Abstract
Metabolic regulation is critical in embryonic development and influences key processes such as fertilization, zygotic genome activation, cell compaction, implantation, gastrulation and organ development. Here we explore the interplay between metabolism and embryonic development in the context of important sequential key embryonic events, highlighting the orchestration of developmental processes by various metabolites and signalling molecules. Key metabolites, including glucose, fatty acids and amino acids, act as modulators of developmental processes, while also serving as energy sources and building blocks for cellular structures. Understanding the intricate relationship between metabolism and embryogenesis may provide insights into developmental disorders and potential therapeutic interventions.
This is a preview of subscription content, access via your institution
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
$32.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
$259.00 per year
only $21.58 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to the full article PDF.
USD 39.95
Prices may be subject to local taxes which are calculated during checkout




Similar content being viewed by others
References
Boyer, L. A. et al. Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122, 947–956 (2005).
Chen, B. et al. Maternal inheritance of glucose intolerance via oocyte TET3 insufficiency. Nature 605, 761–766 (2022).
Sharpley, M. S., Chi, F., Hoeve, J. T. & Banerjee, U. Metabolic plasticity drives development during mammalian embryogenesis. Dev. Cell 56, 2329–2347 e2326 (2021).
Zhao, J. et al. Metabolic remodelling during early mouse embryo development. Nat. Metab. 3, 1372–1384 (2021).
Perez-Ramirez, C. A. et al. Atlas of fetal metabolism during mid-to-late gestation and diabetic pregnancy. Cell 187, 204–215 e214 (2024).
Brown, J. J. & Whittingham, D. G. The roles of pyruvate, lactate and glucose during preimplantation development of embryos from F1 hybrid mice in vitro. Development 112, 99–105 (1991).
Wales, R. G. et al. The metabolism of specifically labelled lactate and pyruvate by two-cell mouse embryos. J. Reprod. Fertil. 33, 207–222 (1973).
Li, J. et al. Metabolic control of histone acetylation for precise and timely regulation of minor ZGA in early mammalian embryos. Cell Discov. 8, 96 (2022).
Zhao, J. et al. Dynamic metabolism during early mammalian embryogenesis. Development 150, dev202148 (2023).
Cao, D. et al. Selective utilization of glucose metabolism guides mammalian gastrulation. Nature 634, 919–928 (2024).
Bulusu, V. et al. Spatiotemporal analysis of a glycolytic activity gradient linked to mouse embryo mesoderm development. Dev. Cell 40, 331–341 (2017).
Ng, S.-F. et al. Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring. Nature 467, 963–966 (2010).
Heard, E. & Martienssen, R. A. Transgenerational epigenetic inheritance: myths and mechanisms. Cell 157, 95–109 (2014).
Li, C. et al. Amylin receptor insensitivity impairs hypothalamic POMC neuron differentiation in the male offspring of maternal high-fat diet-fed mice. Mol. Metab. 44, 101135 (2021).
Biggers, J. D., Whittingham, D. G. & Donahue, R. P. The pattern of energy metabolism in the mouse oöcyte and zygote. Proc. Natl Acad. Sci. USA 58, 560–567 (1967).
Nagaraj, R. et al. Nuclear localization of mitochondrial TCA cycle enzymes as a critical step in mammalian zygotic genome activation. Cell 168, 210–223 (2017).
Conaghan, J., Handyside, A. H., Winston, R. M. & Leese, H. J. Effects of pyruvate and glucose on the development of human preimplantation embryos in vitro. J. Reprod. Fertil. 99, 87–95 (1993).
Baumann, C. G., Morris, D. G., Sreenan, J. M. & Leese, H. J. The quiet embryo hypothesis: molecular characteristics favoring viability. Mol. Reprod. Dev. 74, 1345–1353 (2007).
Brinster, R. L. Incorporation of carbon from glucose and pyruvate into the preimplantation mouse embryo. Exp. Cell. Res. 58, 153–158 (1969).
Ross, J. M. et al. High brain lactate is a hallmark of aging and caused by a shift in the lactate dehydrogenase A/B ratio. Proc. Natl Acad. Sci. USA 107, 20087–20092 (2010).
Doherty, J. R. & Cleveland, J. L. Targeting lactate metabolism for cancer therapeutics. J. Clin. Investig. 123, 3685–3692 (2013).
