Molecular mechanisms of global DNA demethylation to naïve pluripotency in ESC

Global demethylation is part of a conserved program of epigenetic reprogramming to naïve pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naïve hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accurately predicts global DNA demethylation kinetics. Experimentally we show that the main drivers of global demethylation are neither active mechanisms (Aicda, Tdg, Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transit to 2i and so is recruitment of the maintenance methylation machinery to replication foci. Concurrently there is global loss of H3K9me2, which is needed for chromatin binding of UHRF1. These mechanisms synergistically enforce global DNA hypomethylation in a replication-coupled fashion. Our observations establish the molecular mechanism for global demethylation in naïve ESCs, which has key parallels with those operating in primordial germ cells and early embryos. mRNA-seq, RRBS-seq and ChIPSeq of different time-points during serum to 2i conversion of mouse ESCs