Wang, L. et al. Programming and inheritance of parental DNA methylomes in mammals. Cell 157, 979–991 (2014).
Smith, Z. D. et al. DNA methylation dynamics of the human preimplantation embryo. Nature 511, 611–615 (2014).
Xia, W. et al. Resetting histone modifications during human parental-to-zygotic transition. Science 365, 353–360 (2019).
Cantone, I. & Fisher, A. G. Epigenetic programming and reprogramming during development. Nat. Struct. Mol. Biol. 20, 282–289 (2013).
Reik, W. Stability and flexibility of epigenetic gene regulation in mammalian development. Nature 447, 425–432 (2007).
Xiang, Y. et al. Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency. Nat. Genet. 52, 95–105 (2019).
Smith, Z. D., Sindhu, C. & Meissner, A. Molecular features of cellular reprogramming and development. Nat. Rev. Mol. Cell Biol. 17, 139–154 (2016).
Yamanaka, S. & Blau, H. M. Nuclear reprogramming to a pluripotent state by three approaches. Nature 465, 704–712 (2010).
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).
Maenohara, S. et al. Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos. PLoS Genet. 13, e1007042 (2017).
von Meyenn, F. et al. Impairment of DNA methylation maintenance is the main cause of global demethylation in naive embryonic stem cells. Mol. Cell 62, 848–861 (2016).
Funaki, S. et al. Inhibition of maintenance DNA methylation by Stella. Biochem. Biophys. Res. Commun. 453, 455–460 (2014).
Li, Y. et al. Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1. Nature 564, 136–140 (2018).
Mulholland, C. B. et al. Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive demethylation in mammals. Preprint at bioRxiv https://doi.org/10.1101/321604 (2020).
Leitch, H. G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat. Struct. Mol. Biol. 20, 311–316 (2013).
Hackett, J. A. et al. Synergistic mechanisms of DNA demethylation during transition to ground-state pluripotency. Stem Cell Rep. 1, 518–531 (2013).
Amouroux, R. et al. De novo DNA methylation drives 5hmC accumulation in mouse zygotes. Nat. Cell Biol. 18, 225–233 (2016).
Jachowicz, J. W. et al. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo. Nat. Genet. 49, 1502–1510 (2017).
Chow, J. C. et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141, 956–969 (2010).
Percharde, M. et al. A LINE1-Nucleolin partnership regulates early development and ESC identity. Cell 174, 391–405 (2018).
Garcia-Perez, J. L., Widmann, T. J. & Adams, I. R. The impact of transposable elements on mammalian development. Development 143, 4101–4114 (2016).
Rodriguez-Terrones, D. & Torres-Padilla, M. E. Nimble and ready to mingle: transposon outbursts of early development. Trends Genet. 34, 806–820 (2018).
Stelzer, Y., Shivalila, C. S., Soldner, F., Markoulaki, S. & Jaenisch, R. Tracing dynamic changes of DNA methylation at single-cell resolution. Cell 163, 218–229 (2015).
Marks, H. et al. The transcriptional and epigenomic foundations of ground state pluripotency. Cell 149, 590–604 (2012).
Walter, M., Teissandier, A., Perez-Palacios, R. & Bourc’his, D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. Elife 5, e11418 (2016).
Hackett, J. A., Kobayashi, T., Dietmann, S. & Surani, M. A. Activation of lineage regulators and transposable elements across a pluripotent spectrum. Stem Cell Rep. 8, 1645–1658 (2017).
Sharif, J. et al. Activation of endogenous retroviruses in Dnmt1
−/− ESCs involves disruption of SETDB1-mediated repression by NP95 binding to hemimethylated DNA. Cell Stem Cell 19, 81–94 (2016).
Doench, J. G. et al. Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184–191 (2016).
Nady, N. et al. ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. Elife 4, e10150 (2015).
Tu, S. et al. Co-repressor CBFA2T2 regulates pluripotency and germline development. Nature 534, 387–390 (2016).
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).
Li, C., Scott, D. A., Hatch, E., Tian, X. & Mansour, S. L. Dusp6 (Mkp3) is a negative feedback regulator of FGF-stimulated ERK signaling during mouse development. Development 134, 167–176 (2007).
Dornan, D. et al. The ubiquitin ligase COP1 is a critical negative regulator of p53. Nature 429, 86–92 (2004).
Vaisvila, R. et al. EM-seq: detection of DNA methylation at single base resolution from picograms of DNA. Preprint at bioRxiv https://doi.org/10.1101/2019.12.20.884692 (2019).
Ooi, S. K. et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448, 714–717 (2007).
Guo, X. et al. Structural insight into autoinhibition and histone H3-induced activation of DNMT3A. Nature 517, 640–644 (2015).
De Iaco, A., Coudray, A., Duc, J. & Trono, D. DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells. EMBO Rep. 20, e47382 (2019).
Brumbaugh, J. et al. Nudt21 controls cell fate by connecting alternative polyadenylation to chromatin signaling. Cell 172, 106–120 (2018).
Choi, J. et al. Prolonged Mek1/2 suppression impairs the developmental potential of embryonic stem cells. Nature 548, 219–223 (2017).
Choi, J. et al. DUSP9 modulates DNA hypomethylation in female mouse pluripotent stem cells. Cell Stem Cell 20, 706–719 (2017).
Hamilton, W. B. et al. Dynamic lineage priming is driven via direct enhancer regulation by ERK. Nature 575, 355–360 (2019).
Eckersley-Maslin, M. et al. Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program. Genes Dev. 33, 194–208 (2019).
Hernandez, C. et al. Dppa2/4 facilitate epigenetic remodeling during reprogramming to pluripotency. Cell Stem Cell. 23, 396–411 (2018).
Nakamura, T., Nakagawa, M., Ichisaka, T., Shiota, A. & Yamanaka, S. Essential roles of ECAT15-2/Dppa2 in functional lung development. Mol. Cell. Biol. 31, 4366–4378 (2011).
Engelen, E. et al. Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry. Nat. Commun. 6, 7155 (2015).
Eckersley-Maslin, M. A. et al. Dppa2/4 target chromatin bivalency enabling multi-lineage commitment. Preprint at bioRxiv https://doi.org/10.1101/832873 (2019).
Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell Biol. 16, 519–532 (2015).
Noh, K. M. et al. Engineering of a histone-recognition domain in Dnmt3a alters the epigenetic landscape and phenotypic features of mouse ESCs. Mol. Cell 59, 89–103 (2015).
Boulard, M., Edwards, J. R. & Bestor, T. H. FBXL10 protects Polycomb-bound genes from hypermethylation. Nat. Genet. 47, 479–485 (2015).
Reddington, J. P. et al. Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes. Genome Biol. 14, R25 (2013).
Lindroth, A. M. et al. Antagonism between DNA and H3K27 methylation at the imprinted Rasgrf1 locus. PLoS Genet. 4, e1000145 (2008).
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Kano, H. et al. L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism. Genes Dev. 23, 1303–1312 (2009).
Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).
Borowiak, M. et al. Small molecules efficiently direct endodermal differentiation of mouse and human embryonic stem cells. Cell Stem Cell 4, 348–358 (2009).
Hackett, J. A. et al. Tracing the transitions from pluripotency to germ cell fate with CRISPR screening. Nat. Commun. 9, 4292 (2018).
Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).
Chen, B. H. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479–1491 (2013).
Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Li, W. et al. MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biol. 15, 554 (2014).
Berrens, R. V. et al. An endosiRNA-based repression mechanism counteracts transposon activation during global DNA demethylation in embryonic stem cells. Cell Stem Cell 21, 694–703 (2017).
Huang, D. W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).