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Gao C, Gao X, Gao F, Du X, Wu S. A CRISPR/Cas9 screen in embryonic stem cells reveals that Mdm2 regulates totipotency exit. Commun Biol 2024; 7:809. [PMID: 38961268 PMCID: PMC11222520 DOI: 10.1038/s42003-024-06507-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 06/25/2024] [Indexed: 07/05/2024] Open
Abstract
During early embryonic development, the transition from totipotency to pluripotency is a fundamental and critical process for proper development. However, the regulatory mechanisms governing this transition remain elusive. Here, we conducted a comprehensive genome-wide CRISPR/Cas9 screen to investigate the 2-cell-like cells (2CLCs) phenotype in mouse embryonic stem cells (mESCs). This effort led to the identification of ten regulators that play a pivotal role in determining cell fate during this transition. Notably, our study revealed Mdm2 as a significant negative regulator of 2CLCs, as perturbation of Mdm2 resulted in a higher proportion of 2CLCs. Mdm2 appears to influence cell fate through its impact on cell cycle progression and H3K27me3 epigenetic modifications. In summary, the results of our CRISPR/Cas9 screen have uncovered several genes with distinct functions in regulating totipotency and pluripotency at various levels, offering a valuable resource for potential targets in future molecular studies.
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Affiliation(s)
- Chen Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xin Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Fei Gao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Xuguang Du
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
| | - Sen Wu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572025, China.
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2
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Liang P, Li H, Long C, Liu M, Zhou J, Zuo Y. Chromatin region binning of gene expression for improving embryo cell subtype identification. Comput Biol Med 2024; 170:108049. [PMID: 38290319 DOI: 10.1016/j.compbiomed.2024.108049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 01/01/2024] [Accepted: 01/26/2024] [Indexed: 02/01/2024]
Abstract
Mammalian embryonic development is a complex process, characterized by intricate spatiotemporal dynamics and distinct chromatin preferences. However, the quick diversification in early embryogenesis leads to significant cellular diversity and the sparsity of scRNA-seq data, posing challenges in accurately determining cell fate decisions. In this study, we introduce a chromatin region binning method using scChrBin, designed to identify chromatin regions that elucidate the dynamics of embryonic development and lineage differentiation. This method transforms scRNA-seq data into a chromatin-based matrix, leveraging genomic annotations. Our results showed that the scChrBin method achieves high accuracy, with 98.0% and 89.2% on two single-cell embryonic datasets, demonstrating its effectiveness in analyzing complex developmental processes. We also systematically and comprehensively analysis of these key chromatin binning regions and their associated genes, focusing on their roles in lineage and stage development. The perspective of chromatin region binning method enables a comprehensive analysis of transcriptome data at the chromatin level, allowing us to unveil the dynamic expression of chromatin regions across temporal and spatial development. The tool is available as an application at https://github.com/liameihao/scChrBin.
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Affiliation(s)
- Pengfei Liang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Hanshuang Li
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Chunshen Long
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Mingzhu Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Jian Zhou
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Institutes of Biomedical Sciences, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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3
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Chai Z, Wu J, Qi Z, Liu Y, Lv Y, Zhang Y, Yu Z, Jiang C, Liu Z. Molecular characterizations and functional roles of NANOG in early development of porcine embryos. Gene 2024; 892:147856. [PMID: 37778417 DOI: 10.1016/j.gene.2023.147856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/11/2023] [Accepted: 09/28/2023] [Indexed: 10/03/2023]
Abstract
Nanog homeobox (NANOG) is the gateway to the pluripotent ground state in mouse embryonic stem cells and early embryos. However, understanding of the molecular signatures and functional characteristics of porcine NANOG remains limited. In this study, we analyzed the gene structure and sequence characteristics of porcine NANOG and found that the porcine NANOG gene is localized on chromosome 5, while NANOG sequence on chromosome 1 is the processed pseudogene. We explored the expression pattern of NANOG in porcine early embryos by immunofluorescence staining and Realtime-PCR and RNA-seq, the results showed that transcription of porcine NANOG commences at the 4-cell stage, while expression of the NANOG protein is initially observed in the inner cell mass of blastocysts. Furthermore, we identified a NANOG splicing variant in porcine early embryos, which maintain the overall structure of the original NANOG mRNA, except for a deletion of 38 base pairs in the second exon. To further investigate the function of NANOG in early embryo development in pigs, we employed siRNA-mediated deletion of the two specific transcripts on porcine zygotes. The results showed that blastocyst rate was significantly reduced after NANOG deleting. A significant decrease in the expression of DNA methylation-related gene DNMT3B was also observed in D3 embryo from the NANOG deleting group. In conclusion, the porcine NANOG gene, accompanied by a single-exon processed pseudogene, exhibits two transcripts and plays a pivotal role in the development of early-stage embryos.
