An H4K20me3-CTCF switch at stable TAD boundaries enforces reversible cell state transitions

Abstract

Reversible transitions between proliferative and quiescent cell states involve widespread gene expression changes despite stable topologically associating domain (TAD) boundaries. We report a reciprocal antagonism between TAD boundary element CTCF and histone modification H4K20me3 as a central mechanism governing the proliferation-quiescence transition. Genome-wide studies and functional perturbations reveal that elevated H4K20me3 in quiescent fibroblasts displaces CTCF at specific TAD boundaries while CTCF binding predominates in proliferating cells. Increased H4K20me3 reversibly induces a compact chromatin state, elliptical nuclear morphology, and transcriptional programs associated with quiescence. Conversely, elevated CTCF binding drives open chromatin, proliferative gene expression, and cell division despite quiescence signals. Fibroblasts lacking H4K20me3 methyltransferase KMT5C/Suv4-20h2 are hyper-proliferative and KMT5C-deficient mice are larger. Our findings provide a mechanistic framework for how architectural and epigenetic regulators exchange at TAD boundaries to coordinate reversible cell state transitions, a finding with implications for organismal development and diseases of dysregulated proliferation.