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Yu T, Zhang C, Song W, Zhao X, Cheng Y, Liu J, Su J. Single-cell RNA-seq and single-cell bisulfite-sequencing reveal insights into yak preimplantation embryogenesis. J Biol Chem 2024; 300:105562. [PMID: 38097189 PMCID: PMC10821408 DOI: 10.1016/j.jbc.2023.105562] [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: 03/24/2023] [Revised: 11/17/2023] [Accepted: 12/03/2023] [Indexed: 01/13/2024] Open
Abstract
Extensive epigenetic reprogramming occurs during preimplantation embryonic development. However, the impact of DNA methylation in plateau yak preimplantation embryos and how epigenetic reprogramming contributes to transcriptional regulatory networks are unclear. In this study, we quantified gene expression and DNA methylation in oocytes and a series of yak embryos at different developmental stages and at single-cell resolution using single-cell bisulfite-sequencing and RNA-seq. We characterized embryonic genome activation and maternal transcript degradation and mapped epigenetic reprogramming events critical for embryonic development. Through cross-species transcriptome analysis, we identified 31 conserved maternal hub genes and 39 conserved zygotic hub genes, including SIN3A, PRC1, HDAC1/2, and HSPD1. Notably, by combining single-cell DNA methylation and transcriptome analysis, we identified 43 candidate methylation driver genes, such as AURKA, NUSAP1, CENPF, and PLK1, that may be associated with embryonic development. Finally, using functional approaches, we further determined that the epigenetic modifications associated with the histone deacetylases HDAC1/2 are essential for embryonic development and that the deubiquitinating enzyme USP7 may affect embryonic development by regulating DNA methylation. Our data represent an extensive resource on the transcriptional dynamics of yak embryonic development and DNA methylation remodeling, and provide new insights into strategies for the conservation of germplasm resources, as well as a better understanding of mammalian early embryonic development that can be applied to investigate the causes of early developmental disorders.
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Affiliation(s)
- Tong Yu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Chengtu Zhang
- Academician Zhang Yong Innovation Center, Xining Animal Disease Control Center, Xining, Qinghai, China
| | - Weijia Song
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Xinyi Zhao
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Yuyao Cheng
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China
| | - Jun Liu
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
| | - Jianmin Su
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, China.
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Knoblochova L, Duricek T, Vaskovicova M, Zorzompokou C, Rayova D, Ferencova I, Baran V, Schultz RM, Hoffmann ER, Drutovic D. CHK1-CDC25A-CDK1 regulate cell cycle progression and protect genome integrity in early mouse embryos. EMBO Rep 2023; 24:e56530. [PMID: 37694680 PMCID: PMC10561370 DOI: 10.15252/embr.202256530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/17/2023] [Accepted: 08/18/2023] [Indexed: 09/12/2023] Open
Abstract
After fertilization, remodeling of the oocyte and sperm genomes is essential to convert these highly differentiated and transcriptionally quiescent cells into early cleavage-stage blastomeres that are transcriptionally active and totipotent. This developmental transition is accompanied by cell cycle adaptation, such as lengthening or shortening of the gap phases G1 and G2. However, regulation of these cell cycle changes is poorly understood, especially in mammals. Checkpoint kinase 1 (CHK1) is a protein kinase that regulates cell cycle progression in somatic cells. Here, we show that CHK1 regulates cell cycle progression in early mouse embryos by restraining CDK1 kinase activity due to CDC25A phosphatase degradation. CHK1 kinase also ensures the long G2 phase needed for genome activation and reprogramming gene expression in two-cell stage mouse embryos. Finally, Chk1 depletion leads to DNA damage and chromosome segregation errors that result in aneuploidy and infertility.
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Affiliation(s)
- Lucie Knoblochova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Tomas Duricek
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Michaela Vaskovicova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Chrysoula Zorzompokou
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Diana Rayova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Ivana Ferencova
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
| | - Vladimir Baran
- Institute of Animal Physiology, Centre of Biosciences, Slovak Academy of SciencesKosiceSlovakia
| | - Richard M Schultz
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
- Department of Anatomy, Physiology, and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - David Drutovic
- Institute of Animal Physiology and Genetics of the Czech Academy of SciencesLibechovCzech Republic
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Liu F, Wang J, Yue Y, Li C, Zhang X, Xiang J, Wang H, Li X. Derivation of Arbas Cashmere Goat Induced Pluripotent Stem Cells in LCDM with Trophectoderm Lineage Differentiation and Interspecies Chimeric Abilities. Int J Mol Sci 2023; 24:14728. [PMID: 37834175 PMCID: PMC10572416 DOI: 10.3390/ijms241914728] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/22/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
The Arbas cashmere goat is a unique biological resource that plays a vital role in livestock husbandry in China. LCDM is a medium with special small molecules (consisting of human LIF, CHIR99021, (S)-(+)-dimethindene maleate, and minocycline hydrochloride) for generation pluripotent stem cells (PSCs) with bidirectional developmental potential in mice, humans, pigs, and bovines. However, there is no report on whether LCDM can support for generation of PSCs with the same ability in Arbas cashmere goats. In this study, we applied LCDM to generate goat induced PSCs (giPSCs) from goat fetal fibroblasts (GFFs) by reprogramming. The derived giPSCs exhibited stem cell morphology, expressing pluripotent markers, and could differentiate into three germ layers. Moreover, the giPSCs differentiated into the trophectoderm lineage by spontaneous and directed differentiation in vitro. The giPSCs contributed to embryonic and extraembryonic tissue in preimplantation blastocysts and postimplantation chimeric embryos. RNA-sequencing analysis showed that the giPSCs were very close to goat embryos at the blastocyst stage and giPSCs have similar properties to typical extended PSCs (EPSCs). The establishment of giPSCs with LCDM provides a new way to generate PSCs from domestic animals and lays the foundation for basic and applied research in biology and agriculture.