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Affiliation(s)
- Zhuang Chai
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Jing Wu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Zicheng Qi
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Yan Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Yanjiao Lv
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Yuting Zhang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Zhuoran Yu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Chaoqian Jiang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
| | - Zhonghua Liu
- College of Life Science, Northeast Agricultural University, Harbin 150030, China; Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China.
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Todorova PK, Jackson BT, Garg V, Paras KI, Brunner JS, Bridgeman AE, Chen Y, Baksh SC, Yan J, Hadjantonakis AK, Finley LWS. Amino acid intake strategies define pluripotent cell states. Nat Metab 2024; 6:127-140. [PMID: 38172382 PMCID: PMC10842923 DOI: 10.1038/s42255-023-00940-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Mammalian preimplantation development is associated with marked metabolic robustness, and embryos can develop under a wide variety of nutrient conditions, including even the complete absence of soluble amino acids. Here we show that mouse embryonic stem cells (ESCs) capture the unique metabolic state of preimplantation embryos and proliferate in the absence of several essential amino acids. Amino acid independence is enabled by constitutive uptake of exogenous protein through macropinocytosis, alongside a robust lysosomal digestive system. Following transition to more committed states, ESCs reduce digestion of extracellular protein and instead become reliant on exogenous amino acids. Accordingly, amino acid withdrawal selects for ESCs that mimic the preimplantation epiblast. More broadly, we find that all lineages of preimplantation blastocysts exhibit constitutive macropinocytic protein uptake and digestion. Taken together, these results highlight exogenous protein uptake and digestion as an intrinsic feature of preimplantation development and provide insight into the catabolic strategies that enable embryos to sustain viability before implantation.
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Affiliation(s)
- Pavlina K Todorova
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Benjamin T Jackson
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Katrina I Paras
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Julia S Brunner
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anna E Bridgeman
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yanyang Chen
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sanjeethan C Baksh
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jielin Yan
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Louis V. Gerstner Jr Graduate School of Biomedical Sciences, New York, NY, USA
| | | | - Lydia W S Finley
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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5
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. 3D Enhancer-promoter networks provide predictive features for gene expression and coregulation in early embryonic lineages. Nat Struct Mol Biol 2024; 31:125-140. [PMID: 38053013 PMCID: PMC10897904 DOI: 10.1038/s41594-023-01130-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 09/18/2023] [Indexed: 12/07/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages: the trophectoderm, the epiblast and the primitive endoderm. Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements through which transcriptional regulators enact these fates remain understudied. Here, we characterize, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observe extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although distinct groups of genes are irresponsive to topological changes. In each lineage, a high degree of connectivity, or 'hubness', positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a predictive model for transcriptional regulation (3D-HiChAT) that outperforms models using only 1D promoter or proximal variables to predict levels and cell-type specificity of gene expression. Using 3D-HiChAT, we identify, in silico, candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments, we validate several enhancers that control gene expression in their respective lineages. Our study identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to comprehensively understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- 3D Chromatin Conformation and RNA Genomics Laboratory, Center for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Genova, Italy
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY, USA
- Department of Medicine, New York University Langone Health, New York, NY, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Christopher M Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Ly-Sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, USA
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY, USA.
- Department of Medicine, New York University Langone Health, New York, NY, USA.
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY, USA.
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
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Shen Q, Gong W, Pan X, Cai J, Jiang Y, He M, Zhao S, Li Y, Yuan X, Li J. Comprehensive Analysis of CircRNA Expression Profiles in Multiple Tissues of Pigs. Int J Mol Sci 2023; 24:16205. [PMID: 38003395 PMCID: PMC10671760 DOI: 10.3390/ijms242216205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/01/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Circular RNAs (circRNAs) are a class of non-coding RNAs with diverse functions, and previous studies have reported that circRNAs are involved in the growth and development of pigs. However, studies about porcine circRNAs over the past few years have focused on a limited number of tissues. Based on 215 publicly available RNA sequencing (RNA-seq) samples, we conducted a comprehensive analysis of circRNAs in nine pig tissues, namely, the gallbladder, heart, liver, longissimus dorsi, lung, ovary, pituitary, skeletal muscle, and spleen. Here, we identified a total of 82,528 circRNAs and discovered 3818 novel circRNAs that were not reported in the CircAtlas database. Moreover, we obtained 492 housekeeping circRNAs and 3489 tissue-specific circRNAs. The housekeeping circRNAs were enriched in signaling pathways regulating basic biological tissue activities, such as chromatin remodeling, nuclear-transcribed mRNA catabolic process, and protein methylation. The tissue-specific circRNAs were enriched in signaling pathways related to tissue-specific functions, such as muscle system process in skeletal muscle, cilium organization in pituitary, and cortical cytoskeleton in ovary. Through weighted gene co-expression network analysis, we identified 14 modules comprising 1377 hub circRNAs. Additionally, we explored circRNA-miRNA-mRNA networks to elucidate the interaction relationships between tissue-specific circRNAs and tissue-specific genes. Furthermore, our conservation analysis revealed that 19.29% of circRNAs in pigs shared homologous positions with their counterparts in humans. In summary, this extensive profiling of housekeeping, tissue-specific, and co-expressed circRNAs provides valuable insights into understanding the molecular mechanisms of pig transcriptional expression, ultimately deepening our understanding of genetic and biological processes.
