Boyes, J. & Bird, A. Repression of genes by DNA methylation depends on CpG density and promoter strength: evidence for involvement of a methyl-CpG binding protein. EMBO J. 11, 327–333 (1992).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet. 39, 457–466 (2007).

Article  PubMed  CAS  Google Scholar 

Mikkelsen, T. S. et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448, 553–560 (2007).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hawkins, R. D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479–491 (2010).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Reddington, J. P. et al. Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol. 14, R25 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Holoch, D. et al.A cis-acting mechanism mediates transcriptional memory at Polycomb target genes in mammals. Nat. Genet. 53, 1686–1697 (2021).

Article  PubMed  CAS  Google Scholar 

Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).

Article  PubMed  CAS  Google Scholar 

Faust, C., Schumacher, A., Holdener, B. & Magnuson, T. The eed mutation disrupts anterior mesoderm production in mice. Development 121, 273–285 (1995).

Article  PubMed  CAS  Google Scholar 

Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).

Article  PubMed  CAS  Google Scholar 

O’Carroll, D. et al. The Polycomb-group gene Ezh2 is required for early mouse development. Mol. Cell. Biol. 21, 4330–4336 (2001).

Article  PubMed  PubMed Central  Google Scholar 

Grosswendt, S. et al. Epigenetic regulator function through mouse gastrulation. Nature 584, 102–108 (2020).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Reddington, J. P., Sproul, D. & Meehan, R. R. DNA methylation reprogramming in cancer: does it act by re-configuring the binding landscape of Polycomb repressive complexes? Bioessays 36, 134–140 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Wassef, M. & Margueron, R. The multiple facets of PRC2 alterations in cancers. J. Mol. Biol. 429, 1978–1993 (2017).

Article  PubMed  CAS  Google Scholar 

Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. Nat. Rev. Mol. Cell Biol. 20, 590–607 (2019).

Article  PubMed  CAS  Google Scholar 

Tanay, A., O’Donnell, A. H., Damelin, M. & Bestor, T. H. Hyperconserved CpG domains underlie Polycomb-binding sites. Proc. Natl Acad. Sci. USA 104, 5521–5526 (2007).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Brinkman, A. B. et al. Sequential ChIP–bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk. Genome Res. 22, 1128–1138 (2012).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Statham, A. L. et al. Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA. Genome Res. 22, 1120–1127 (2012).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Bird, A., Taggart, M., Frommer, M., Miller, O. J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated, CpG-rich DNA. Cell 40, 91–99 (1985).

Article  PubMed  CAS  Google Scholar 

Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 15, 979–991 (2014).

Article  Google Scholar 

Zheng, H. et al. Resetting epigenetic memory by reprogramming of histone modifications in mammals. Mol. Cell 63, 1066–1079 (2016).

Article  PubMed  CAS  Google Scholar 

Liu, X. et al. Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos. Nature 537, 558–562 (2016).

Article  PubMed  CAS  Google Scholar 

Cooper, S. et al. Targeting Polycomb to pericentric heterochromatin in embryonic stem cells reveals a role for H2AK119u1 in PRC2 recruitment. Cell Rep. 7, 1456–1470 (2014).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).

Article  PubMed  CAS  Google Scholar 

Chen, H. et al. H3K36 dimethylation shapes the epigenetic interaction landscape by directing repressive chromatin modifications in embryonic stem cells. Genome Res. 32, 825–837 (2022).

PubMed  PubMed Central  Google Scholar 

Tsumura, A. et al. Maintenance of self‐renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805–814 (2006).

Article  PubMed  CAS  Google Scholar 

Montgomery, N. D. et al. The murine Polycomb group protein Eed is required for global histone H3 lysine-27 methylation. Curr. Biol. 15, 942–947 (2005).

Article  PubMed  CAS  Google Scholar 

Smith, A. Formative pluripotency: the executive phase in a developmental continuum. Development 144, 365–373 (2017).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Kolodziejczyk, A. A. et al. Single cell RNA-sequencing of pluripotent states unlocks modular transcriptional variation. Cell Stem Cell 17, 471–485 (2015).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Hayashi, K., Ohta, H., Kurimoto, K., Aramaki, S. & Saitou, M. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146, 519–532 (2011).

Article  PubMed  CAS  Google Scholar 

Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).

Article  PubMed  PubMed Central  CAS  Google Scholar 

Habibi, E. et al. Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell 13, 360–369 (2013).

Article  PubMed