HDAC2-Mediated Recruitment of METTL3 to Chromatin Regulates Human Embryonic Stem Cell Differentiation

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. We performed RNA-seq and m6A-seq in wildtype, METTL3-KO, and HDAC2-KO hESCs, while ChIP-seq were conducted in wildtype and HDAC2-KO hESCs.