mRNA isoform switches during mouse zygotic genome activation

References

[1] Jukam D, Shariati SAM, Skotheim JM. Zygotic genome activation in vertebrates. Dev Cell. 2017;42(4):316-332.

[2] Schulz KN, Harrison MM. Mechanisms regulating zygotic genome activation. Nat Rev Genet. 2019;20(4):221-234.

[3] Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol. 2018;19(7):436-450.

[4] Abe KI, Funaya S, Tsukioka D, et al. Minor zygotic gene activation is essential for mouse preimplantation development. Proc Natl Acad Sci U S A. 2018;115(29):E6780-E6788.

[5] Mazin PV, Khaitovich P, Cardoso-Moreira M, Kaessmann H. Alternative splicing during mammalian organ development. Nat Genet. 2021;53(6):925-934.

[6] Baralle FE, Giudice J. Alternative splicing as a regulator of development and tissue identity. Nat Rev Mol Cell Biol. 2017;18(7):437-451.

[7] Wright CJ, Smith CWJ, Jiggins CD. Alternative splicing as a source of phenotypic diversity. Nat Rev Genet. 2022;23(11):697-710.

[8] Kornblihtt AR, Schor IE, Alló M, Dujardin G, Petrillo E, Muñoz MJ. Alternative splicing: a pivotal step between eukaryotic transcription and translation. Nat Rev Mol Cell Biol. 2013;14(3):153-165.

[9] Feng G, Tong M, Xia B, et al. Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage. EMBO Rep. 2016;17(9):1304-1313.

[10] Nepal C, Andersen JB. Alternative promoters in CpG depleted regions are prevalently associated with epigenetic misregulation of liver cancer transcriptomes. Nat Commun. 2023;14(1):2712.

[11] Wang J, Zhang S, Lu H, Xu H. Differential regulation of alternative promoters emerges from unified kinetics of enhancer-promoter interaction. Nat Commun. 2022;13(1):2714.

[12] Hamaya Y, Suzuki A, Suzuki Y, Tsuchihara K, Yamashita R. Classification and characterization of alternative promoters in 26 lung adenocarcinoma cell lines. Jpn J Clin Oncol. 2023;53(2):97-104.

[13] Zhu LY, Zhu YR, Dai DJ, Wang X, Jin HC. Epigenetic regulation of alternative splicing. Am J Cancer Res. 2018;8(12):2346-2358.

[14] Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T. Epigenetics in alternative pre-mRNA splicing. Cell. 2011;144(1):16-26.

[15] Lee Y, Rio DC. Mechanisms and regulation of alternative pre-mRNA splicing. Annu Rev Biochem. 2015;84:291-323.

[16] Li ZK, Wang LY, Wang LB, et al. Generation of bimaternal and bipaternal mice from hypomethylated haploid ESCs with imprinting region deletions. Cell Stem Cell. 2018;23(5):665.e4-676.e4.

[17] Sasaki H, Matsui Y. Epigenetic events in mammalian germ-cell development: reprogramming and beyond. Nat Rev Genet. 2008;9(2):129-140.

[18] Xu Q, Xie W. Epigenome in early mammalian development: inheritance reprogramming and establishment. Trends Cell Biol. 2018;28(3):237-253.

[19] Aanes H, Østrup O, Andersen IS, et al. Differential transcript isoform usage pre- and post-zygotic genome activation in zebrafish. BMC Genomics. 2013;14:331.

[20] Torre D, Francoeur NJ, Kalma Y, et al. Isoform-resolved transcriptome of the human preimplantation embryo. Nat Commun. 2023;14(1):6902.

[21] Xing Y, Yang W, Liu G, et al. Dynamic alternative splicing during mouse preimplantation embryo development. Front Bioeng Biotechnol. 2020;8:35.

[22] Chen J, He Y, Chen L, et al. Differential alternative splicing landscape identifies potentially functional RNA binding proteins in early embryonic development in mammals. iScience. 2024;27:109104.

[23] Gabut M, Samavarchi-Tehrani P, Wang X, et al. An alternative splicing switch regulates embryonic stem cell pluripotency and reprogramming. Cell. 2011;147(1):132-146.

[24] Leng L, Sun J, Huang J, et al. Single-cell transcriptome analysis of uniparental embryos reveals parent-of-origin effects on human preimplantation development. Cell Stem Cell. 2019;25(5):697.e6-697.e712.

[25] Zito A, Roberts AL, Visconti A, et al. Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable. PLoS Genet. 2023;19(2):e1010556.

[26] Trincado JL, Entizne JC, Hysenaj G, et al. SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. Genome Biol. 2018;19(1):40.

[27] Shen S, Park JW, Lu ZX, et al. rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-seq data. Proc Natl Acad Sci U S A. 2014;111(51):E5593-E5601.

[28] Florea L, Song L, Salzberg SL. Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues. F1000Res. 2013;2:188.

[29] Kim P, Yang M, Yiya K, Zhao W, Zhou X. ExonSkipDB: functional annotation of exon skipping event in human. Nucleic Acids Res. 2020;48(D1):D896-D907.

[30] Flemr M, Malik R, Franke V, et al. A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell. 2013;155(4):807-816.

[31] Guo AX, Cui JJ, Wang LY, Yin JY. The role of CSDE1 in translational reprogramming and human diseases. Cell Commun Signal. 2020;18(1):14.

[32] Kakumani PK, Harvey LM, Houle F, Guitart T, Gebauer F, Simard MJ. CSDE1 controls gene expression through the miRNA-mediated decay machinery. Life Sci Alliance. 2020;3(4):e201900632.

[33] Buschauer R, Matsuo Y, Sugiyama T, et al. The Ccr4-not complex monitors the translating ribosome for codon optimality. Science. 2020;368(6488):eaay6912.

[34] Sha QQ, Zhu YZ, Li S, et al. Characterization of zygotic genome activation-dependent maternal mRNA clearance in mouse. Nucleic Acids Res. 2020;48(2):879-894.

[35] Galan A, Rodriguez-Navarro S. Sus1/ENY2: a multitasking protein in eukaryotic gene expression. Crit Rev Biochem Mol Biol. 2012;47(6):556-568.

[36] Yang YW, Flynn RA, Chen Y, et al. Essential role of lncRNA binding for WDR5 maintenance of active chromatin and embryonic stem cell pluripotency. Elife. 2014;3:e02046.

[37] Laptenko O, Shiff I, Freed-Pastor W, et al. The p53 C terminus controls site-specific DNA binding and promotes structural changes within the central DNA binding domain. Mol Cell. 2015;57(6):1034-1046.

[38] Jin XL, O'Neill C. The presence and activation of two essential transcription factors (cAMP response element-binding protein and cAMP-dependent transcription factor ATF1) in the two-cell mouse embryo. Biol Reprod. 2010;82(2):459-468.

[39] Yan L, Yang M, Guo H, et al. Single-cell RNA-seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol. 2013;20(9):1131-1139.

[40] Yuan S, Zhan J, Zhang J, et al. Human zygotic genome activation is initiated from paternal genome. Cell Discov. 2023;9(1):13.

[41] Wang C, Liu X, Gao Y, et al. Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development. Nat Cell Biol. 2018;20(5):620-631.

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