Álvarez-Carretero S, Kapli P, Yang Z. Beginner’s guide on the use of PAML to detect positive selection. Mol Biol Evolut. 2023;40(4):msad041. https://doi.org/10.1093/molbev/msad041.

Article  CAS  Google Scholar 

Andrews S, Krueger C, Mellado-Lopez M, Hemberger M, Dean W, Perez-Garcia V, Hanna CW. Mechanisms and function of de novo DNA methylation in placental development reveals an essential role for DNMT3B. Nat Commun. 2023;14(1):371. https://doi.org/10.1038/s41467-023-36019-9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barau J, Teissandier A, Zamudio N, Roy S, Nalesso V, Hérault Y, Guillou F, Bourc’his D. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity. Science. 2016;354(6314):909–12. https://doi.org/10.1126/science.aah5143.

Article  CAS  PubMed  Google Scholar 

Bourc’his D, Bestor TH. Meiotic catastrophe and retrotransposon reactivation in male germ cells lacking Dnmt3L. Nature. 2004;431(7004):96–9. https://doi.org/10.1038/nature02886.

Article  CAS  PubMed  Google Scholar 

Bourc’his D, Xu G-L, Lin C-S, Bollman B, Bestor Timothy H. Dnmt3L and the establishment of maternal genomic imprints. Science. 2001;294(5551):2536–9. https://doi.org/10.1126/science.1065848.

Article  CAS  PubMed  Google Scholar 

Brind’Amour J, Kobayashi H, Richard Albert J, Shirane K, Sakashita A, Kamio A, Bogutz A, Koike T, Karimi MM, Lefebvre L, Kono T, Lorincz MC. LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation. Nat Commun. 2018;9(1):3331–3331. https://doi.org/10.1038/s41467-018-05841-x.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Carter AM. Animal models of human pregnancy and placentation: alternatives to the mouse. Reproduction. 2020;160(6):R129–43. https://doi.org/10.1530/REP-20-0354.

Article  CAS  PubMed  Google Scholar 

Chen Z, Zhang Y. Role of mammalian DNA methyltransferases in development. Annu Rev Biochem. 2020;89(1):135–58. https://doi.org/10.1146/annurev-biochem-103019-102815.

Article  CAS  PubMed  Google Scholar 

Chitwood JL, Burruel VR, Halstead MM, Meyers SA, Ross PJ. Transcriptome profiling of individual rhesus macaque oocytes and preimplantation embryos†. Biol Reprod. 2017;97(3):353–64. https://doi.org/10.1093/biolre/iox114.

Article  PubMed  PubMed Central  Google Scholar 

Ciccone DN, Su H, Hevi S, Gay F, Lei H, Bajko J, Xu G, Li E, Chen T. KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints. Nature. 2009;461(7262):415–8. https://doi.org/10.1038/nature08315.

Article  CAS  PubMed  Google Scholar 

Clarke HJ, Vieux K-F. Epigenetic inheritance through the female germ-line: the known, the unknown, and the possible. Semin Cell Dev Biol. 2015;43:106–16. https://doi.org/10.1016/j.semcdb.2015.07.003.

Article  PubMed  Google Scholar 

Dang Y, Zhu L, Yuan P, Liu Q, Guo Q, Chen X, Gao S, Liu X, Ji S, Yuan Y, Lian Y, Li R, Yan L, Wong CCL, Qiao J. Functional profiling of stage-specific proteome and translational transition across human pre-implantation embryo development at a single-cell resolution. Cell Discov. 2023;9(1):10. https://doi.org/10.1038/s41421-022-00491-2.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Demond H, Kelsey G. The enigma of DNA methylation in the mammalian oocyte [version 1; peer review: 4 approved]. F1000 Res. 2020;9:146. https://doi.org/10.12688/f1000research.21513.1.

Article  CAS  Google Scholar 

Dhayalan A, Rajavelu A, Rathert P, Tamas R, Jurkowska RZ, Ragozin S, Jeltsch A. The Dnmt3a PWWP domain reads histone 3 lysine 36 trimethylation and guides DNA methylation*. J Biol Chem. 2010;285(34):26114–20. https://doi.org/10.1074/jbc.M109.089433.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Duymich CE, Charlet J, Yang X, Jones PA, Liang G. DNMT3B isoforms without catalytic activity stimulate gene body methylation as accessory proteins in somatic cells. Nat Commun. 2016;7(1):11453. https://doi.org/10.1038/ncomms11453.

