The enigma of DNA methylation in the mammalian oocyte

Abstract

The mammalian genome experiences profound setting and resetting of epigenetic patterns during the life-course. This is understood best for DNA methylation: the specification of germ cells, gametogenesis, and early embryo development are characterised by phases of widespread erasure and rewriting of methylation. While mitigating against intergenerational transmission of epigenetic information, these processes must also ensure correct genomic imprinting that depends on faithful and long-term memory of gamete-derived methylation states in the next generation. This underscores the importance of understanding the mechanisms of methylation programming in the germline. De novo methylation in the oocyte is of particular interest because of its intimate association with transcription, which results in a bimodal methylome unique amongst mammalian cells. Moreover, this methylation landscape is entirely set up in a non-dividing cell, making the oocyte a fascinating model system in which to explore mechanistic determinants of methylation. Here, we summarise current knowledge on the oocyte DNA methylome and how it is established, focussing on recent insights from knockout models in the mouse that explore the interplay between methylation and chromatin states. We also highlight some remaining paradoxes and enigmas, in particular the involvement of non-nuclear factors for correct de novo methylation.

Keywords: DNA methylation; chromatin; oocyte.

Figure 1.. Schematic depicting the typical DNA methylation pattern of fully grown oocytes over active gene bodies and distribution of associated chromatin marks.

While H3K36me3 is enriched over methylated domains, H3K27me3 and H3K9me2 are enriched in unmethylated domains. H3K4me3 has an unusual pattern in the oocyte in that peaks can be found at both active and inactive gene promoters (dark red) as well as enrichment over broad domains in untranscribed regions (light red). H3K27me3 is also broadly distributed over non-transcribed regions in oocytes but generally mutually exclusive to H3K4me3.

Figure 2.. Models showing chromatin factors involved in DNA methyltransferase (DNMT) 3A/DNMT3L recruitment in methylated regions and factors inhibiting DNMT3A/DNMT3L binding at unmethylated regions.

A) At actively transcribed gene bodies, SETD2-mediated H3K36me3 has been proposed to recruit DNMT3A/DNMT3L, whilst lysine demethylase 1B (KDM1B) seems to be required to prevent or remove histone 3 lysine 4 (H3K4) methylation. DNMT1 is needed for methylation of hemimethylated DNA. B) Ubiquitin-like, plant homeodomain and ring finger-containing 1 (UHRF1) is required for intermediate DNA methylation of some genic and intergenic regions, likely by recruiting one of the DNMT proteins, but the chromatin requirements are unknown. C) At active promoters, H3K4me3 is thought to prevent DNMT3A/DNMT3L binding. D) Transcriptionally inactive regions can be marked by mixed lineage leukaemia-2 protein (MLL2)-mediated H3K4me3 and/or polycomb repressive complex 2 (PRC2)-mediated H3K27me3, preventing recruitment of DNMT3A/DNMT3L to these regions. EED, embryonic ectoderm development; EZHIP, EZH inhibitory protein; SETD2, SET domain containing 2.

Figure 3.. The role of STELLA in regulating methylation in the oocyte.

In the oocyte, STELLA is required for the cytoplasmic localisation of the majority of DNA methyltransferase 1 (DNMT1)/ubiquitin-like, plant homeodomain and ring finger-containing 1 (UHRF1). Ablation of STELLA results in UHRF1/DNMT1 redistribution into the nucleus, resulting in increased DNA methylation at regions that are normally unmethylated. KO, knockout.