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Affiliation(s)
- Qingpeng Shen
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Wentao Gong
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiali Cai
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yao Jiang
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
- School of Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA 6149, Australia
| | - Mingran He
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Shanghui Zhao
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Yipeng Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Swine and Poultry Breeding Industry, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou 510642, China; (Q.S.); (W.G.); (X.P.); (J.C.); (Y.J.); (M.H.); (S.Z.); (Y.L.)
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7
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Gao D, Wang X, Yan YL, Li C, Tan YP, Liu QC, Zhang MY, Zhang JV, Sun QY, Cao ZB, Zhang YH. CircKDM5B sponges miR-128 to regulate porcine blastocyst development by modulating trophectoderm barrier function. Mol Hum Reprod 2023; 29:gaad027. [PMID: 37471586 DOI: 10.1093/molehr/gaad027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/05/2023] [Indexed: 07/22/2023] Open
Abstract
Circular RNAs (circRNAs), which exert critical functions in the regulation of transcriptional and post-transcriptional gene expression, are found in mammalian cells but their functions in mammalian preimplantation embryo development remain poorly understood. Here, we showed that circKDM5B mediated miRNA-128 (miR-128) to regulate porcine early embryo development. We screened circRNAs potentially expressed in porcine embryos through an integrated analysis of sequencing data from mouse and human embryos, as well as porcine oocytes. An authentic circRNA originating from histone demethylase KDM5B (referred to as circKDM5B) was abundantly expressed in porcine embryos. Functional studies revealed that circKDM5B knockdown not only significantly reduced blastocyst formation but also decreased the number of total cells and trophectoderm (TE) cells. Moreover, the knockdown of circKDM5B resulted in the disturbance of tight junction assembly and impaired paracellular sealing within the TE epithelium. Mechanistically, miR-128 inhibitor injection could rescue the early development of circKDM5B knockdown embryos. Taken together, the findings revealed that circKDM5B functions as a miR-128 sponge, thereby facilitating early embryonic development in pigs through the modulation of gene expression linked to tight junction assembly.
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Affiliation(s)
- Di Gao
- Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong Shenzhen Hospital, Shenzhen, China
- Research Center for Reproduction and Health Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advance Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xin Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ye-Lian Yan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Chao Li
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Yong-Peng Tan
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Qiu-Chen Liu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Meng-Ya Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jian V Zhang
- Research Center for Reproduction and Health Development, Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advance Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Qing-Yuan Sun
- Fertility Preservation Lab, Guangdong-Hong Kong Metabolism & Reproduction Joint Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zu-Bing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yun-Hai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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8
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Huayhua C, Rodríguez M, Vega J, Briones M, Rodriguez-Alvarez L, Mellisho E. Blastulation time measured with time-lapse system can predict in vitro viability of bovine blastocysts. PLoS One 2023; 18:e0289751. [PMID: 37561791 PMCID: PMC10414680 DOI: 10.1371/journal.pone.0289751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 07/26/2023] [Indexed: 08/12/2023] Open
Abstract
The objective of this study was to evaluate the time of blastulation monitored by time-lapse technology to predict in vitro viability of bovine blastocysts. This technology can be a powerful tool for bovine embryos selection with higher implantation capacity and competence. Also, in humans an early blastulation is associated with higher quality and pregnancy rate. Cumulus oocyte complexes (COCs) were matured for 20 to 22 h and then fertilized by co-incubation of COCs and spermatozoa (10,000 sperm per oocyte) for 18 h. Presumptive zygotes were placed individually in microwells, in droplets of commercial culture medium. The Primo Vision TL system (EVO+; Vitrolife) captured digital images of developing embryos every 15 minutes. The time frame from IVF to the start of blastulation (tSB) and to blastocyst development (tB) was recorded. After day 7.5, the blastocysts were in vitro culture for 48 h until day 9.5 after IVF to evaluate post hatching development. In vitro viability was evaluated at day 9.5: those with a diameter greater than 200 μm and a total cell count greater than 180 were classified as viable (value 1), while the rest were classified as non in vitro viable (value 0). The area under the ROC curve (AUC) was estimated to determine the predictive power of in vitro viability through blastulation time. In addition, binary logistic regression analysis was used to generate a mathematical model with morphokinetic variables that allow the best prediction of in vitro viability. In 13 sessions, the blastocyst production rate was 46.2% (96/208). The cut-off time to discriminate early or late blastulation was 149.8 h. The post-hatching development of the embryos with early blastulation was 63.3% (31/49), being statistically superior (p = 0.001) than the late blastulation group 14.9% (7/47). Likewise, the time of blastulation showed an accuracy of 90.8% (p < 0.001) in predicting in vitro viability of bovine blastocysts. In conclusion, the selection of blastocysts based on blastulation time (< 155 h) and blastocyst diameter measured on day 7.5 after IVF (> 180 μm) maximizes the in vitro viability.
