Li, W. et al. Androgenetic haploid embryonic stem cells produce live transgenic mice. Nature 490, 407–411 (2012).
Yang, H. et al. Generation of genetically modified mice by oocyte injection of androgenetic haploid embryonic stem cells. Cell 149, 605–617 (2012).
Li, W. et al. Genetic modification and screening in rat using haploid embryonic stem cells. Cell Stem Cell 14, 404–414 (2014).
Lin, J. C. & Van Eenennaam, A. L. Electroporation-mediated genome editing of livestock zygotes. Front. Genet. 12, 648482 (2021).
Hai, T., Teng, F., Guo, R., Li, W. & Zhou, Q. One-step generation of knockout pigs by zygote injection of CRISPR/Cas system. Cell Res. 24, 372–375 (2014).
He, W., Chen, J. & Gao, S. Mammalian haploid stem cells: establishment, engineering and applications. Cell. Mol. Life Sci. 76, 2349–2367 (2019).
Elling, U. et al. Forward and reverse genetics through derivation of haploid mouse embryonic stem cells. Cell Stem Cell 9, 563–574 (2011).
Lu, J. et al. Structure-activity relationship studies of small-molecule inhibitors of Wnt response. Bioorg. Med. Chem. Lett. 19, 3825–3827 (2009).
Huang, S. M. et al. Tankyrase inhibition stabilizes axin and antagonizes Wnt signalling. Nature 461, 614–620 (2009).
Smith, A. Formative pluripotency: the executive phase in a developmental continuum. Development 144, 365–373 (2017).
Graf, A. et al. Fine mapping of genome activation in bovine embryos by RNA sequencing. Proc. Natl Acad. Sci. USA 111, 4139–4144 (2014).
Jiang, Z. et al. Transcriptional profiles of bovine in vivo pre-implantation development. BMC Genomics 15, 756 (2014).
Bogliotti, Y. S. et al. Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts. Proc. Natl Acad. Sci. USA 115, 2090–2095 (2018).
Zhao, L. et al. Establishment of bovine expanded potential stem cells. Proc. Natl Acad. Sci. USA 118, e2018505118 (2021).
Zhong, C. et al. CRISPR-Cas9-mediated genetic screening in mice with haploid embryonic stem cells carrying a guide RNA library. Cell Stem Cell 17, 221–232 (2015).
Yang, L., Song, L., Liu, X., Bai, L. & Li, G. KDM6A and KDM6B play contrasting roles in nuclear transfer embryos revealed by MERVL reporter system. EMBO Rep. 19, e46240 (2018).
Czernik, M., Iuso, D., Toschi, P., Khochbin, S. & Loi, P. Remodeling somatic nuclei via exogenous expression of protamine 1 to create spermatid-like structures for somatic nuclear transfer. Nat. Protoc. 11, 2170–2188 (2016).
He, W. et al. Reduced self-diploidization and improved survival of semi-cloned mice produced from androgenetic haploid embryonic stem cells through overexpression of Dnmt3b. Stem Cell Rep. 10, 477–493 (2018).
Anzalone, A. V. et al. Search-and-replace genome editing without double-strand breaks or donor DNA. Nature 576, 149–157 (2019).
Rodgers, B. D. & Garikipati, D. K. Clinical, agricultural, and evolutionary biology of myostatin: a comparative review. Endocr. Rev. 29, 513–534 (2008).
Irie, N. et al. SOX17 is a critical specifier of human primordial germ cell fate. Cell 160, 253–268 (2015).
Ishii, T. & Pera, R. A. Creating human germ cells for unmet reproductive needs. Nat. Biotechnol. 34, 470–473 (2016).
Hwang, Y. S. et al. Reconstitution of prospermatogonial specification in vitro from human induced pluripotent stem cells. Nat. Commun. 11, 5656 (2020).
He, Z. Q. et al. Generation of mouse haploid somatic cells by small molecules for genome-wide genetic screening. Cell Rep. 20, 2227–2237 (2017).