Veech, R. L. et al. The ‘great’ controlling nucleotide coenzymes. IUBMB Life 71, 565–579 (2019).
Streffer, C., Elias, S. & van Beuningen, D. Influence of NAD+ on development of mouse blastocysts in vitro. Nature 250, 434–435 (1974).
Intlekofer, A. M. et al. l-2-hydroxyglutarate production arises from noncanonical enzyme function at acidic pH. Nat. Chem. Biol. 13, 494–500 (2017).
Oldham, W. M., Clish, C. B., Yang, Y. & Loscalzo, J. Hypoxia-mediated increases in l-2-hydroxyglutarate coordinate the metabolic response to reductive stress. Cell Metab. 22, 291–303 (2015).
Intlekofer, A. M. et al. Hypoxia induces production of l-2-hydroxyglutarate. Cell Metab. 22, 304–311 (2015).
Hamatani, T., Carter, M. G., Sharov, A. A. & Ko, M. S. Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell 6, 117–131 (2004).
Wang, Q. T. et al. A genome-wide study of gene activity reveals developmental signaling pathways in the preimplantation mouse embryo. Dev. Cell 6, 133–144 (2004).
Li, J. et al. Lactate regulates major zygotic genome activation by H3K18 lactylation in mammals. Natl Sci. Rev. 11, nwad295 (2024).
Zhang, D. et al. Metabolic regulation of gene expression by histone lactylation. Nature 574, 575–580 (2019).
Mouchiroud, L. et al. The NAD+/sirtuin pathway modulates longevity through activation of mitochondrial UPR and FOXO signaling. Cell 154, 430–441 (2013).
Haigis, M. C. & Sinclair, D. A. Mammalian sirtuins: biological insights and disease relevance. Annu. Rev. Pathol. 5, 253–295 (2010).
Wang, M., Chen, Z. & Zhang, Y. CBP/p300 and HDAC activities regulate H3K27 acetylation dynamics and zygotic genome activation in mouse preimplantation embryos. EMBO J. 41, e112012 (2022).
Liu, B. et al. Mapping putative enhancers in mouse oocytes and early embryos reveals TCF3/12 as key folliculogenesis regulators. Nat. Cell Biol. 26, 962–974 (2024).
Lane, M. & Gardner, D. K. Mitochondrial malate-aspartate shuttle regulates mouse embryo nutrient consumption. J. Biol. Chem. 280, 18361–18367 (2005).
Houghton, F. D., Thompson, J. G., Kennedy, C. J. & Leese, H. J. Oxygen consumption and energy metabolism of the early mouse embryo. Mol. Reprod. Dev. 44, 476–485 (1996).
Martin, K. L. & Leese, H. J. Role of glucose in mouse preimplantation embryo development. Mol. Reprod. Dev. 40, 436–443 (1995).
Rossant, J. Genetic control of early cell lineages in the mammalian embryo. Annu. Rev. Genet. 52, 185–201 (2018).
White, M. D., Zenker, J., Bissiere, S. & Plachta, N. Instructions for assembling the early mammalian embryo. Dev. Cell 45, 667–679 (2018).
Chi, F., Sharpley, M. S., Nagaraj, R., Roy, S. S. & Banerjee, U. Glycolysis-independent glucose metabolism distinguishes TE from ICM fate during mammalian embryogenesis. Dev. Cell 53, 9–26 e24 (2020).
Tu, W. B., Christofk, H. R. & Plath, K. Nutrient regulation of development and cell fate decisions. Development 150, dev199961 (2023).
Cornacchia, D. et al. Lipid deprivation induces a stable, naive-to-primed intermediate state of pluripotency in human PSCs. Cell Stem Cell 25, 120–136 (2019).
Aizawa, R. et al. Synthesis and maintenance of lipid droplets are essential for mouse preimplantation embryonic development. Development 146, dev181925 (2019).
Mau, K. H. T. et al. Dynamic enlargement and mobilization of lipid droplets in pluripotent cells coordinate morphogenesis during mouse peri-implantation development. Nat. Commun. 13, 3861 (2022).
Liu, K. & Czaja, M. J. Regulation of lipid stores and metabolism by lipophagy. Cell Death Differ 20, 3–11 (2013).
Zhang, S. et al. The regulation, function and role of lipophagy, a form of selective autophagy, in metabolic disorders. Cell Death Dis. 13, 132 (2022).
