Dynamic changes in histone modifications precede de novo DNA methylation in oocytes

Abstract

Erasure and subsequent reinstatement of DNA methylation in the germline, especially at imprinted CpG islands (CGIs), is crucial to embryogenesis in mammals. The mechanisms underlying DNA methylation establishment remain poorly understood, but a number of post-translational modifications of histones are implicated in antagonizing or recruiting the de novo DNA methylation complex. In mouse oogenesis, DNA methylation establishment occurs on a largely unmethylated genome and in nondividing cells, making it a highly informative model for examining how histone modifications can shape the DNA methylome. Using a chromatin immunoprecipitation (ChIP) and genome-wide sequencing (ChIP-seq) protocol optimized for low cell numbers and novel techniques for isolating primary and growing oocytes, profiles were generated for histone modifications implicated in promoting or inhibiting DNA methylation. CGIs destined for DNA methylation show reduced protective H3K4 dimethylation (H3K4me2) and trimethylation (H3K4me3) in both primary and growing oocytes, while permissive H3K36me3 increases specifically at these CGIs in growing oocytes. Methylome profiling of oocytes deficient in H3K4 demethylase KDM1A or KDM1B indicated that removal of H3K4 methylation is necessary for proper methylation establishment at CGIs. This work represents the first systematic study performing ChIP-seq in oocytes and shows that histone remodeling in the mammalian oocyte helps direct de novo DNA methylation events.

Humanized H19/Igf2 locus reveals diverged imprinting mechanism between mouse and human and reflects Silver–Russell syndrome phenotypes

“…Consequently, the establishment of DNA methylation at hIC1 is inhibited. This finding adds to the growing consensus that H3K4 methylation marks are inhibitory to de novo DNA methylation in the germ line, whereas repressive histone marks do not play major role in the establishment of methylation at ICRs (14,(16)(17)(18)20). However, it is equally possible that the hypomethylated state of DNA attracts H3K4me2 at hIC1 by an unknown mechanism.…”

“…To investigate factors that may inhibit complete establishment of DNA methylation at hIC1 during spermatogenesis, we examined histone posttranslational modifications at hIC1. Parental allelespecific histone modifications have been described at mIC1 in both somatic and germ cells (14)(15)(16)(17)(18). Several studies have suggested an antagonistic relationship between "activating marks," such as dimethylation and trimethylation of histone H3 at lysine 4 (H3K4me2 and H3K4me3, respectively), and DNA methylation (17)(18)(19)(20).…”

“…Parental allelespecific histone modifications have been described at mIC1 in both somatic and germ cells (14)(15)(16)(17)(18). Several studies have suggested an antagonistic relationship between "activating marks," such as dimethylation and trimethylation of histone H3 at lysine 4 (H3K4me2 and H3K4me3, respectively), and DNA methylation (17)(18)(19)(20). Other studies have shown a strong relationship between "repressive marks," such as trimethylation of histone H3 at lysine 9 (H3K9me3), and DNA methylation (21).…”

Blocked transcription through KvDMR1 results in absence of methylation and gene silencing resembling Beckwith-Wiedemann syndrome

“…Although generally not resulting from studies using oocytes, several lines of evidence suggest that transcription through gene bodies and associated intragenic CGI and gDMRs brings about a specific chromatin structure that promotes the binding and action of the DMNT3A/ DMNT3L complex. The model suggests that transcription-coupled recruitment of histone modifying enzymes, such as the H3K4me1/2 demethylase KDM1B and the H3K36 methylase SETD2, yields a chromatin template with unmethylated H3K4 and trimethylated H3K36, histone modifications that are 'preferred' by the DNMT3A/ DNMT3L complex (reviewed by Kelsey and Feil, 2013;Stewart et al, 2015). The number of transcription units and intragenic CGIs that are methylated throughout their gene body in oocytes is far greater than the number of known imprinted gDMRs (Kobayashi et al, 2012;Smallwood et al, 2011).…”

Deconstructing the winding path to the recapitulation of mammalian oogenesis ex vivo

“…For example, this group long ago recognized that the competence to acquire and exercise completion of the process of meiosis took place during the growth phase of oogenesis and required epigenetic modifications in oocyte chromatin (10). Keep in mind that the processes of growth and transcriptional efficiency, coupled to histone modifications required for the expression of housekeeping and maternal effect gene products (11), involve dynamic histone changes that precede imprinting methylations (12). Moreover, these stage-specific methylation marks of both imprinted and nonimprinted varieties control later developmental events bearing directly on implantation and trophectoderm development (13).…”