Repression of germline genes by PRC1.6 and SETDB1 in the early embryo precedes DNA methylation-mediated silencing

• Published in: Nature communications Vol. 12; no. 1; pp. 7020 - 15
• Main Authors: Mochizuki, Kentaro, Sharif, Jafar, Shirane, Kenjiro, Uranishi, Kousuke, Bogutz, Aaron B., Janssen, Sanne M., Suzuki, Ayumu, Okuda, Akihiko, Koseki, Haruhiko, Lorincz, Matthew C.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 02-12-2021; Nature Publishing Group; Nature Portfolio
• Subjects: 13/106; 13/31; 38/1; 38/15; 38/39; 42/100; 45; 631/136/2086/1986; 631/208/176/2016; 631/208/177; Animals; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - genetics; Basic Helix-Loop-Helix Leucine Zipper Transcription Factors - metabolism; Basic Helix-Loop-Helix Transcription Factors - genetics; Basic Helix-Loop-Helix Transcription Factors - metabolism; Binding; Deoxyribonucleic acid; DNA; DNA Methylation; E2F6 Transcription Factor - genetics; E2F6 Transcription Factor - metabolism; Embryo cells; Embryo Implantation; Embryo, Mammalian; Embryos; Epigenesis, Genetic; Female; Gene Expression Regulation, Developmental; Gene Silencing; Genes; Genes, Reporter; Genomes; Green Fluorescent Proteins - genetics; Green Fluorescent Proteins - metabolism; Histone-Lysine N-Methyltransferase - genetics; Histone-Lysine N-Methyltransferase - metabolism; Histones; Histones - genetics; Histones - metabolism; Humanities and Social Sciences; Implantation; Male; Methyltransferase; Mice; Mice, Inbred C57BL; Mice, Transgenic; Mouse Embryonic Stem Cells - cytology; Mouse Embryonic Stem Cells - metabolism; multidisciplinary; Polycomb Repressive Complex 1 - genetics; Polycomb Repressive Complex 1 - metabolism; Polycomb-Group Proteins - genetics; Polycomb-Group Proteins - metabolism; Protein Subunits - genetics; Protein Subunits - metabolism; Science; Science (multidisciplinary); Signal Transduction; Stem cells; Ubiquitin-Protein Ligases - genetics; Ubiquitin-Protein Ligases - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-27345-x

Silencing of a subset of germline genes is dependent upon DNA methylation (DNAme) post-implantation. However, these genes are generally hypomethylated in the blastocyst, implicating alternative repressive pathways before implantation. Indeed, in embryonic stem cells (ESCs), an overlapping set of genes, including germline “genome-defence” (GGD) genes, are upregulated following deletion of the H3K9 methyltransferase SETDB1 or subunits of the non-canonical PRC1 complex PRC1.6. Here, we show that in pre-implantation embryos and naïve ESCs (nESCs), hypomethylated promoters of germline genes bound by the PRC1.6 DNA-binding subunits MGA/MAX/E2F6 are enriched for RING1B-dependent H2AK119ub1 and H3K9me3. Accordingly, repression of these genes in nESCs shows a greater dependence on PRC1.6 than DNAme. In contrast, GGD genes are hypermethylated in epiblast-like cells (EpiLCs) and their silencing is dependent upon SETDB1, PRC1.6/RING1B and DNAme, with H3K9me3 and DNAme establishment dependent upon MGA binding. Thus, GGD genes are initially repressed by PRC1.6, with DNAme subsequently engaged in post-implantation embryos.
Germline genes are repressed by DNA methylation and histone marks. Here, the authors show that specific germline genes hypomethylated pre-implantation are enriched for PRC1.6, H2AK119ub1 and H3K9me3, which coordinately repress their expression.