Takahashi, S. et al. Induction of the G2/M transition stabilizes haploid embryonic stem cells. Development 141, 3842–3847 (2014).
Gao, G. et al. Transcriptome-wide analysis of the SCNT bovine abnormal placenta during mid- to late gestation. Sci. Rep. 9, 20035 (2019).
Cheng, R. et al. Modification of alternative splicing in bovine somatic cell nuclear transfer embryos using engineered CRISPR-Cas13d. Sci. China Life Sci. 65, 2257–2268 (2022).
Kinoshita, M. et al. Pluripotent stem cells related to embryonic disc exhibit common self-renewal requirements in diverse livestock species. Development 148, dev199901 (2021).
Kim, H. et al. Modulation of beta-catenin function maintains mouse epiblast stem cell and human embryonic stem cell self-renewal. Nat. Commun. 4, 2403 (2013).
Ross, P. J. & Cibelli, J. B. Bovine somatic cell nuclear transfer. Methods Mol. Biol. 636, 155–177 (2010).
Zhang, J. et al. Dissecting the molecular features of bovine-arrested eight-cell embryos using single-cell multi-omics sequencingdagger. Biol. Reprod. 108, 871–886 (2023).
Alberio, R., Motlik, J., Stojkovic, M., Wolf, E. & Zakhartchenko, V. Behavior of M-phase synchronized blastomeres after nuclear transfer in cattle. Mol. Reprod. Dev. 57, 37–47 (2000).
German, S. D., Lee, J. H., Campbell, K. H., Sweetman, D. & Alberio, R. Actin depolymerization is associated with meiotic acceleration in cycloheximide-treated ovine oocytes. Biol. Reprod. 92, 103 (2015).
Yang, L. et al. Transient Dux expression facilitates nuclear transfer and induced pluripotent stem cell reprogramming. EMBO Rep. 21, e50054 (2020).
Zhou, Q. et al. Generation of fertile cloned rats by regulating oocyte activation. Science 302, 1179 (2003).
Furusawa, T. et al. Characteristics of bovine inner cell mass-derived cell lines and their fate in chimeric conceptuses. Biol. Reprod. 89, 28 (2013).
Ying, Q. L. et al. The ground state of embryonic stem cell self-renewal. Nature 453, 519–523 (2008).
Takashima, Y. et al. Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158, 1254–1269 (2014).
Theunissen, T. W. et al. Systematic identification of culture conditions for induction and maintenance of naive human pluripotency. Cell Stem Cell 15, 471–487 (2014).
Bao, S. et al. Derivation of hypermethylated pluripotent embryonic stem cells with high potency. Cell Res. 28, 22–34 (2018).
Yang, Y. et al. Derivation of pluripotent stem cells with in vivo embryonic and extraembryonic potency. Cell 169, 243–257 (2017).
Yang, J. et al. Establishment of mouse expanded potential stem cells. Nature 550, 393–397 (2017).
Gao, X. et al. Establishment of porcine and human expanded potential stem cells. Nat. Cell Biol. 21, 687–699 (2019).
Vilarino, M. et al. Derivation of sheep embryonic stem cells under optimized conditions. Reproduction 160, 761–772 (2020).
Oh, S. K. et al. Methods for expansion of human embryonic stem cells. Stem Cells 23, 605–609 (2005).
De Los Angeles, A., Okamura, D. & Wu, J. Highly efficient derivation of pluripotent stem cells from mouse preimplantation and postimplantation embryos in serum-free conditions. Methods Mol. Biol. 2005, 29–36 (2019).
Ludwig, T. E. et al. Feeder-independent culture of human embryonic stem cells. Nat. Methods 3, 637–646 (2006).
Zhang, X. M. et al. In vitro expansion of human sperm through nuclear transfer. Cell Res. 30, 356–359 (2020).
Zhong, C. et al. Generation of human haploid embryonic stem cells from parthenogenetic embryos obtained by microsurgical removal of male pronucleus. Cell Res. 26, 743–746 (2016).