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Affiliation(s)
- Carmen Huayhua
- Centro de Investigación en Tecnología de Embriones (CIETE), Animal Improvement Program, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Misael Rodríguez
- Centro de Investigación en Tecnología de Embriones (CIETE), Animal Improvement Program, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Jhorjhi Vega
- Centro de Investigación en Tecnología de Embriones (CIETE), Animal Improvement Program, Universidad Nacional Agraria La Molina, Lima, Perú
| | - Mario Briones
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Chillán, Concepción, Chile
| | - Lleretny Rodriguez-Alvarez
- Department of Animal Science, Faculty of Veterinary Sciences, Universidad de Concepción, Chillán, Concepción, Chile
| | - Edwin Mellisho
- Centro de Investigación en Tecnología de Embriones (CIETE), Animal Improvement Program, Universidad Nacional Agraria La Molina, Lima, Perú
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9
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Murphy D, Salataj E, Di Giammartino DC, Rodriguez-Hernaez J, Kloetgen A, Garg V, Char E, Uyehara CM, Ee LS, Lee U, Stadtfeld M, Hadjantonakis AK, Tsirigos A, Polyzos A, Apostolou E. Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549714. [PMID: 37577543 PMCID: PMC10422694 DOI: 10.1101/2023.07.19.549714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Mammalian embryogenesis commences with two pivotal and binary cell fate decisions that give rise to three essential lineages, the trophectoderm (TE), the epiblast (EPI) and the primitive endoderm (PrE). Although key signaling pathways and transcription factors that control these early embryonic decisions have been identified, the non-coding regulatory elements via which transcriptional regulators enact these fates remain understudied. To address this gap, we have characterized, at a genome-wide scale, enhancer activity and 3D connectivity in embryo-derived stem cell lines that represent each of the early developmental fates. We observed extensive enhancer remodeling and fine-scale 3D chromatin rewiring among the three lineages, which strongly associate with transcriptional changes, although there are distinct groups of genes that are irresponsive to topological changes. In each lineage, a high degree of connectivity or "hubness" positively correlates with levels of gene expression and enriches for cell-type specific and essential genes. Genes within 3D hubs also show a significantly stronger probability of coregulation across lineages, compared to genes in linear proximity or within the same contact domains. By incorporating 3D chromatin features, we build a novel predictive model for transcriptional regulation (3D-HiChAT), which outperformed models that use only 1D promoter or proximal variables in predicting levels and cell-type specificity of gene expression. Using 3D-HiChAT, we performed genome-wide in silico perturbations to nominate candidate functional enhancers and hubs in each cell lineage, and with CRISPRi experiments we validated several novel enhancers that control expression of one or more genes in their respective lineages. Our study comprehensively identifies 3D regulatory hubs associated with the earliest mammalian lineages and describes their relationship to gene expression and cell identity, providing a framework to understand lineage-specific transcriptional behaviors.
