated protein kinase 1 (MSK1) specifically phosphorylates KDM3A at Ser264 (pKDM3A), which is enriched in the regulatory regions of gene loci in the human genome under heat shock conditions. p-KDM3A directly interacts with and is recruited by the transcription factor Stat1 to activate KDM3A target genes. The demethylation of H3K9me2 at the Stat1 binding site specifically depends on the co-expression of p-KDM3A under heat shock conditions. In contrast to heat shock treatment, IFN-M-NM-3 treatment does not phosphorylate KDM3A via MSK1, thereby abrogating its downstream effects. To our knowledge, this is the first evidence that a KDM can be modified via phosphorylation to determine its specific binding to target genes in response to cellular stress. 3 ChIP samples and two input as controls

2014-10-15 | E-GEOD-62309 | biostudies-arrayexpress

The histone demethylase Kdm3a is essential to progression through differentiation

Project description:Histone demethylation has important roles in regulating gene expression and forms part of the epigenetic memory system that regulates cell fate and identity, by still poorly understood mechanisms. Here we examined the role played by the histone demethylase Kdm3a, which demethylates lysine 9 of histone H3, during cellular differentiation. Using F9 mouse embryonal carcinoma cells as a model for progression through terminal differentiation, we showed that Kdm3a is essential to differentiation into parietal endoderm-like (PE) cells. On gene expression microarrays, we found several genes whose expression is upregulated by Kdm3a during endoderm differentiation, including the three developmental master players Dab2, Pdlim4, and FoxQ1. The role of Kdm3a as a transcriptional activator of these genes was correlated with its effect by demethylating dimethyl-lysine 9 of histone H3 (H3K9me2) at their promoters. We further demonstrated that Dab2 depletion, like Kdm3a depletion, prevents F9 cells from fully differentiating into PE cells. Nevertheless, the only overexpression of Dab2 in Kdm3a-depleted cells is not sufficient to completely restore the PE differentiation in Kdm3a-knockdown cells. Overall, our findings reveal that Kdm3a is crucial for progression through terminal differentiation, likely by regulating the expression of a set of master players in endoderm differentiation. The emergence of Kdm3a as a key modulator of cell fate decision strengthens the notion that histone demethylases are at the nexus of cell differentiation and development.

2012-06-15 | GSE33841 | GEO

Systematic characterization of epigenetic modifying enzymes identifies KDM3B as a key regulator in castration resistant prostate cancer

Project description:Androgen deprivation therapy (ADT) is the standard care for prostate cancer patients who fail surgery and radiotherapy. While initially effective, the cancer almost always recurs into a more aggressive Castration Resistant Prostate Cancer (CRPC). Despite the existing evidence on the role of epigenetic modifiers in CRPC, only a handful of enzymes have been tested. In this study, we conducted a systematic shRNA library screen, focusing of epigenetic modifiers linked to stem-cell reprogramming, in LNCaP-abl cells, a model of CRPC. Amongst the shRNA hits, KDM3B, a histone H3K9 demethylase, was identified to have the most significant anti-proliferative effect on LNCaP-abl cells. KDM3B CRISPR/Cas9 knockout phenocopied the shRNA treatment, proving the observed phenotype was not due to shRNA off-target effects. Interestingly, this decrease in proliferation was remarkably specific to androgen-independent cells. Additionally, genetic rescue experiment showed that only enzymatically active KDM3B recovers the phenotype. No alterations in the cell cycle distribution or expression of AR downstream effectors were observed, but RNASeq revealed subtle changes in the genes expression profile for cells treated with KDM3A shRNA, including in metabolome-related enzymes such as ARG2, RDH11. However, metabolomic analysis in KDM3B knockout cells showed little change overall compared to untreated cells. Interestingly, we observed a decrease in the availability of amino acids in the absence of KDM3B which requires further investigation. Overall, our studies are the first ones to show the specificity of KDM3B in CRPC.

2020-03-16 | GSE127904 | GEO

Epigenetic safeguards are coordinately removed to reverse cell identity [5hmC Enrichment]

Project description:Epigenetic modifications operate in concert to maintain cell identity, yet how these interconnected networks suppress alternative cell fates remains unknown. Here we uncover a link between the removal of repressive histone H3K9 methylation and DNA methylation during the reprogramming of somatic cells to pluripotency. The H3K9me2 demethylase, Kdm3b, transcriptionally controls DNA demethylase Tet1 expression. Unexpectedly, in the absence of Kdm3b, loci that have to be DNA demethylated are trapped in an intermediate hydroxymethylated (5hmC) state and do not resolve to unmethylated cytosine. Ectopic 5hmC trapping precludes the chromatin association of master pluripotency factor, POU5F1, and pluripotent gene activation. Tet1 but not Tet2 is critical for this defining event in the reprogramming process. Taken together we uncover a mechanism of coordinated chromatin modification removal in disrupting cell identity.

2019-09-26 | GSE119076 | GEO

Epigenetic safeguards are coordinately removed to reverse cell identity [RNA-Seq]

2019-09-26 | GSE119075 | GEO

Histone H3 lysine-to-methionine mutants as a paradigm to study chromatin signaling

Project description:Histone H3 lysine27-to-methionine (H3K27M) gain-of-function mutations occur in highly aggressive pediatric gliomas. Here, we establish a Drosophila animal model for the pathogenic histone H3K27M mutation and show that its overexpression resembles Polycomb repressive complex 2 (PRC2) loss-of-function phenotypes, causing de-repression of PRC2 target genes and developmental perturbations. Similarly, a H3K9M mutant depletes H3K9 methylation levels and suppresses position-effect variegation in various Drosophila tissues. The histone H3K9 demethylase KDM3B/JHDM2 associates with H3K9M nucleosomes and its overexpression in Drosophila results in loss of H3K9 methylation levels and heterochromatic silencing defects. Here we establish histone lysine-to-methionine mutants as robust in vivo tools for inhibiting methylation pathways that also function as biochemical reagents for capturing site-specific histone-modifying enzymes, thus providing molecular insight into chromatin-signaling pathways. RNA-seq of wing imaginal discs expressing either H3.3WT-FLAG-HA or H3.3K27M-FLAG-HA.

2014-09-02 | E-GEOD-59891 | biostudies-arrayexpress

Genome-wide maps of chromatin state in HCT116 cells.

Project description:We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription. We identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes. We found that H3K27ac upregulation is highly correlated with gene activation, but not H3K4me3; and transcription repression of certain TEAD1 target genes, such as BBC3, is important for the pathway function. KDM3A knockout caused upregulation of H3K9me2 mainly on TEAD1-binding enhancers rather than gene bodies, leading to decrease of H3K27ac and TEAD1 binding on enhancers and impaired transcription.

2019-03-20 | GSE108920 | GEO

Expression data from pre-iPSCs with a control, histone methyltransferase or Cbx3 (HP1g) knockdown

Project description:Transition from a partially reprogrammed pre-iPSC state to iPSC state can be achieved by modulating levels of histone modifying enzymes or proteins that can bind to histone modifications We used microarrays to determine the gene expression profile of pre-iPSCs depleted for either 3 histone methyltransferases together or the HP1gamma protein pre-iPSCs were subjected to simultaneous siRNA mediated knockdown of Ehmt1, Ehmt2 and Setdb1- which is the 3XHMT sample that mediate H3k9me2/me3 or Cbx3( HP1gamma) or control siRNA to luciferase

2013-06-05 | E-GEOD-44084 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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