DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells

Abstract

DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de novo methylation during embryogenesis, which is mainly mediated by DNMT3B. How DNMT3L regulates DNA methylation and what determines its functional specificity are not well understood. Here we show that DNMT3L-deficient mouse embryonic stem cells (mESCs) exhibit downregulation of DNMT3A, especially DNMT3A2, the predominant DNMT3A isoform in mESCs. DNA methylation analysis of DNMT3L-deficient mESCs reveals hypomethylation at many DNMT3A target regions. These results confirm that DNMT3L is a positive regulator of DNA methylation, contrary to a previous report that, in mESCs, DNMT3L regulates DNA methylation positively or negatively, depending on genomic regions. Mechanistically, DNMT3L forms a complex with DNMT3A2 and prevents DNMT3A2 from being degraded. Restoring the DNMT3A protein level in DNMT3L-deficient mESCs partially recovers DNA methylation. Thus, our work uncovers a role for DNMT3L in maintaining DNMT3A stability, which contributes to the effect of DNMT3L on DNMT3A-dependent DNA methylation.

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

“…For instance, a previous study has demonstrated that DNMT3L modulates cellular de novo methylation activities through focusing the DNA methylation machineries on wellchromatinized DNA templates 32 . In addition, despite that structural analysis of both DNMT3B-DNA and DNMT3A-DNA complexes reveals that DNMT3L does not directly engage in the DNA interaction, the role of DNMT3L in stimulating the enzymatic activity and/or stability of DNMT3A and DNMT3B has been well established [6][7][8]42,45 , which may attenuate the impact of the intrinsic sequence specificities of these enzymes on the landscape of DNA methylation 32 . How the intrinsic preferences of DNMT3A and DNMT3B interplay with other cellular factors in regulating genomic DNA methylation awaits further investigation.…”

DNA Methylation Reprogramming during Mammalian Development

“…DNMT3L substantially stimulates the catalytic activity of DNMT3A and DNMT3B in vitro [59,60,61]. Recent work suggests that DNMT3L is also involved in maintaining DNMT3A stability [62]. In addition, the ADD domain of DNMT3L binds H3K4me0 and likely plays a role in determining the specificity of DNMT3A-mediated DNA methylation [63].…”

Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation

“…DNMT3A and DNMT3B mediate DNA methylation establishment during gametogenesis and embryogenesis [16,87], and subsequently participate in methylation maintenance [88,89,90]. The enzymatic activity of DNMT3A/3B in germ cells and embryonic stem cells is further regulated by DNMT3-like (DNMT3L) protein, which lacks DNA methylation activity but functions to stimulate the cofactor binding and enzymatic activity of DNMT3A/3B [7,91,92,93] and to maintain DNMT3A stability in cells [94]. DNMT3A and DNMT3B are highly related in sequence, both containing a largely disordered NTD, followed by a Pro-Trp-Trp-Pro (PWWP) domain, an Atrx-Dnmt3-Dnmt3l (ADD) domain and a highly homologous MTase domain (Figure 1).…”