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Affiliation(s)
- Dylan Murphy
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Eralda Salataj
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Dafne Campigli Di Giammartino
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
- 3D Chromatin Conformation and RNA genomics laboratory, Instituto Italiano di Tecnologia (IIT), Center for Human Technologies (CHT), Genova, Italy (current affiliation)
| | - Javier Rodriguez-Hernaez
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Andreas Kloetgen
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Vidur Garg
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Erin Char
- Tri-Institutional Training Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, 10065, New York, USA
| | - Christopher M. Uyehara
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Ly-sha Ee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - UkJin Lee
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Matthias Stadtfeld
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Anna-Katerina Hadjantonakis
- Developmental Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biochemistry Cell and Molecular Biology Program, Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA
| | - Aristotelis Tsirigos
- Department of Pathology, New York University Langone Health, New York, NY 10016, USA
- Applied Bioinformatics Laboratory, New York University Langone Health, New York, NY 10016, USA
| | - Alexander Polyzos
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Effie Apostolou
- Sanford I. Weill Department of Medicine, Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
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10
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Li Z, Xu H, Li J, Xu X, Wang J, Wu D, Zhang J, Liu J, Xue Z, Zhan G, Tan BCP, Chen D, Chan YS, Ng HH, Liu W, Hsu CH, Zhang D, Shen Y, Liang H. Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network. Nat Commun 2023; 14:3646. [PMID: 37339952 DOI: 10.1038/s41467-023-39344-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 06/08/2023] [Indexed: 06/22/2023] Open
Abstract
Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown. In this study, we identify the unexpected role of a highly expressed 2-cell (2C) embryo specific transcription factor, ZFP352, in facilitating the dissolution of the totipotency network. We find that ZFP352 has selective binding towards two different retrotransposon sub-families. ZFP352 coordinates with DUX to bind the 2C specific MT2_Mm sub-family. On the other hand, without DUX, ZFP352 switches affinity to bind extensively onto SINE_B1/Alu sub-family. This leads to the activation of later developmental programs like ubiquitination pathways, to facilitate the dissolution of the 2C state. Correspondingly, depleting ZFP352 in mouse embryos delays the 2C to morula transition process. Thus, through a shift of binding from MT2_Mm to SINE_B1/Alu, ZFP352 can trigger spontaneous dissolution of the totipotency network. Our study highlights the importance of different retrotransposons sub-families in facilitating the timely and programmed cell fates transition during early embryogenesis.
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Affiliation(s)
- Zhengyi Li
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Haiyan Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Jiaqun Li
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Xiao Xu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Junjiao Wang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Danya Wu
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Jiateng Zhang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Juan Liu
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Ziwei Xue
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Guankai Zhan
- Women's Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Bobby Cheng Peow Tan
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore
| | - Di Chen
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Yun-Shen Chan
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou, 510005, Guangdong Province, China
| | - Huck Hui Ng
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117597, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 639798, Singapore
| | - Wanlu Liu
- Department of Orthopedic Surgery of the Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
- Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Rd., Haining, 314400, China
| | - Chih-Hung Hsu
- Women's Hospital, Institute of Genetics, and Department of Environmental Medicine, Zhejiang University School of Medicine, Hangzhou, 310006, China
| | - Dan Zhang
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
- Zhejiang Provincial Clinical Research Center for Child Health, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
| | - Yang Shen
- Laboratory of Precision Disease Therapeutics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, 138672, Singapore, Singapore.
- Vision Medicals Co., Ltd, G10 BLDG, Huaxin Park, 31 Kefeng Ave, Gaungzhou, 510000, China.
| | - Hongqing Liang
- Division of Human Reproduction and Developmental Genetics, Women's Hospital, and Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, 310006, China.
- Key Laboratory of Reproductive Genetics (Ministry of Education) and Department of Reproductive Endocrinology, Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310006, China.
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11
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Zhu J, Chen K, Sun YH, Ye W, Liu J, Zhang D, Su N, Wu L, Kou X, Zhao Y, Wang H, Gao S, Kang L. LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei. Nat Commun 2023; 14:957. [PMID: 36810573 PMCID: PMC9944933 DOI: 10.1038/s41467-023-36584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic reprogramming of the parental genome is essential for zygotic genome activation and subsequent embryo development in mammals. Asymmetric incorporation of histone H3 variants into the parental genome has been observed previously, but the underlying mechanism remains elusive. In this study, we discover that RNA-binding protein LSM1-mediated major satellite RNA decay plays a central role in the preferential incorporation of histone variant H3.3 into the male pronucleus. Knockdown of Lsm1 disrupts nonequilibrium pronucleus histone incorporation and asymmetric H3K9me3 modification. Subsequently, we find that LSM1 mainly targets major satellite repeat RNA (MajSat RNA) for decay and that accumulated MajSat RNA in Lsm1-depleted oocytes leads to abnormal incorporation of H3.1 into the male pronucleus. Knockdown of MajSat RNA reverses the anomalous histone incorporation and modifications in Lsm1-knockdown zygotes. Our study therefore reveals that accurate histone variant incorporation and incidental modifications in parental pronuclei are specified by LSM1-dependent pericentromeric RNA decay.
