HDAC2-Mediated Recruitment of METTL3 to Chromatin Regulates Human Embryonic Stem Cell Differentiation
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PROVIDER: PRJNA1216271 | ENA |
REPOSITORIES: ENA
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Project description:N6-methyladenosine (m6A) methylation and its methyltransferase METTL3 are crucial for maintaining pluripotency and regulating stem cell differentiation. In this study, we demonstrate that METTL3 directly interacts with the histone deacetylase HDAC2. Notably, knockout of HDAC2 reduces METTL3 binding to chromatin, leading to a downregulation of m6A modifications on HDAC2 target genes, which were associated with stem cell lineage differentiation. Conversely, deletion of METTL3 does not affect HDAC2 expression or histone acetylation levels. Disrupting the interaction between HDAC2 and METTL3, either by knocking out HDAC2 or METTL3, significantly impairs differentiation of human embryonic stem cells (hESCs). Additionally, we observe a marked decrease in the RNA stability and translation of genes in which m6A levels were downregulated. Mechanistically, HDAC2 recruits METTL3 to regulate the m6A levels of its target genes, and these changes in m6A modification subsequently influence RNA stability and translation, ultimately contributing to hESC differentiation. Our findings identify a novel interactor of METTL3 and elucidate the functional and mechanistic roles of the HDAC2-METTL3 interaction axis in hESCs.
2025-09-01 | GSE288140 | GEO
Project description:Analysis of heart ventricles from Hopx, Hdac2, and both Hopx-Hdac2 deficient embryos at embryonic day E16.5. Results provide insight into the role of Hopx and Hdac2 in cardiac development. We used microarrays to detail the global programme of gene expression underlying cardiac development by Hopx and Hdac2 and identified distinct classes of up-regulated and down-regulated genes during this process. Mouse embryonic ventricles were selected at E16.5 for RNA extraction and hybridization on Affymetrix microarrays. We obtained three independent embryonic ventricles for WT, Hopx-null, Hdac2-null, and Hopx-Hdac2 double null genotypes.
2010-08-19 | E-GEOD-23700 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) is the most prevalent mRNA modification with diverse regulatory roles in mammalian cells. While its functions are well-documented in mouse embryonic stem cells (mESCs), its role in human pluripotent stem cells (hPSCs) remains to be fully explored. METTL3 is the main enzyme responsible for m6A deposition. Here, using a METTL3 inducible knockout (iKO) system, we uncovered that, unlike in mESCs, METTL3 was indispensable for hPSC maintenance. Importantly, loss of METTL3 caused significant upregulation of pluripotency factors including naïve pluripotency genes and failure to exit pluripotency, thus impaired stem cell differentiation towards embryonic and extraembryonic cells including trophoblasts. Mechanistically, METTL3 iKO in hPSCs substantially increased expression and enhancer activities of two primate-specific transposable elements (TEs), SVA_D and HERVK/LTR5_Hs, which are normally modified by METTL3-dependent m6A. METTL3 loss activated SVA_D by lowering H3K9me3 deposition, and increased chromatin accessibility at LTR5_Hs through the naïve and other pluripotency factors. Conversely, we discovered that the activated SVA_D and LTR5_Hs loci positively regulated naïve gene expression by directly interacted with their promoters. These findings thus reveal that METTL3-dependent m6A RNA methylation has critical roles in suppressing TE expression and in the human pluripotency regulatory network.
2025-05-07 | PXD056046 | Pride
Project description:Analysis of heart ventricles from Hopx, Hdac2, and both Hopx-Hdac2 deficient embryos at embryonic day E16.5. Results provide insight into the role of Hopx and Hdac2 in cardiac development. We used microarrays to detail the global programme of gene expression underlying cardiogenesis by Hopx and Hdac2 and identified distinct classes of up-regulated and down-regulated genes during this process.
2010-08-19 | GSE23700 | GEO
Project description:The histone deacetylase HDAC2, which negatively regulates neuronal plasticity and synaptic gene expression, is upregulated both in Alzheimer’s disease (AD) patients and mouse models (Graff et al., 2012). Therapeutics targeting HDAC2 are speculated to be a promising avenue for ameliorating AD related cognitive impairment. However, attempts to generate HDAC2-specific inhibitors have not been successful. Here, we take a novel approach utilizing integrative genomics to identify proteins that mediate HDAC2 recruitment to synaptic plasticity genes. Functional screening revealed that knockdown of the transcription factor Sp3 phenocopied HDAC2 knockdown, and that Sp3 facilitated the recruitment of HDAC2 to synaptic genes. Importantly, like HDAC2, Sp3 expression was elevated in AD patients and mouse models, where Sp3 knockdown ameliorated synaptic dysfunction. Furthermore, exogenous expression of an HDAC2 fragment containing the Sp3 binding domain fully restored synaptic plasticity and memory in a mouse model with severe neurodegeneration. Our findings indicate that targeting the HDAC2-Sp3 complex could enhance synaptic and cognitive function, without affecting HDAC2 function in other processes.
