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Fan J, Liu C, Zhao Y, Xu Q, Yin Z, Liu Z, Mu Y. Single-Cell RNA Sequencing Reveals Differences in Chromatin Remodeling and Energy Metabolism among In Vivo-Developed, In Vitro-Fertilized, and Parthenogenetically Activated Embryos from the Oocyte to 8-Cell Stages in Pigs. Animals (Basel) 2024; 14:465. [PMID: 38338108 PMCID: PMC10854501 DOI: 10.3390/ani14030465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/26/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
In vitro-fertilized (IVF) and parthenogenetically activated (PA) embryos, key to genetic engineering, face more developmental challenges than in vivo-developed embryos (IVV). We analyzed single-cell RNA-seq data from the oocyte to eight-cell stages in IVV, IVF, and PA porcine embryos, focusing on developmental differences during early zygotic genome activation (ZGA), a vital stage for embryonic development. (1) Our findings reveal that in vitro embryos (IVF and PA) exhibit more similar developmental trajectories compared to IVV embryos, with PA embryos showing the least gene diversity at each stage. (2) Significant differences in maternal mRNA, particularly affecting mRNA splicing, energy metabolism, and chromatin remodeling, were observed. Key genes like SMARCB1 (in vivo) and SIRT1 (in vitro) played major roles, with HDAC1 (in vivo) and EZH2 (in vitro) likely central in their complexes. (3) Across different types of embryos, there was minimal overlap in gene upregulation during ZGA, with IVV embryos demonstrating more pronounced upregulation. During minor ZGA, global epigenetic modification patterns diverged and expanded further. Specifically, in IVV, genes, especially those linked to H4 acetylation and H2 ubiquitination, were more actively regulated compared to PA embryos, which showed an increase in H3 methylation. Additionally, both types displayed a distinction in DNA methylation. During major ZGA, IVV distinctively upregulated genes related to mitochondrial regulation, ATP synthesis, and oxidative phosphorylation. (4) Furthermore, disparities in mRNA degradation-related genes between in vivo and in vitro embryos were more pronounced during major ZGA. In IVV, there was significant maternal mRNA degradation. Maternal genes regulating phosphatase activity and cell junctions, highly expressed in both in vivo and in vitro embryos, were degraded in IVV in a timely manner but not in in vitro embryos. (5) Our analysis also highlighted a higher expression of many mitochondrially encoded genes in in vitro embryos, yet their nucleosome occupancy and the ATP8 expression were notably higher in IVV.
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Affiliation(s)
- Jianlin Fan
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Chang Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yunjing Zhao
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
| | - Qianqian Xu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhi Yin
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Zhonghua Liu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
| | - Yanshuang Mu
- Key Laboratory of Animal Cellular and Genetic Engineering of Heilongjiang Province, Northeast Agricultural University, Harbin 150030, China; (J.F.); (C.L.); (Y.Z.); (Q.X.); (Z.Y.)
- College of Life Science, Northeast Agricultural University, Harbin 150030, China
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Takahashi N, Franciosi F, Daldello EM, Luong XG, Althoff P, Wang X, Conti M. CPEB1-dependent disruption of the mRNA translation program in oocytes during maternal aging. Nat Commun 2023; 14:416. [PMID: 36697412 PMCID: PMC9877008 DOI: 10.1038/s41467-023-35994-3] [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: 04/12/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
The molecular causes of deteriorating oocyte quality during aging are poorly defined. Since oocyte developmental competence relies on post-transcriptional regulations, we tested whether defective mRNA translation contributes to this decline in quality. Disruption in ribosome loading on maternal transcripts is present in old oocytes. Using a candidate approach, we detect altered translation of 3'-UTR-reporters and altered poly(A) length of the endogenous mRNAs. mRNA polyadenylation depends on the cytoplasmic polyadenylation binding protein 1 (CPEB1). Cpeb1 mRNA translation and protein levels are decreased in old oocytes. This decrease causes de-repression of Ccnb1 translation in quiescent oocytes, premature CDK1 activation, and accelerated reentry into meiosis. De-repression of Ccnb1 is corrected by Cpeb1 mRNA injection in old oocytes. Oocyte-specific Cpeb1 haploinsufficiency in young oocytes recapitulates all the translation phenotypes of old oocytes. These findings demonstrate that a dysfunction in the oocyte translation program is associated with the decline in oocyte quality during aging.
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Affiliation(s)
- Nozomi Takahashi
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Federica Franciosi
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,Reproductive and Developmental Biology Lab, Department of Veterinary Medicine and Animal Science, Università degli Studi di Milano, 20133, Milan, Italy
| | - Enrico Maria Daldello
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,Sorbonne Université, CNRS, Laboratoire de Biologie du Développement-Institut de Biologie Paris Seine, LBD-IBPS, Paris, France
| | - Xuan G Luong
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Peter Althoff
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Xiaotian Wang
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA.,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA
| | - Marco Conti
- Center for Reproductive Sciences, University of California, San Francisco, CA, 94143, USA. .,USA Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, 94143, USA. .,Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA, 94143, USA.
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