Zhang, L. et al. Low-input lipidomics reveals lipid metabolism remodelling during early mammalian embryo development. Nat. Cell Biol. 26, 278–293 (2024).
Murphy, B. D. Under arrest: the embryo in diapause. Dev. Cell 52, 139–140 (2020).
Hamatani, T. et al. Global gene expression analysis identifies molecular pathways distinguishing blastocyst dormancy and activation. Proc. Natl Acad. Sci. USA 101, 10326–10331 (2004).
Fenelon, J. C., Banerjee, A. & Murphy, B. D. Embryonic diapause: development on hold. Int. J. Dev. Biol. 58, 163–174 (2014).
Hussein, A. M. et al. Metabolic control over mTOR-dependent diapause-like state. Dev. Cell 52, 236–250 e237 (2020).
van der Weijden, V. A. et al. FOXO1-mediated lipid metabolism maintains mammalian embryos in dormancy. Nat. Cell Biol. 26, 181–193 (2024).
Lee, J.-E. et al. Autophagy regulates embryonic survival during delayed implantation. Endocrinology 152, 2067–2075 (2011).
He, B. et al. Blastocyst activation engenders transcriptome reprogram affecting X-chromosome reactivation and inflammatory trigger of implantation. Proc. Natl Acad. Sci. USA 116, 16621–16630 (2019).
Bulut-Karslioglu, A. et al. Inhibition of mTOR induces a paused pluripotent state. Nature 540, 119–123 (2016).
Scognamiglio, R. et al. Myc depletion induces a pluripotent dormant state mimicking diapause. Cell 164, 668–680 (2016).
Shaw, R. J. et al. The tumor suppressor LKB1 kinase directly activates AMP-activated kinase and regulates apoptosis in response to energy stress. Proc. Natl Acad. Sci. USA 101, 3329–3335 (2004).
Iyer, D. P. et al. mTOR activity paces human blastocyst stage developmental progression. Cell 187, 6566–6583 (2024).
Ye, Q., Zeng, X., Cai, S., Qiao, S. & Zeng, X. Mechanisms of lipid metabolism in uterine receptivity and embryo development. Trends Endocrinol. Metab. 32, 1015–1030 (2021).
Yang, T., Zhao, J., Liu, F. & Li, Y. Lipid metabolism and endometrial receptivity. Hum. Reprod. Update 28, 858–889 (2022).
Fattahi, A. et al. Effects of dietary omega-3 and -6 supplementations on phospholipid fatty acid composition in mice uterus during window of pre-implantation. Theriogenology 108, 97–102 (2018).
Vasquez, Y. M. & DeMayo, F. J. Role of nuclear receptors in blastocyst implantation. Semin. Cell Dev. Biol. 24, 724–735 (2013).
Sun, X. & Dey, S. K. Aspects of endocannabinoid signaling in periimplantation biology. Mol. Cell. Endocrinol. 286, S3–S11 (2008).
Lu, Y. et al. Excessive lipid peroxidation in uterine epithelium causes implantation failure and pregnancy loss. Adv. Sci. (Weinh.) 11, e2302887 (2024).
Ruane, P. T. et al. Glucose influences endometrial receptivity to embryo implantation through O-GlcNAcylation-mediated regulation of the cytoskeleton. Am. J. Physiol. Cell Physiol. 327, C634–C645 (2024).
Ruane, P. T. et al. Protein O-GlcNAcylation promotes trophoblast differentiation at implantation. Cells 9, 2246 (2020).
Zhang, H. et al. O-GlcNAc modification mediates aquaporin 3 to coordinate endometrial cell glycolysis and affects embryo implantation. J. Adv. Res. 37, 119–131 (2022).
Van Winkle, L. J., Tesch, J. K., Shah, A. & Campione, A. L. System B0,+ amino acid transport regulates the penetration stage of blastocyst implantation with possible long-term developmental consequences through adulthood. Hum. Reprod. Update 12, 145–157 (2006).
Van Winkle, L. J. Amino acid transport regulation and early embryo development. Biol. Reprod. 64, 1–12 (2001).
Hubaud, A. & Pourquié, O. Signalling dynamics in vertebrate segmentation. Nat. Rev. Mol. Cell Biol. 15, 709–721 (2014).
Dequéant, M.-L. & Pourquié, O. Segmental patterning of the vertebrate embryonic axis. Nat. Rev. Genet. 9, 370–382 (2008).
