GSE203606
H3K36 methylation maintains cell identity by regulating opposing lineage programs
While epigenetic regulation in early development and differentiation is relatively well-characterized, the precise mechanisms that subsequently maintain specialized cell states remain largely unexplored. Here, we employed histone H3.3 mutants to uncover a crucial role for H3K36 methylation in the maintenance of cell identities across diverse developmental contexts. Focusing on the experimentally induced conversion of fibroblasts to pluripotent stem cells, we show that H3K36M-mediated disruption of H3K36 methylation endowed reprogramming intermediates with a plastic state poised to acquire pluripotency in virtually every cell. At a cellular level, H3K36M rendered mesenchymal cells insensitive to TGF? signals and thus facilitated epithelial plasticity. At a molecular level, H3K36M led to the downregulation of mesenchymal genes by depleting H3K36me2 and H3K27ac at associated enhancers. In parallel, H3K36M led to the upregulation of epithelial and stem cell genes by enabling enhancer accessibility and hypomethylation. Mechanistically, we found that Tet-dependent demethylation uncouples pluripotency enhancer activation from somatic enhancer decommissioning in K36M cells. This dynamic switch of enhancer activities redirects Sox2 binding from promiscuous somatic targets to bona fide stem cell targets crucial for the establishment of the pluripotency network. Together, our findings reveal a dual role for H3K36 methylation in the maintenance of cell identity, by integrating a key developmental pathway into sustained expression of cell type-specific programs, and by opposing the expression of alternative lineage programs through continual enhancer methylation. Our results provide crucial insight into the impact of dynamic H3K36 methylation patterns on physiological and pathological cell fate transitions, including development, tissue regeneration and cancer. Overall design: Reprogramming for sequencing samples was performed in AGi conditions. RRBS was performed for d0 samples (MEFs), d4 and d8 reprogramming intermediates, and passaged iPSCs of both backgrounds (S/L, no dox). All reads aligned to mm9 genome.