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Affiliation(s)
- Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu H Sun
- Departments of Biology, University of Rochester, 14642, Rochester, NY, USA
| | - Wen Ye
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Juntao Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Dandan Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Nan Su
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Li Wu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China. .,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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12
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Shao W, Ning W, Liu C, Zou Y, Yao Y, Kang J, Cao Z. Histone Methyltransferase SETD2 Is Required for Porcine Early Embryonic Development. Animals (Basel) 2022; 12:ani12172226. [PMID: 36077946 PMCID: PMC9454584 DOI: 10.3390/ani12172226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022] Open
Abstract
Simple Summary Normal early embryonic development is important for ensuring sow fertility. Low quality of in vitro production embryos severely limits extensive application of porcine embryo engineering technologies in animal agriculture and the biomedicine field. Histone H3K36 methyltransferase SETD2 reportedly regulates oocyte maturation and preimplantation embryonic development in mice. However, the specific substrate and function of SETD2 in porcine early embryonic development remains unclear. Here, we show that SETD2 preferentially catalyzes H3K36me3 in porcine early embryos. SETD2 knockdown severely impeded blastocyst cavitation and perturbed normal allocation of inner cell mass and trophectoderm. SETD2 knockdown caused the apoptosis of cells within blastocysts. Therefore, SETD2 is essential for porcine early embryonic development. These findings provide a better understanding of porcine early embryonic development and lay a potential basis for improving the quality of porcine in vitro production embryos. Abstract SET domain-containing 2 (SETD2) is a methyltransferase that can catalyze the di- and tri-methylation of lysine 36 on histone H3 (H3K36me2/me3). SETD2 frequently mediates H3K36me3 modification to regulate both oocyte maturation and preimplantation embryonic development in mice. However, the specific substrate and function of SETD2 in porcine early embryonic development are still unclear. In this study, SETD2 preferentially catalyzed H3K36me3 to regulate porcine early embryonic development. SETD2 mRNA is dynamically expressed during early embryonic development. Functional studies using an RNA interference (RNAi) approach revealed that the expression levels of SETD2 mRNA were effectively knocked down by siRNA microinjection. Immunofluorescence analysis indicated that SETD2 knockdown (KD) did not affect H3K36me2 modification but significantly reduced H3K36me3 levels, suggesting a preferential H3K36me3 recognition of SETD2 in porcine embryos. Furthermore, SETD2 KD significantly reduced blastocyst rate and disrupted allocation between inner cell mass (ICM) and trophectoderm (TE) lineage. The expression levels of key genes important for specification of the first two lineages apparently decreased in SETD2 KD blastocysts. SETD2 KD markedly increased the apoptotic percentage of cells within embryos and altered the expression of pro- and anti-apoptotic genes. Therefore, our data indicate that SETD2 is essential for porcine early embryonic development.
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Affiliation(s)
| | | | | | | | | | | | - Zubing Cao
- Correspondence: ; Tel.: +86-551-6578-6537
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13
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Jing J, Feng J, Yuan Y, Guo T, Lei J, Pei F, Ho TV, Chai Y. Spatiotemporal single-cell regulatory atlas reveals neural crest lineage diversification and cellular function during tooth morphogenesis. Nat Commun 2022; 13:4803. [PMID: 35974052 PMCID: PMC9381504 DOI: 10.1038/s41467-022-32490-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 08/02/2022] [Indexed: 11/10/2022] Open
Abstract
Cranial neural crest cells are an evolutionary innovation of vertebrates for craniofacial development and function, yet the mechanisms that govern the cell fate decisions of postmigratory cranial neural crest cells remain largely unknown. Using the mouse molar as a model, we perform single-cell transcriptome profiling to interrogate the cell fate diversification of postmigratory cranial neural crest cells. We reveal the landscape of transcriptional heterogeneity and define the specific cellular domains during the progression of cranial neural crest cell-derived dental lineage diversification, and find that each domain makes a specific contribution to distinct molar mesenchymal tissues. Furthermore, IGF signaling-mediated cell-cell interaction between the cellular domains highlights the pivotal role of autonomous regulation of the dental mesenchyme. Importantly, we reveal cell-type-specific gene regulatory networks in the dental mesenchyme and show that Foxp4 is indispensable for the differentiation of periodontal ligament. Our single-cell atlas provides comprehensive mechanistic insight into the cell fate diversification process of the cranial neural crest cell-derived odontogenic populations.
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Affiliation(s)
- Junjun Jing
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA ,grid.13291.380000 0001 0807 1581State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Chengdu, Sichuan 610041 China
| | - Jifan Feng
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yuan Yuan
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Tingwei Guo
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Jie Lei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Fei Pei
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Thach-Vu Ho
- grid.42505.360000 0001 2156 6853Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA 90033 USA
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, CA, 90033, USA.
