Translational regulation plays a pivotal role during pre-implantation development. However, the mechanisms by which messenger RNAs (mRNAs) are selectively regulated over time, along with their dynamic utilization and fate during this period, remain largely unknown. Here, we performed fraction-resolved polysome profiling and characterized translational dynamics across oocytes and early embryo development. This approach allowed us to examine the changes in translation during pre-implantation development in high resolution and uncover previously unrecognized modes of translational selectivity. We observed a stage-specific delay in translation, characterized by the postponed recruitment of stored mRNAs-either unbound or associated with light ribosomal fractions-into actively translating polysomes (heavy fraction). Comparative analysis of translatome with proteomics, RNA N6-methyladenosine modifications, and mRNA features further revealed both coordinated and distinct regulatory mechanisms during pre-implantation development. Furthermore, we identified a eukaryotic initiation factor 1A domain containing 3, Eif1ad3, which is exclusively translated at the two-cell stage and is essential for embryonic development by regulating ribosome biogenesis and protein synthesis. Collectively, our study provides a valuable resource of spatiotemporal translational regulation in mammalian pre-implantation development and highlights a previously uncharacterized translation initiation factor critical for early embryos.

Department of Animal Sciences Institute of Food and Agricultural Sciences University of Florida Gainesville FL 32610 United States

Genetics Institute University of Florida Gainesville FL 32610 United States

Laboratory of Biochemistry and Molecular Biology of Germ Cells Institute of Animal Physiology and Genetics of the Czech Academy of Sciences Libechov 27721 Czech Republic

bioRxiv. 2024 Oct 28:2024.10.28.620693. doi: 10.1101/2024.10.28.620693. PubMed

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Sonenberg  N, Hinnebusch  AG  Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Genes Dev. 2009; 136:418–31. 10.1016/j.cell.2009.01.042. PubMed DOI PMC

Iyyappan  R, Aleshkina  D, Ming  H  et al.  The translational oscillation in oocyte and early embryo development. Nucleic Acids Res. 2023; 51:12076–91. 10.1093/nar/gkad996. PubMed DOI PMC

Yang  G, Xin  Q, Dean  J  Degradation and translation of maternal mRNA for embryogenesis. Trends Genet. 2024; 40:238–49. 10.1016/j.tig.2023.12.008. PubMed DOI

Susor  A, Kubelka  M  Translational regulation in the mammalian oocyte. Results Probl Cell Differ. 2017; 63:257–95. PubMed

Becker  K, Bluhm  A, Casas-Vila  N  et al.  Quantifying post-transcriptional regulation in the development of PubMed DOI PMC

Dang  Y, Zhu  L, Yuan  P  et al.  Functional profiling of stage-specific proteome and translational transition across human pre-implantation embryo development at a single-cell resolution. Cell Discov. 2023; 9:10. 10.1038/s41421-022-00491-2. PubMed DOI PMC

Gao  Y, Liu  X, Tang  B  et al.  Protein expression landscape of mouse embryos during pre-implantation development. Cell Rep. 2017; 21:3957–69. 10.1016/j.celrep.2017.11.111. PubMed DOI

Banliat  C, Mahe  C, Lavigne  R  et al.  The proteomic analysis of bovine embryos developed PubMed DOI PMC

Banliat  C, Mahe  C, Lavigne  R  et al.  Dynamic changes in the proteome of early bovine embryos developed PubMed DOI PMC

Zhang  C, Wang  M, Li  Y  et al.  Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition. Sci Adv. 2022; 8:eabj3967. 10.1126/sciadv.abj3967. PubMed DOI PMC

Xiong  Z, Xu  K, Lin  Z  et al.  Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development. Nat Cell Biol. 2022; 24:968–80. 10.1038/s41556-022-00928-6. PubMed DOI

Masek  T, Del  Llano E, Gahurova  L  et al.  Identifying the translatome of mouse NEBD-stage oocytes via SSP-profiling; a novel polysome fractionation method. Int J Mol Sci. 2020; 21:1254. 10.3390/ijms21041254. PubMed DOI PMC

Zhu  L, Zhou  T, Iyyappan  R  et al.  High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development. 2022; 149: 10.1242/dev.200819. PubMed DOI PMC

Jansova  D, Aleshkina  D, Jindrova  A  et al.  Single molecule RNA localization and translation in the mammalian oocyte and embryo. J Mol Biol. 2021; 433:167166. 10.1016/j.jmb.2021.167166. PubMed DOI

Hamatani  T, Carter  MG, Sharov  AA  et al.  Dynamics of global gene expression changes during mouse preimplantation development. Dev Cell. 2004; 6:117–31. 10.1016/S1534-5807(03)00373-3. PubMed DOI

Teixeira  FK, Lehmann  R  Translational control during developmental transitions. Cold Spring Harb Perspect Biol. 2019; 11: 10.1101/cshperspect.a032987. PubMed DOI PMC

Li  D, Wang  J  Ribosome heterogeneity in stem cells and development. J Cell Biol. 2020; 219:e202001108. 10.1083/jcb.202001108. PubMed DOI PMC

Knott  JG, Gardner  AJ, Madgwick  S  et al.  Calmodulin-dependent protein kinase II triggers mouse egg activation and embryo development in the absence of Ca PubMed DOI

Pakrasi  PL, Dey  SK  Role of calmodulin in blastocyst formation in the mouse. J Reprod Fertil. 1984; 71:513–7. 10.1530/jrf.0.0710513. PubMed DOI

Poueymirou  WT, Schultz  RM  Regulation of mouse preimplantation development: inhibitory effect of the calmodulin antagonist W-7 on the first cleavage. Mol Reprod Dev. 1990; 26:211–6. 10.1002/mrd.1080260303. PubMed DOI

