Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

Abstract

SummaryGlobal demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive 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, and Tet1-3) nor the reduction of de novo methylation. UHRF1 protein, the essential targeting factor for DNMT1, is reduced upon transition 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 naive ESCs, which has key parallels with those operating in primordial germ cells and early embryos.

X-chromosome dosage as a modulator of pluripotency, signalling and differentiation?

“…The reduced levels of Dnmt3a/b in 2i conditions contribute to the markedly reduced DNA methylation levels that are observed in 2i in a genome-wide manner [32][33][34]. In addition, also the maintenance of DNA methylation after DNA replication seem to be less efficient in 2i due to reduced protein expression of UHRF1, which targets the maintenance DNA methyltransferase Dnmt1 to replication foci [35]. Taken together, blocking two differentiation-associated signal transduction pathways can lock mESCs in the naive pluripotent ground state, where they express homogenously high levels of all pluripotency factors and are globally DNA hypomethylated (figure 2).…”

EHMT1/GLP; Biochemical Function and Association with Brain Disorders

“…There is some evidence of DNMT1 interacting with G9a, regulating H3K9 methylation in the HCT116 cancerous colon immortalised cells, where knocking out DNMT1 lead to a reduction in H3K9me2 [25]. Low DNA methylation in embryonic stem cells (ESCs) cultured in 2i serum was associated with decreased DNA methylation maintenance and associated protein E3 ubiquitin-protein ligase (UHRF1) and decreased GLP/G9a expression, coupled with an upregulation of several H3K9 demethylases [26]. However, the exact mechanism by which GLP mediates the maintenance of DNA methylation is not fully understood.…”

Signalling pathways in UHRF1-dependent regulation of tumor suppressor genes in cancer

“…One of the most interesting is a sensor role for interstrand crosslinks, showing that UHRF1 is also involved in DNA repair processes [20–22]. Of note, it was also shown that the decrease of UHRF1 protein levels is a major cause of DNA demethylation in embryonic stems cells [23]. Therefore, UHRF1 appears to have a triple role during cell proliferation, i.e., in DNA methylation pattern inheritance, sensor of DNA crosslinks and a facilitator of DNA demethylation during development.…”