Oginuma, M. et al. A gradient of glycolytic activity coordinates FGF and Wnt signaling during elongation of the body axis in amniote embryos. Dev. Cell 40, 342–353.e10 (2017).
Solmonson, A. et al. Compartmentalized metabolism supports midgestation mammalian development. Nature 604, 349–353 (2022).
Øyen, N. et al. Prepregnancy diabetes and offspring risk of congenital heart disease: a nationwide cohort study. Circulation 133, 2243–2253 (2016).
Lázaro, J. et al. A stem cell zoo uncovers intracellular scaling of developmental tempo across mammals. Cell Stem Cell 30, 938–949 (2023).
Matsuda, M. et al. Recapitulating the human segmentation clock with pluripotent stem cells. Nature 580, 124–129 (2020).
Diaz-Cuadros, M. et al. Metabolic regulation of species-specific developmental rates. Nature 613, 550–557 (2023).
Yost, R. A. & Enke, C. G. Triple quadrupole mass spectrometry for direct mixture analysis and structure elucidation. Anal. Chem. 51, 1251–1264 (1979).
Sarafian, M. H. et al. Objective set of criteria for optimization of sample preparation procedures for ultra-high throughput untargeted blood plasma lipid profiling by ultra performance liquid chromatography-mass spectrometry. Anal. Chem. 86, 5766–5774 (2014).
Lam, S. M. et al. A multi-omics investigation of the composition and function of extracellular vesicles along the temporal trajectory of COVID-19. Nat. Metab. 3, 909–922 (2021).
Zhu, H. et al. Moderate UV exposure enhances learning and memory by promoting a novel glutamate biosynthetic pathway in the brain. Cell 173, 1716–1727 e1717 (2018).
Cao, J. et al. Deciphering the metabolic heterogeneity of hematopoietic stem cells with single-cell resolution. Cell Metab. 36, 209–221 e206 (2024).
Shi, L. et al. Mid-infrared metabolic imaging with vibrational probes. Nat. Methods 17, 844–851 (2020).
Wei, L. et al. Super-multiplex vibrational imaging. Nature 544, 465–470 (2017).
Perevedentseva, E., Krivokharchenko, A., Karmenyan, A. V., Chang, H.-H. & Cheng, C.-L. Raman spectroscopy on live mouse early embryo while it continues to develop into blastocyst in vitro. Sci. Rep. 9, 6636 (2019).
Huang, J. et al. Lipid metabolic heterogeneity during early embryogenesis revealed by hyper-3D stimulated Raman imaging. Chem. Biomed. Imaging 3, 15–24 (2025).
Bradley, J. et al. Quantitative imaging of lipids in live mouse oocytes and early embryos using CARS microscopy. Development 143, 2238–2247 (2016).
Zhang, X., Dorlhiac, G., Landry, M. P. & Streets, A. Phototoxic effects of nonlinear optical microscopy on cell cycle, oxidative states and gene expression. Sci. Rep. 12, 18796 (2022).
Ottosen, L. D. M., Hindkjaer, J. & Ingerslev, J. Light exposure of the ovum and preimplantation embryo during ART procedures. J. Assist Reprod. Genet. 24, 99–103 (2007).
Alexandrov, T. Spatial metabolomics: from a niche field towards a driver of innovation. Nat. Metab. 5, 1443–1445 (2023).
Chandrasekaran, S. et al. Comprehensive mapping of pluripotent stem cell metabolism using dynamic genome-scale network modeling. Cell Rep. 21, 2965–2977 (2017).
Lin, D. W., Zhang, L., Zhang, J. & Chandrasekaran, S. Inferring metabolic objectives and trade-offs in single cells during embryogenesis. Cell Syst 16, 101164 (2024).
Zhai, J., Xiao, Z., Wang, Y. & Wang, H. Human embryonic development: from peri-implantation to gastrulation. Trends Cell Biol. 32, 18–29 (2022).
Ji, S. et al. OBOX regulates mouse zygotic genome activation and early development. Nature 620, 1047–1053 (2023).
De Iaco, A. et al. DUX-family transcription factors regulate zygotic genome activation in placental mammals. Nat. Genet. 49, 941–945 (2017).
Hendrickson, P. G. et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat. Genet. 49, 925–934 (2017).
