E2F6 initiates stable epigenetic silencing of germline genes during embryonic development

Thomas Dahlet,Uschi Luz,Peter N Robinson,Jochen Hecht,Johana Chicher,Anaïs F Bardet,Judith Vallet,Peter Hansen,Christian Hagemeier,Matthias Truss,Ghislain Auclair,Michael Weber,Ute Frede,Michael Dumas,Sarah Kottnik,Philippe Hammann,Hala Al Adhami,Gonzalo Alvarez

doi:10.1038/s41467-021-23596-w

Abstract

In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development.

Highlights

In mouse development, long-term silencing by CpG island DNA methylation is targeted to germline genes; the molecular mechanisms of this specificity remain unclear
Gene Ontology (GO) analysis of E2F6-bound gene promoters revealed an enrichment for gene functions associated with cell cycle, DNA replication, response to DNA damage, and meiosis (Supplementary Data 2), which is in line with known functions of E2F6 that binds to genes activated by E2F transcription factors (TFs) during the G1/S transition of the cell cycle[17,35]
Genome-wide studies of DNA methylation during embryonic development revealed that CpG islands (CGIs) promoters are constitutively protected from DNA methylation, whereas de novo DNA methylation is targeted to a small subset of promoter CGIs of germline genes[1,2,3]

Summary

Introduction

Long-term silencing by CpG island DNA methylation is targeted to germline genes; the molecular mechanisms of this specificity remain unclear. We demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNAbinding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development. We investigated the biological functions of E2F6 in the mouse and the hypothesis that E2F6 may play an essential role in initiating long-term epigenetic repression of germline genes during embryogenesis

Methods

Results

Conclusion