Much like a set of helping hands can guide, support, and protect a toddler taking their first steps, the guiding force of epigenetics during embryonic development ensures genome stability and supports healthy development by regulating the expression of key genes.
Such genes include DNA methylation-sensitive “germline genome-defense” genes, which undergo DNA demethylation and become expressed in primordial germ cells (PGCs), which eventually give rise to sperm and eggs. Previous studies have described how DNA methylation deposited by DNMT3A/3B, H3K9me3 deposited by SETDB1, and H2AK119ub1 deposited by RING1A/B (subunits of the non-canonical PRC1 complex PRC1.6) repressed germline genes at other development stages (where their expression could be deleterious); however, we lacked an understanding at what specific developmental stages each epigenetic “baby-step” occurred and how each step interconnected to ensure silencing of these CpG island promoter-driven genes.
To answer these questions, researchers led by Matthew Lorincz (University of British Columbia, Canada) characterized the epigenetic baby-steps taken by the developing early mouse embryo and an in vitro model system in which naïve embryonic stem cells (nESC) can be differentiated into epiblast-like cells (EpiLC) and then PGC-like cells, to describe the critical mechanisms involved in the regulation of germline genome-defense genes.
So, let’s go step-by-step through this exciting new study from Mochizuki and colleagues:
- CpG island promoters of germline genome-defense genes bound by the PRC1.6 DNA-binding subunits MGA/MAX/E2F6 display enrichment for RING1B-dependent H2AK119ub1 followed by H3K9me3 and H3K27me3 in preimplantation embryos and naïve ESCs (nESCs possess no differentiation bias, representing cells at a preimplantation stage of development)
- Like most genes, the CpG island promoters of these genes lack DNA methylation at this stage
- These findings show that gene repression in the preimplantation embryo depends on PRC1.6 (which directs both H2AK119ub1 and H3K9me3) to a greater degree than DNA methylation
- Germline genome-defense genes exhibit an increase in DNA methylation levels in the epiblast of post-implantation embryos as well as in EpiLCs (representing the post-implantation developmental stage)
- Gene silencing at this stage depends on PRC1.6/RING1B, SETDB1, and DNMT3A/3B, with H3K9me3 and DNA methylation reliant on MGA binding
- Thus, while PRC1.6 initially represses germline genome-defense genes during preimplantation development, DNA methylation subsequently engages at post-implantation stages
The authors suggest that the atypical combination of H2AK119ub1 and H3K9me3, which generally mark distinct genomic regions, silences germline genome-defense genes by targeting their CpG island promoters during early development, thanks to the all-important guiding influence of PRC1.6; meanwhile, DNA methylation plays a role in their silencing later in development, where the expression of these genes could have deleterious consequences.
First author Kentaro Mochizuki shares, “Our study shows that different repressive mechanisms orchestrated by PRC1.6 orderly emerge, creating a multilayered ‘safety net’ that represses germline genes. Since the orthologs of PRC1.6 subunits, as well as SETDB1, have recently been reported to be involved in germline gene repression in Drosophila and C. elegans, H2AK119ub1 and H3K9 methylation seem to play an ancestral role in silencing of germline genes in metazoans, with DNA methylation engaged in the process in mammals only after implantation.” Senior author Matthew Lorincz concludes, “This study clearly shows that epigenetic marks typically found in distinct genomic regions are sequentially established at the promoters of germline genes during early embryonic development to maintain them in a repressed state, with DNA methylation engaged in the process only after implantation. Why germline genes, in particular those involved in genomic defense, are subject to such multilayered repression remains an open question.”