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14
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Dang Y, Luo L, Shi Y, Li S, Wang S, Zhang K. KDM5-mediated redistribution of H3K4me3 is required for oocyte-to-embryonic transition in cattle. Biol Reprod 2022; 106:1059-1071. [PMID: 35243485 DOI: 10.1093/biolre/ioac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/12/2022] Open
Abstract
Reprogramming of histone modifications is critical to safeguard correct gene expression profile during preimplantation development. Of interest, trimethylation of lysine 4 on histone 3 (H3K4me3) exhibits a unique and dynamic landscape with a potential species-specific feature. Here, we address how it is reprogrammed and its functional significance during oocyte maturation and early embryonic development in cows. Notably, the overall signal of H3K4me3 decreased sharply during embryonic genome activation (EGA). By using low input ChIP-seq, we find widespread broad H3K4me3 domains in oocytes and early cleaved embryos. The broad domains are gradually removed after fertilization, which is obviously seen during EGA. Meanwhile, H3K4me3 become enriched at promoter regions after the removal of broad H3K4me3. Interestingly, the gene expression level displays a positive correlation with the relative H3K4me3 signal of their promoters when embryos reach 16-cell stage. Importantly, disruption of H3K4me3 demethylases KDM5 increases H3K4me3 level, decreases the embryonic developmental rate and results in dysregulation of over a thousand genes. Meanwhile, KDM5 deficiency causes a redistribution of H3K4me3 across genome. In particular, H3K4me3 in gene body or intergenic regions can't be removed and H3K4me3 in promoter regions is aberrantly reduced. Besides, the positive correlation between promoter H3K4me3 enrichment and gene expression level disappear. Overall, we describe the genomic reprogramming of H3K4me3 with a greater resolution during bovine preimplantation development and propose that KDM5-mediated redistribution of H3K4me3 plays an important role in modulating oocyte-to-embryonic transition.
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Affiliation(s)
- Yanna Dang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lei Luo
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yan Shi
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shuang Li
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Shaohua Wang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Kun Zhang
- Laboratory of Mammalian Molecular Embryology, College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Bora P, Gahurova L, Hauserova A, Stiborova M, Collier R, Potěšil D, Zdráhal Z, Bruce AW. DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification. Open Biol 2021; 11:210092. [PMID: 34255976 PMCID: PMC8277471 DOI: 10.1098/rsob.210092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Successful navigation of the mouse preimplantation stages of development, during which three distinct blastocyst lineages are derived, represents a prerequisite for continued development. We previously identified a role for p38-mitogen-activated kinases (p38-MAPK) regulating blastocyst inner cell mass (ICM) cell fate, specifically primitive endoderm (PrE) differentiation, that is intimately linked to rRNA precursor processing, polysome formation and protein translation regulation. Here, we develop this work by assaying the role of DEAD-box RNA helicase 21 (DDX21), a known regulator of rRNA processing, in the context of p38-MAPK regulation of preimplantation mouse embryo development. We show nuclear DDX21 protein is robustly expressed from the 16-cell stage, becoming exclusively nucleolar during blastocyst maturation, a localization dependent on active p38-MAPK. siRNA-mediated clonal Ddx21 knockdown within developing embryos is associated with profound cell-autonomous and non-autonomous proliferation defects and reduced blastocyst volume, by the equivalent peri-implantation blastocyst stage. Moreover, ICM residing Ddx21 knockdown clones express the EPI marker NANOG but rarely express the PrE differentiation marker GATA4. These data contribute further significance to the emerging importance of lineage-specific translation regulation, as identified for p38-MAPK, during mouse preimplantation development.
