Transient Polycomb activity represses developmental genes in growing oocytes

Abstract

Background Non-genetic disease inheritance and offspring phenotype are substantially influenced by germline epigenetic programming, including genomic imprinting. Loss of Polycomb Repressive Complex 2 (PRC2) function in oocytes causes non-genetically inherited effects on offspring, including embryonic growth restriction followed by post-natal offspring overgrowth. While PRC2-dependent non-canonical imprinting is likely to contribute, less is known about germline epigenetic programming of non-imprinted genes during oocyte growth. In addition, de novo germline mutations in genes encoding PRC2 lead to overgrowth syndromes in human patients, but the extent to which PRC2 activity is conserved in human oocytes is poorly understood. Results In this study, we identify a discrete period of early oocyte growth during which PRC2 is expressed in mouse growing oocytes. Deletion of Eed during this window led to the de-repression of 343 genes. A high proportion of these were developmental regulators, and the vast majority were not imprinted genes. Many of the de-repressed genes were also marked by the PRC2-dependent epigenetic modification histone 3 lysine 27 trimethylation (H3K27me3) in primary–secondary mouse oocytes, at a time concurrent with PRC2 expression. In addition, we found H3K27me3 was also enriched on many of these genes by the germinal vesicle (GV) stage in human oocytes, strongly indicating that this PRC2 function is conserved in the human germline. However, while the 343 genes were de-repressed in mouse oocytes lacking EED, they were not de-repressed in pre-implantation embryos and lost H3K27me3 during pre-implantation development. This implies that H3K27me3 is a transient feature that represses a wide range of genes in oocytes. Conclusions Together, these data indicate that EED has spatially and temporally distinct functions in the female germline to repress a wide range of developmentally important genes and that this activity is conserved in the mouse and human germlines.

Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth

“…While loss of EED in oocytes disrupts H3K27me3 imprints ( Hanna and Kelsey, 2021 ; Inoue et al, 2017 ), our data suggest that other genes may also be affected, perhaps through altered DNA methylation ( Jarred et al, 2022 ). We, therefore, analysed DNA methylation in placentas of E17.5 female WT-wt, HET-het, and HET-hom offspring using RRBS.…”

“…Heterozygous offspring generated from Eed heterozygous oocytes (HET-het offspring) or from Eed homozygous null oocytes (HET-hom offspring) are isogenic. However, the HET-hom offspring were generated from oocytes that completely lacked functional EED and the HET-het offspring were generated from oocytes that had one functional copy of EED and maintained essentially normal gene repression ( Prokopuk et al, 2018 ; Jarred et al, 2022 ). As they are isogenic and heterozygous for Eed , comparison of HET-hom with HET-het offspring allowed the identification of differences that resulted specifically from a loss of EED in oocytes in the absence of confounding genetic differences ( Figure 1A ).…”

“…However, we found that while preimplantation development progressed at similar rates in embryos from Eed wild-type and Eed -null oocytes, blastocysts derived from Eed- null oocytes contained low cell numbers, primarily due to fewer inner cell mass cells. This deficit may be due to low cell proliferation during pre-implantation development caused by loss of EED-dependent oocyte programming or to loss of maternal EED supplied in the mature oocyte ( Inoue et al, 2017 ; Inoue et al, 2018 ; Jarred et al, 2022 ; Harris et al, 2019 ; Erhardt et al, 2003 ). While the latter is consistent with the established role of PRC2 in driving cell division in stem cells and other cell types ( Bracken et al, 2003 ), other EED-dependent effects in the oocyte may also contribute.…”

“… During oocyte growth, all three subunits of polycomb repressive complex 2 (PRC2) are present at the primary to secondary stages, which is important for the silencing of developmental genes and Histone 3 Lysine 27 trimethylation (H3K27me3)-dependent imprinting ( Inoue et al, 2017 ; Inoue et al, 2018 ; Matoba et al, 2022 ; Jarred et al, 2022 ). Deletion of Eed in oocyte results in loss of maternal H3K27me3 and PRC2, early growth restriction, followed by placental hyperplasia and late gestation fetal catch-up growth, outcomes consistent with loss of H3K27me3-dependent imprinting observed in SCNT offspring ( Matoba et al, 2018 ; Inoue et al, 2020 ; Wang et al, 2020 ).…”