Plasticity in Dnmt3L-dependent and -independent modes of de novo methylation in the developing mouse embryo

Abstract

SUMMARYA stimulatory DNA methyltransferase co-factor, Dnmt3L, has evolved in mammals to assist the process of de novo methylation, as genetically demonstrated in the germline. The function of Dnmt3L in the early embryo remains unresolved. By combining developmental and genetic approaches, we find that mouse embryos begin development with a maternal store of Dnmt3L, which is rapidly degraded and does not participate in embryonic de novo methylation. A zygotic-specific promoter of Dnmt3l is activated following gametic methylation loss and the potential recruitment of pluripotency factors just before implantation. Importantly, we find that zygotic Dnmt3L deficiency slows down the rate of de novo methylation in the embryo by affecting methylation density at some, but not all, genomic sequences. Dnmt3L is not strictly required, however, as methylation patterns are eventually established in its absence, in the context of increased Dnmt3A protein availability. This study proves that the postimplantation embryo is more plastic than the germline in terms of DNA methylation mechanistic choices and, importantly, that de novo methylation can be achieved in vivo without Dnmt3L.

Stable Methylation at Promoters Distinguishes Epiblast Stem Cells from Embryonic Stem Cells and the In Vivo Epiblasts

“…The zygotic promoter of Dnmt3l, which controls its expression during preimplantation stages, was also methylated in EpiSCs (Supplementary Fig. S3D), as is the case in the postimplantation epiblast [16]. Expression of these genes are quickly downregulated during conversion of ESCs to EpiSCs [38]; (see below).…”

“…Three have been isolated in mammals: Dnmt3a and Dnmt3b are catalytically active, while Dnmt3l, is a cofactor for both. In the epiblast, Dnmt3b is the first to be expressed at E3.5 while Dnmt3a expression starts 1 day later [16][17][18]. Dnmt3l is expressed transitorily in the epiblast, between E4.5 and E6.5 [16,18].…”

“…In the epiblast, Dnmt3b is the first to be expressed at E3.5 while Dnmt3a expression starts 1 day later [16][17][18]. Dnmt3l is expressed transitorily in the epiblast, between E4.5 and E6.5 [16,18]. The ICM of E3.5 blastocyst is globally hypomethylated, while a massive wave of de novo methylation occurs between the epiblast stages E3.5 and E6.5 [13].…”

De novoDNA methylation through 5'-segment of theH19ICR maintains its imprint during early embryogenesis

“…Even in the presence of these enzymes (Fig. S2) (Guenatri et al, 2013;Hirasawa et al, 2008), the maternally inherited transgenic (Fig. 1C,D) and endogenous H19 ICRs do not acquire methylation.…”

“…S2) (Guenatri et al, 2013;Hu et al, 2008) would compensate for a loss of maternally provided DNMT3L in transgenic H19 ICR methylation during embryogenesis. The paternally inherited transgenic H19 ICR remained unmethylated in blastocyst-stage embryos derived from Dnmt3l −/− mothers (Fig.…”