Elling, U. et al. Derivation and maintenance of mouse haploid embryonic stem cells. Nat. Protoc. 14, 1991–2014 (2019).
Shirasawa, A. et al. Efficient derivation of embryonic stem cells and primordial germ cell-like cells in cattle. J. Reprod. Dev. 70, 82–95 (2024).
Ross, P. J. et al. Activation of bovine somatic cell nuclear transfer embryos by PLCZ cRNA injection. Reproduction 137, 427–437 (2009).
Owen, J. R. et al. One-step generation of a targeted knock-in calf using the CRISPR-Cas9 system in bovine zygotes. BMC Genomics 22, 118 (2021).
Bustin, S. A. et al. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55, 611–622 (2009).
Hajkova, P. et al. DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. Methods Mol. Biol. 200, 143–154 (2002).
Xie, Y. et al. An episomal vector-based CRISPR/Cas9 system for highly efficient gene knockout in human pluripotent stem cells. Sci. Rep. 7, 2320 (2017).
Chow, R. D., Chen, J. S., Shen, J. & Chen, S. A web tool for the design of prime-editing guide RNAs. Nat. Biomed. Eng. 5, 190–194 (2021).
Palazzese, L., Czernik, M., Iuso, D., Toschi, P. & Loi, P. Nuclear quiescence and histone hyper-acetylation jointly improve protamine-mediated nuclear remodeling in sheep fibroblasts. PLoS ONE 13, e0193954 (2018).
Grobet, L. et al. A deletion in the bovine myostatin gene causes the double-muscled phenotype in cattle. Nat. Genet. 17, 71–74 (1997).
Clop, A. et al. A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat. Genet. 38, 813–818 (2006).
Chen, Y., Spitzer, S., Agathou, S., Karadottir, R. T. & Smith, A. Gene editing in rat embryonic stem cells to produce in vitro models and in vivo reporters. Stem Cell Rep. 9, 1262–1274 (2017).
Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res. 42, e168 (2014).
Patch, A. M. et al. Whole-genome characterization of chemoresistant ovarian cancer. Nature 521, 489–494 (2015).
Xie, C. & Tammi, M. T. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10, 80 (2009).
Shen, H. et al. Mouse totipotent stem cells captured and maintained through spliceosomal repression. Cell 184, 2843–2859 (2021).
Kaya-Okur, H. S. et al. CUT&Tag for efficient epigenomic profiling of small samples and single cells. Nat. Commun. 10, 1930 (2019).
Trapnell, C., Pachter, L. & Salzberg, S. L. TopHat: discovering splice junctions with RNA-seq. Bioinformatics 25, 1105–1111 (2009).
Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).
Huang da, W., Sherman, B. T. & Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4, 44–57 (2009).
Zhao, T. et al. Single-cell RNA-seq reveals dynamic early embryonic-like programs during chemical reprogramming. Cell Stem Cell 23, 31–45 (2018).
Peng, G. et al. Spatial transcriptome for the molecular annotation of lineage fates and cell identity in Mid-gastrula Mouse Embryo. Dev. Cell 36, 681–697 (2016).
Zhi, M. et al. Generation and characterization of stable pig pregastrulation epiblast stem cell lines. Cell Res. 32, 383–400 (2022).
Wen, J. et al. Single-cell analysis reveals lineage segregation in early post-implantation mouse embryos. J. Biol. Chem. 292, 9840–9854 (2017).
Nakamura, T. et al. A developmental coordinate of pluripotency among mice, monkeys and humans. Nature 537, 57–62 (2016).
van Leeuwen, J., Berg, D. K. & Pfeffer, P. L. Morphological and gene expression changes in cattle embryos from hatched blastocyst to early gastrulation stages after transfer of in vitro produced embryos. PLoS ONE https://doi.org/10.1371/journal.pone.0129787 (2015).
Pérez-Gómez, A., González-Brusi, L., Bermejo-Álvarez, P. & Ramos-Ibeas, P. Lineage differentiation markers as a proxy for embryo viability in farm ungulates. Front. Vet. Sci. 8, 680539 (2021).