Article  PubMed  PubMed Central  Google Scholar 

Emperle M, Bangalore DM, Adam S, Kunert S, Heil HS, Heinze KG, Bashtrykov P, Tessmer I, Jeltsch A. Structural and biochemical insight into the mechanism of dual CpG site binding and methylation by the DNMT3A DNA methyltransferase. Nucleic Acids Res. 2021;49(14):8294–308. https://doi.org/10.1093/nar/gkab600.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Franke V, Ganesh S, Karlic R, Malik R, Pasulka J, Horvat F, Kuzman M, Fulka H, Cernohorska M, Urbanova J, Svobodova E, Ma J, Suzuki Y, Aoki F, Schultz RM, Vlahovicek K, Svoboda P. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 2017. https://doi.org/10.1101/gr.216150.116.

Article  PubMed  PubMed Central  Google Scholar 

Gahurova L, Tomizawa S-I, Smallwood SA, Stewart-Morgan KR, Saadeh H, Kim J, Andrews SR, Chen T, Kelsey G. Transcription and chromatin determinants of de novo DNA methylation timing in oocytes. Epigenet Chromatin. 2017;10:25–25. https://doi.org/10.1186/s13072-017-0133-5.

Article  CAS  Google Scholar 

Hanna CW, Demond H, Kelsey G. Epigenetic regulation in development: is the mouse a good model for the human? Hum Reprod Update. 2018;24(5):556–76. https://doi.org/10.1093/humupd/dmy021.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hanna CW, Huang J, Belton C, Reinhardt S, Dahl A, Andrews S, Stewart AF, Kranz A, Kelsey G. Loss of histone methyltransferase SETD1B in oogenesis results in the redistribution of genomic histone 3 lysine 4 trimethylation. Nucleic Acids Res. 2022;50(4):1993–2004. https://doi.org/10.1093/nar/gkac051.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hanna CW, Taudt A, Huang J, Gahurova L, Kranz A, Andrews S, Dean W, Stewart AF, Colomé-Tatché M, Kelsey G. MLL2 conveys transcription-independent H3K4 trimethylation in oocytes. Nat Struct Mol Biol. 2018;25(1):73–82. https://doi.org/10.1038/s41594-017-0013-5.

Article  CAS  PubMed  Google Scholar 

Inoue A. Noncanonical imprinting: intergenerational epigenetic inheritance mediated by Polycomb complexes. Curr Opin Genet Dev. 2023;78:102015. https://doi.org/10.1016/j.gde.2022.102015.

Article  CAS  PubMed  Google Scholar 

Jia D, Jurkowska RZ, Zhang X, Jeltsch A, Cheng X. Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation. Nature. 2007;449(7159):248–51. https://doi.org/10.1038/nature06146.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jin Y, Tam OH, Paniagua E, Hammell M. TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics. 2015;31(22):3593–9. https://doi.org/10.1093/bioinformatics/btv422.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kaneda M, Okano M, Hata K, Sado T, Tsujimoto N, Li E, Sasaki H. Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting. Nature. 2004;429(6994):900–3. https://doi.org/10.1038/nature02633.

Article  CAS  PubMed  Google Scholar 

Kibe K, Shirane K, Ohishi H, Uemura S, Toh H, Sasaki H. The DNMT3A PWWP domain is essential for the normal DNA methylation landscape in mouse somatic cells and oocytes. PLoS Genet. 2021;17(5):e1009570. https://doi.org/10.1371/journal.pgen.1009570.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kobayashi H, Sakurai T, Imai M, Takahashi N, Fukuda A, Yayoi O, Sato S, Nakabayashi K, Hata K, Sotomaru Y, Suzuki Y, Kono T. Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet. 2012;8(1):e1002440. https://doi.org/10.1371/journal.pgen.1002440.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li J-Y, Pu M-T, Hirasawa R, Li B-Z, Huang Y-N, Zeng R, Jing N-H, Chen T, Li E, Sasaki H, Xu G-L. Synergistic function of DNA methyltransferases Dnmt3a and Dnmt3b in the methylation of Oct4 and Nanog. Mol Cell Biol. 2007;27(24):8748–59. https://doi.org/10.1128/MCB.01380-07.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lu X, Zhang Y, Wang L, Wang L, Wang H, Xu Q, Xiang Y, Chen C, Kong F, Xia W, Lin Z, Ma S, Liu L, Wang X, Ni H, Li W, Guo Y, Xie W. Evolutionary epigenomic analyses in mammalian early embryos reveal species-specific innovations and conserved principles of imprinting. Sci Adv. 2021;7(48):eabi6178. https://doi.org/10.1126/sciadv.abi6178.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Madeira F, Pearce M, Tivey ARN, Basutkar P, Lee J, Edbali O, Madhusoodanan N, Kolesnikov A, Lopez R. Search and sequence analysis tools services from EMBL-EBI in 2022. Nucleic Acids Res. 2022. https://doi.org/10.1093/nar/gkac240.

Article  PubMed  PubMed Central  Google Scholar