2017-08-08 | GSE87441 | GEO
Project description:Human myeloid leukemia cell line, HL-60 cells, have a potential to differentiate into monocytes with treatment of 12-O-tetradecanoylphorbol-13-acetate (TPA). However, the underlying mechanism of differentiation by TPA is not fully elucidated yet. Here, we performed ChIP-seq profiling using RNA Pol II, HDAC2, AcH3 and H3K27me3, and analyzed the differential chromatin state changes during HL-60 differentiation by TPA. In this study, we focused on the atypical active genes, which showed enhanced H3 acetylation occupancies despite increased HDAC2 recruitment. We found that HDAC2 regulates the expression of these genes positively via histone deacetylase activity-independent manner. HDAC2 interacted and recruited Paired Box 5 (PAX5) to promoter of the target genes and regulated PAX5-mediated gene activation. Taken together, these data demonstrated the profiling of differentiation specific-chromatin status during the differentiation in HL-60 cells by TPA and suggested that HDAC2 activates certain genes through the interaction with PAX5 in enzyme activity independent pathway.
2018-08-15 | GSE110566 | GEO
Project description:Histone acetylation is a dynamic modification regulated by the opposing actions of histone acetyltransferases and histone deacetylases (HDACs). Deacetylation of histone tails results in chromatin tightening and therefore HDACs are generally regarded as transcriptional repressors. Counterintuitively, simultaneous deletion of HDAC1 and HDAC2 in embryonic stem cells (ESC) reduced expression of pluripotent transcription factors, Oct4, Sox2 and Nanog (OSN). By shaping global histone acetylation HDACs indirectly regulate the activity of acetyl-lysine readers, such as BRD4. To examine the direct effects of HDAC (LBH589) and BRD4 (JQ1) inhibition on the ESC transcriptome, we performed precision nuclear run-on and sequencing (PRO-seq) analysis. Both LBH589 and JQ1 caused a marked reduction in the pluripotent network. However, while JQ1 treatment induced widespread transcriptional pausing of genes, HDAC inhibition caused a reduction in both paused and elongating polymerase, suggesting an overall reduction in recruitment of RNAPII. Using enhancer RNA (eRNA) expression to measure enhancer activity, we found that while HDAC activity regulates fewer enhancers than JQ1, LBH589 sensitive eRNAs were preferentially associated with super-enhancers and OSN binding sites. These findings suggest that HDAC activity is required for maintenance of pluripotency by regulating the OSN enhancer network via optimal recruitment of RNA polymerase II. Comparative gene expression using the Illumina mouseWG-6 v2 expression BeadChip platform. Wild type (Day 0) ESC compared to HDAC1-/-; HDAC2-/wt; CreER ESCs on day 4 following for OHT treatment in presence (+LIF) or absence (-LIF) of Leukemia inhibitory factor (LIF).
2020-08-01 | GSE136620 | GEO
Project description:we find METTL3 associates with polyribosomes and promotes translation. METTL3 depletion inhibits translation, and both wild-type and catalytically inactive METTL3 promote translation when tethered to the 3' untranslated region (UTR) of a reporter mRNA. Mechanistically, METTL3 enhances mRNA translation through an interaction with the translation initiation machinery. m6A seq in A549 and H1299 cells, RNA seq in METTL3 knockdown cells
2016-07-03 | E-GEOD-76367 | biostudies-arrayexpress
Project description:N6-methyladenosine (m6A) methylation of mRNA by the methyltransferase complex (MTC), with core components including METTL3-METTL14 heterodimers and Wilms’ tumor 1-associated protein (WTAP), contributes to breast tumorigenesis, but the mechanism of MTC assembly remains elusive. Here, we identify a novel cleaved form METTL3a (residues 239-580 of METTL3), that is highly expressed in breast cancer. Furthermore, we find that both METTL3a and full-length METTL3 are required for MTC assembly, RNA m6A deposition, as well as cancer cell proliferation. Mechanistically, we find that METTL3a is required for METTL3-METTL3 interaction, which is a prerequisite step for recruitment of WTAP in MTC assembly. Analysis of m6A sequencing data shows that depletion of METTL3a globally disrupts m6A methylation, and METTL3a mediates mTOR activation via m6A-mediated suppression of TMEM127 expression. Consequently, we find that METTL3 cleavage is mediated by proteasome in an mTOR-dependent manner, revealing positive regulatory feedback between METTL3a and mTOR signaling. Our findings reveal METTL3a as an important component for MTC assembly, and suggest the METTL3a-mTOR axis as a potential therapeutic target for breast cancer.
2023-08-18 | PXD036899 | Pride
Project description:We used microarrays to detail the global programme of gene expression underlying cardiac development by HDAC2 and identified distinct classes of up-regulated and down-regulated genes during this process. Experiment Overall Design: Embryonic heart ventricles were dissected at E17.5 for RNA extraction and hybridization on Affymetrix microarrays. Wild type and HDAC2-deficient littermates were used. Tissue from 2-3 individual animals of identical genotype was pooled for each micro-array.
2008-06-15 | E-GEOD-6770 | biostudies-arrayexpress