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Affiliation(s)
- Pablo Bora
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Lenka Gahurova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic.,Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, Rumburská 89, 27721 Liběchov, Czech Republic
| | - Andrea Hauserova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Martina Stiborova
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Rebecca Collier
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Alexander W Bruce
- Laboratory of Early Mammalian Developmental Biology (LEMDB), Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branišovská 31, 37005 České Budějovice, Czech Republic
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16
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Cao Z, Tong X, Yin H, Zhou N, Zhang X, Zhang M, Wang X, Liu Q, Yan Y, Ma Y, Yu T, Li Y, Zhang Y. Histone Arginine Methyltransferase CARM1-Mediated H3R26me2 Is Essential for Morula-to-Blastocyst Transition in Pigs. Front Cell Dev Biol 2021; 9:678282. [PMID: 34150772 PMCID: PMC8206646 DOI: 10.3389/fcell.2021.678282] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/10/2021] [Indexed: 01/08/2023] Open
Abstract
Coactivator-associated arginine methyltransferase 1 (CARM1) is involved in both establishment of first pluripotent lineage and pluripotency maintenance of embryonic stem cells (ESCs) in mice. However, the histone substrates and role of CARM1 in early embryonic development remain largely unknown. Here, we show that CARM1 specifically catalyzes H3R26me2 to promote porcine blastocyst formation. The putative histone substrates of CARM1, including H3R2me2, H3R17me2, and H3R26me2, are present in pig early embryos. The changes of CARM1 mRNA during early embryogenesis parallel that of H3R26me2. Functional studies using a combinational approach of chemical inhibition and RNA interference (RNAi) showed that catalytic activity inhibition of CARM1 protein or knockdown (KD) of CARM1 mRNA did not alter the levels of both H3R2me2 and H3R17me2, but significantly reduced H3R26me2 levels in porcine embryos. Furthermore, CARM1 inhibition or KD did not affect embryo development to the 2-cell, 4-cell, 8-cell, and morula stages, but severely compromised blastocyst development. CARM1 knocked down embryos that developed to the blastocyst stage had fewer total cells, inner cell mass (ICM), and trophectoderm (TE) cells. Mechanistically, single embryo RNA-sequencing analysis revealed that CARM1 KD altered the transcriptome characterized by downregulation of key genes associated with Hippo and PI3K-AKT signaling pathways. Taken together, these results demonstrate that CARM1 specifically catalyzes H3R26me2 in porcine embryos and participates in blastocyst development.
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Affiliation(s)
- Zubing Cao
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xu Tong
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Huiqun Yin
- Reproductive Medicine Center, The 901st Hospital, Hefei, China
| | - Naru Zhou
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Reproductive and Genetic Branch, The First Affiliated Hospital of University of Science and Technology of China, Hefei, China
| | - Xiangdong Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Mengya Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Xin Wang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qiuchen Liu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yelian Yan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yangyang Ma
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Tong Yu
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yunsheng Li
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yunhai Zhang
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
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Springer C, Wolf E, Simmet K. A New Toolbox in Experimental Embryology-Alternative Model Organisms for Studying Preimplantation Development. J Dev Biol 2021; 9:15. [PMID: 33918361 PMCID: PMC8167745 DOI: 10.3390/jdb9020015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 02/06/2023] Open
Abstract
Preimplantation development is well conserved across mammalian species, but major differences in developmental kinetics, regulation of early lineage differentiation and implantation require studies in different model organisms, especially to better understand human development. Large domestic species, such as cattle and pig, resemble human development in many different aspects, i.e., the timing of zygotic genome activation, mechanisms of early lineage differentiations and the period until blastocyst formation. In this article, we give an overview of different assisted reproductive technologies, which are well established in cattle and pig and make them easily accessible to study early embryonic development. We outline the available technologies to create genetically modified models and to modulate lineage differentiation as well as recent methodological developments in genome sequencing and imaging, which form an immense toolbox for research. Finally, we compare the most recent findings in regulation of the first lineage differentiations across species and show how alternative models enhance our understanding of preimplantation development.
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Affiliation(s)
- Claudia Springer
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (E.W.)
| | - Eckhard Wolf
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (E.W.)
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
- Center for Innovative Medical Models (CiMM), Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany
| | - Kilian Simmet
- Chair for Molecular Animal Breeding and Biotechnology, Gene Center and Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, 85764 Oberschleissheim, Germany; (C.S.); (E.W.)
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Carreiro LE, Santos GSD, Luedke FE, Goissis MD. Cell differentiation events in pre-implantation mouse and bovine embryos. Anim Reprod 2021; 18:e20210054. [PMID: 35035540 PMCID: PMC8747937 DOI: 10.1590/1984-3143-ar2021-0054] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/02/2021] [Indexed: 12/20/2022] Open
Abstract
Early mammal embryogenesis starts with oocyte fertilization, giving rise to the zygote. The events that the newly formed zygote surpasses are crucial to the embryo developmental success. Shortly after activation of its genome, cells of the embryo segregate into the inner cell mass (ICM) or the trophectoderm (TE). The first will give rise to the embryo while the latter will become the placenta. This first segregation involves cellular and molecular processes that include cell polarity linked to intracellular pathway activation, which will regulate the transcription of trophectoderm-related genes. Then, cells of the ICM undergo the second event of mammalian cell differentiation, which consists of the separation between epiblast (EPI) and hypoblast or primitive endoderm (PrE). This second segregation involves paracrine signaling, leading to differential expression of key genes that will dictate the fate of the cell. Although these processes are described in detail in the mouse, recent studies suggest that the bovine embryo could also be an interesting model for early development, since there are differences to the mouse and similarities with early human embryogenesis. In this review, we gathered the main data available in the literature upon bovine and mouse early development events, suggesting that both models should be analyzed and studied in a complementary way, to better model early events occurring in human development.
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