Whiddon, J. L., Langford, A. T., Wong, C.-J., Zhong, J. W. & Tapscott, S. J. Conservation and innovation in the DUX4-family gene network. Nat. Genet. 49, 935–940 (2017).
Lee, S. H., Liu, X., Jimenez-Morales, D. & Rinaudo, P. F. Murine blastocysts generated by in vitro fertilization show increased Warburg metabolism and altered lactate production. eLife 11, e79153 (2022).
Jia, Y. et al. Melatonin supplementation in the culture medium rescues impaired glucose metabolism in IVF mice offspring. J. Pineal Res. 72, e12778 (2022).
Gardner, D. K. & Leese, H. J. The role of glucose and pyruvate transport in regulating nutrient utilization by preimplantation mouse embryos. Development 104, 423–429 (1988).
Fu, J. et al. Non-invasive metabolomic profiling of day 3 embryo culture media using near-infrared spectroscopy to assess the development potential of embryos. Acta Biochim. Biophys. Sin. (Shanghai) 45, 1074–1078 (2013).
Botros, L., Sakkas, D. & Seli, E. Metabolomics and its application for non-invasive embryo assessment in IVF. Mol. Hum. Reprod. 14, 679–690 (2008).
Agarwal, A., Gupta, S. & Sharma, R. K. Role of oxidative stress in female reproduction. Reprod. Biol. Endocrinol. 3, 28 (2005).
Guérin, P., El Mouatassim, S. & Ménézo, Y. Oxidative stress and protection against reactive oxygen species in the pre-implantation embryo and its surroundings. Hum. Reprod. Update 7, 175–189 (2001).
Dunning, K. R. et al. Beta-oxidation is essential for mouse oocyte developmental competence and early embryo development. Biol. Reprod. 83, 909–918 (2010).
Abe, H. et al. Fine structure of bovine morulae and blastocysts in vivo and in vitro. Anat. Embryol. (Berl.) 199, 519–527 (1999).
de Andrade Melo-Sterza, F. & Poehland, R. Lipid metabolism in bovine oocytes and early embryos under in vivo, in vitro, and stress conditions. Int. J. Mol. Sci. 22, 3421 (2021).
Ren, L. et al. Dynamic comparisons of high-resolution expression profiles highlighting mitochondria-related genes between in vivo and in vitro fertilized early mouse embryos. Hum. Reprod. 30, 2892–2911 (2015).
Belli, M. et al. Oxygen concentration alters mitochondrial structure and function in in vitro fertilized preimplantation mouse embryos. Hum. Reprod. 34, 601–611 (2019).
Rhon-Calderon, E. A. et al. Trophectoderm biopsy of blastocysts following IVF and embryo culture increases epigenetic dysregulation in a mouse model. Hum. Reprod. 39, 154–176 (2024).
Rodriguez-Terrones, D. et al. A distinct metabolic state arises during the emergence of 2-cell-like cells. EMBO Rep. 21, e48354 (2020).
Teslaa, T. & Teitell, M. A. Pluripotent stem cell energy metabolism: an update. EMBO J. 34, 138–153 (2015).
Zhang, J. et al. Metabolism in pluripotent stem cells and early mammalian development. Cell Metab. 27, 332–338 (2018).
Zhang, J., Nuebel, E., Daley, G. Q., Koehler, C. M. & Teitell, M. A. Metabolic regulation in pluripotent stem cells during reprogramming and self-renewal. Cell Stem Cell 11, 589–595 (2012).
Folmes, C. D. L. et al. Somatic oxidative bioenergetics transitions into pluripotency-dependent glycolysis to facilitate nuclear reprogramming. Cell Metab. 14, 264–271 (2011).
Author information
Authors and Affiliations
Contributions
J.Z. conceived, supervised and revised the Review, Y.X. completed all the writing and drawing, and W.X. provided valuable suggestions and revised the Review.
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing interests.
Peer review
Peer review information
Nature Cell Biology thanks Qingran Kong and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Additional information
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Xu, Y., Xie, W. & Zhang, J. Metabolic regulation of key developmental events during mammalian embryogenesis. Nat Cell Biol 27, 1219–1229 (2025). https://doi.org/10.1038/s41556-025-01720-y
Received:
Accepted:
Published:
Version of record:
Issue date:
DOI: https://doi.org/10.1038/s41556-025-01720-y