Biziaev  N, Shuvalov  A, Salman  A  et al.  The impact of mRNA poly(A) tail length on eukaryotic translation stages. Nucleic Acids Res. 2024; 52:7792–808. 10.1093/nar/gkae510. PubMed DOI PMC

Mao  Y, Dong  L, Liu  XM  et al.  m(6)A in mRNA coding regions promotes translation via the RNA helicase-containing YTHDC2. Nat Commun. 2019; 10:5332. PubMed PMC

Jain  S, Koziej  L, Poulis  P  et al.  Modulation of translational decoding by m(6)A modification of mRNA. Nat Commun. 2023; 14:4784. 10.1038/s41467-023-40422-7. PubMed DOI PMC

Lee  K, Cho  K, Morey  R  et al.  An extended wave of global mRNA deadenylation sets up a switch in translation regulation across the mammalian oocyte-to-embryo transition. Cell Rep. 2024; 43:113710. 10.1016/j.celrep.2024.113710. PubMed DOI PMC

Wang  Y, Li  Y, Skuland  T  et al.  The RNA m(6)A landscape of mouse oocytes and preimplantation embryos. Nat Struct Mol Biol. 2023; 30:703–9. 10.1038/s41594-023-00969-x. PubMed DOI PMC

Sun  H, Sun  G, Zhang  H  et al.  Proteomic profiling reveals the molecular control of oocyte maturation. Mol Cell Proteomics. 2023; 22:100481. 10.1016/j.mcpro.2022.100481. PubMed DOI PMC

Tanguay  RL, Gallie  DR  Translational efficiency is regulated by the length of the 3' untranslated region. Mol Cell Biol. 1996; 16:146–56. 10.1128/MCB.16.1.146. PubMed DOI PMC

West  JD, Smith  HJ, Vu  LT  et al.  The quantitative impact of 3'UTRs on gene expression. Nucleic Acids Res. 2025; 53:1362–4962. 10.1093/nar/gkaf568. PubMed DOI PMC

Jackson  RJ, Hellen  CU, Pestova  TV  The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol. 2010; 11:113–27. 10.1038/nrm2838. PubMed DOI PMC

Susor  A, Jelinkova  L, Karabinova  P  et al.  Regulation of cap-dependent translation initiation in the early stage porcine parthenotes. Mol Reprod Dev. 2008; 75:1716–25. 10.1002/mrd.20913. PubMed DOI

Schulz  KN, Harrison  MM  Mechanisms regulating zygotic genome activation. Nat Rev Genet. 2019; 20:221–34. 10.1038/s41576-018-0087-x. PubMed DOI PMC

Ozadam  H, Tonn  T, Han  CM  et al.  Single-cell quantification of ribosome occupancy in early mouse development. Nature. 2023; 618:1057–64. 10.1038/s41586-023-06228-9. PubMed DOI PMC

Sachs  A  The role of poly(A) in the translation and stability of mRNA. Curr Opin Cell Biol. 1990; 2:1092–8. 10.1016/0955-0674(90)90161-7. PubMed DOI

Passmore  LA, Tang  TT  The long and short of it. eLife. 2021; 10:e66493. 10.7554/eLife.70757. PubMed DOI PMC

Passmore  LA, Coller  J  Roles of mRNA poly(A) tails in regulation of eukaryotic gene expression. Nat Rev Mol Cell Biol. 2022; 23:93–106. 10.1038/s41580-021-00417-y. PubMed DOI PMC

Clegg  KB, Piko  L  Poly(A) length, cytoplasmic adenylation and synthesis of poly(A)+ RNA in early mouse embryos. Dev Biol. 1983; 95:331–41. 10.1016/0012-1606(83)90034-9. PubMed DOI

Xiang  K, Ly  J, Bartel  DP  Control of poly(A)-tail length and translation in vertebrate oocytes and early embryos. Dev Cell. 2024; 59:1058–1074. 10.1016/j.devcel.2024.02.007. PubMed DOI

Fierro  L, Ishii  A, Aoyama  H  et al.  Comprehensive analysis of mRNA 3' ends during early zebrafish development reveals dynamics of 3'UTR changes on a genome-wide scale. FEBS Lett. 2025; 2129–41. 10.1002/1873-3468.70106. PubMed DOI

Lamacova  L, Jansova  D, Jiang  Z  et al.  CPEB3 maintains developmental competence of the oocyte. Cells. 2024; 13:850–68. 10.3390/cells13100850. PubMed DOI PMC

Paulson  EE, Fishman  EL, Schultz  RM  et al.  Embryonic microRNAs are essential for bovine preimplantation embryo development. Proc Natl Acad Sci USA. 2022; 119:e2212942119. 10.1073/pnas.2212942119. PubMed DOI PMC

Liu  Y, Sun  J, Su  Y  et al.  Nuclear-localized eukaryotic translation initiation factor 1A is involved in mouse preimplantation embryo development. J Mol Histol. 2021; 52:965–73. 10.1007/s10735-021-10014-0. PubMed DOI

Sadato  D, Ono  T, Gotoh-Saito  S  et al.  Eukaryotic translation initiation factor 3 (eIF3) subunit e is essential for embryonic development and cell proliferation. FEBS Open Bio. 2018; 8:1188–201. 10.1002/2211-5463.12482. PubMed DOI PMC

Yang  G, Xin  Q, Feng  I  et al.  Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation. Genes Dev. 2023; 37:418–31. 10.1101/gad.350400.123. PubMed DOI PMC