Zhao, B. S., Roundtree, I. A. & He, C. Post-transcriptional gene regulation by mRNA modifications. Nat. Rev. Mol. Cell Biol. 18, 31–42 (2017).
Article CAS PubMed Google Scholar
Zaccara, S., Ries, R. J. & Jaffrey, S. R. Reading, writing and erasing mRNA methylation. Nat. Rev. Mol. Cell Biol. 20, 608–624 (2019).
Article CAS PubMed Google Scholar
Klungland, A., Dahl, J. A., Greggains, G., Fedorcsak, P. & Filipczyk, A. Reversible RNA modifications in meiosis and pluripotency. Nat. Methods 14, 18–22 (2016).
Dominissini, D. et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 485, 201–206 (2012).
Article CAS PubMed Google Scholar
Meyer, K. D. et al. Comprehensive analysis of mRNA methylation reveals enrichment in 3′ UTRs and near stop codons. Cell 149, 1635–1646 (2012).
Article CAS PubMed PubMed Central Google Scholar
Atlasi, Y. & Stunnenberg, H. G. The interplay of epigenetic marks during stem cell differentiation and development. Nat. Rev. Genet. 18, 643–658 (2017).
Article CAS PubMed Google Scholar
Dahl, J. A. et al. Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition. Nature 537, 548–552 (2016).
Article CAS PubMed PubMed Central Google Scholar
Sui, X. et al. METTL3-mediated m6A is required for murine oocyte maturation and maternal-to-zygotic transition. Cell Cycle 19, 391–404 (2020).
Article CAS PubMed PubMed Central Google Scholar
Falco, G. et al. Zscan4: a novel gene expressed exclusively in late 2-cell embryos and embryonic stem cells. Dev. Biol. 307, 539–550 (2007).
Article CAS PubMed PubMed Central Google Scholar
Marikawa, Y. & Alarcon, V. B. Establishment of trophectoderm and inner cell mass lineages in the mouse embryo. Mol. Reprod. Dev. 76, 1019–1032 (2009).
Article CAS PubMed PubMed Central Google Scholar
Batista, P. J. et al. m6A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell Stem Cell 15, 707–719 (2014).
Article CAS PubMed PubMed Central Google Scholar
Wang, Y. et al. N6-methyladenosine modification destabilizes developmental regulators in embryonic stem cells. Nat. Cell Biol. 16, 191–198 (2014).
Article CAS PubMed PubMed Central Google Scholar
Geula, S. et al. m6A mRNA methylation facilitates resolution of naive pluripotency toward differentiation. Science 347, 1002–1006 (2015).
Article CAS PubMed Google Scholar
Jin, K. X. et al. N6-methyladenosine (m6A) depletion regulates pluripotency exit by activating signaling pathways in embryonic stem cells. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.2105192118 (2021).
Oron, E. & Ivanova, N. Cell fate regulation in early mammalian development. Phys. Biol. 9, 045002 (2012).
Ivanova, I. et al. The RNA m6A reader YTHDF2 is essential for the post-transcriptional regulation of the maternal transcriptome and oocyte competence. Mol. Cell 67, 1059–1067 e1054 (2017).
Article CAS PubMed PubMed Central Google Scholar
Li, M. et al. Ythdf2-mediated m6A mRNA clearance modulates neural development in mice. Genome Biol. 19, 69 (2018).
Article PubMed PubMed Central Google Scholar
Lasman, L. et al. Context-dependent functional compensation between Ythdf m6A reader proteins. Genes Dev. 34, 1373–1391 (2020).
Article CAS PubMed PubMed Central Google Scholar
Sha, Q. Q. et al. Characterization of zygotic genome activation-dependent maternal mRNA clearance in mouse. Nucleic Acids Res. 48, 879–894 (2020).
Article CAS PubMed Google Scholar
Mu, H. et al. METTL3-mediated mRNA N6-methyladenosine is required for oocyte and follicle development in mice. Cell Death Dis. 12, 989 (2021).
Article CAS PubMed PubMed Central Google Scholar
Chen, T. et al. m6A RNA methylation is regulated by microRNAs and promotes reprogramming to pluripotency. Cell Stem Cell 16, 289–301 (2015).
Article CAS PubMed Google Scholar
Yang, Q. et al. Highly sensitive sequencing reveals dynamic modifications and activities of small RNAs in mouse oocytes and early embryos. Sci. Adv. 2, e1501482 (2016).
Article PubMed PubMed Central Google Scholar
Deniz, O., Frost, J. M. & Branco, M. R. Regulation of transposable elements by DNA modifications. Nat. Rev. Genet. 20, 417–431 (2019).
Article CAS PubMed Google Scholar
Franke, V. et al. Long terminal repeats power evolution of genes and gene expression programs in mammalian oocytes and zygotes. Genome Res. 27, 1384–1394 (2017).
Article CAS PubMed PubMed Central Google Scholar
Chen, C. et al. Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos. Protein Cell 12, 455–474 (2021).
Article CAS PubMed PubMed Central Google Scholar
Liu, J. et al. The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity. Nature 591, 322–326 (2021).
Article CAS PubMed Google Scholar
Chelmicki, T. et al. m6A RNA methylation regulates the fate of endogenous retroviruses. Nature 591, 312–316 (2021).
Article CAS PubMed Google Scholar
Xu, W. et al. METTL3 regulates heterochromatin in mouse embryonic stem cells. Nature 591, 317–321 (2021).
Article CAS PubMed Google Scholar
Xiong, F. et al. RNA m6A modification orchestrates a LINE-1–host interaction that facilitates retrotransposition and contributes to long gene vulnerability. Cell Res. 31, 861–885 (2021).
Article CAS PubMed PubMed Central Google Scholar
Lanciano, S. & Cristofari, G. Measuring and interpreting transposable element expression. Nat. Rev. Genet. 21, 721–736 (2020).
Article CAS PubMed Google Scholar
Svoboda, P. Why mouse oocytes and early embryos ignore miRNAs? RNA Biol. 7, 559–563 (2010).
Article CAS PubMed PubMed Central Google Scholar
DeVeale, B., Swindlehurst-Chan, J. & Blelloch, R. The roles of microRNAs in mouse development. Nat. Rev. Genet. 22, 307–323 (2021).
Article CAS PubMed Google Scholar
Marcel, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal https://doi.org/10.14806/ej.17.1.200 (2011).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Article CAS PubMed PubMed Central Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Article PubMed PubMed Central Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
Article CAS PubMed PubMed Central Google Scholar
Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015).
Article CAS PubMed PubMed Central Google Scholar
Wu, Z. et al. NormExpression: an R package to normalize gene expression data using evaluated methods. Front. Genet. 10, 400 (2019).
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