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Affiliation(s)
- Fang Liu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jing Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Yongli Yue
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Chen Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xuemin Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Jinzhu Xiang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Hanning Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
| | - Xueling Li
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot 010070, China
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Gao L, Zhang Z, Zheng X, Wang F, Deng Y, Zhang Q, Wang G, Zhang Y, Liu X. The Novel Role of Zfp296 in Mammalian Embryonic Genome Activation as an H3K9me3 Modulator. Int J Mol Sci 2023; 24:11377. [PMID: 37511136 PMCID: PMC10379624 DOI: 10.3390/ijms241411377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/05/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
The changes in epigenetic modifications during early embryonic development significantly impact mammalian embryonic genome activation (EGA) and are species-conserved to some degree. Here, we reanalyzed the published RNA-Seq of human, mouse, and goat early embryos and found that Zfp296 (zinc finger protein 296) expression was higher at the EGA stage than at the oocyte stage in all three species (adjusted p-value < 0.05 |log2(foldchange)| ≥ 1). Subsequently, we found that Zfp296 was conserved across human, mouse, goat, sheep, pig, and bovine embryos. In addition, we identified that ZFP296 interacts with the epigenetic regulators KDM5B, SMARCA4, DNMT1, DNMT3B, HP1β, and UHRF1. The Cys2-His2(C2H2) zinc finger domain TYPE2 TYPE3 domains of ZFP296 co-regulated the modification level of the trimethylation of lysine 9 on the histone H3 protein subunit (H3K9me3). According to ChIP-seq analysis, ZFP296 was also enriched in Trim28, Suv39h1, Setdb1, Kdm4a, and Ehmt2 in the mESC genome. Then, knockdown of the expression of Zfp296 at the late zygote of the mouse led to the early developmental arrest of the mouse embryos and failure resulting from a decrease in H3K9me3. Together, our results reveal that Zfp296 is an H3K9me3 modulator which is essential to the embryonic genome activation of mouse embryos.
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Affiliation(s)
- Lu Gao
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Zihan Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Xiaoman Zheng
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Fan Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Yi Deng
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Qian Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Guoyan Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
| | - Xu Liu
- College of Veterinary Medicine, Northwest A&F University, Xianyang 712100, China
- State Key Laboratory for Biology of Livestock, Northwest A&F University, Xianyang 712100, China
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Fu P, Zhang D, Yang C, Yuan X, Luo X, Zheng H, Deng Y, Liu Q, Cui K, Gao F, Shi D. Whole-genome transcriptome and DNA methylation dynamics of pre-implantation embryos reveal progression of embryonic genome activation in buffaloes. J Anim Sci Biotechnol 2023; 14:94. [PMID: 37430306 DOI: 10.1186/s40104-023-00894-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/11/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND During mammalian pre-implantation embryonic development (PED), the process of maternal-to-zygote transition (MZT) is well orchestrated by epigenetic modification and gene sequential expression, and it is related to the embryonic genome activation (EGA). During MZT, the embryos are sensitive to the environment and easy to arrest at this stage in vitro. However, the timing and regulation mechanism of EGA in buffaloes remain obscure. RESULTS Buffalo pre-implantation embryos were subjected to trace cell based RNA-seq and whole-genome bisulfite sequencing (WGBS) to draw landscapes of transcription and DNA-methylation. Four typical developmental steps were classified during buffalo PED. Buffalo major EGA was identified at the 16-cell stage by the comprehensive analysis of gene expression and DNA methylation dynamics. By weighted gene co-expression network analysis, stage-specific modules were identified during buffalo maternal-to-zygotic transition, and key signaling pathways and biological process events were further revealed. Programmed and continuous activation of these pathways was necessary for success of buffalo EGA. In addition, the hub gene, CDK1, was identified to play a critical role in buffalo EGA. CONCLUSIONS Our study provides a landscape of transcription and DNA methylation in buffalo PED and reveals deeply the molecular mechanism of the buffalo EGA and genetic programming during buffalo MZT. It will lay a foundation for improving the in vitro development of buffalo embryos.
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Affiliation(s)
- Penghui Fu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- College of Animal Science and Technology, Southwest University, Chongqing, 402460, China
| | - Du Zhang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Chunyan Yang
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, 530001, China
| | - Xiang Yuan
- Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, 530016, China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Haiying Zheng
- Guangxi Key Laboratory of Buffalo Genetics, Reproduction and Breeding, Guangxi Buffalo Research Institute, Chinese Academy of Agricultural Science, Nanning, 530001, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Kuiqing Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Fei Gao
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, DK 1870 C, Frederiksberg, Denmark.
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources & Guangxi Key Laboratory of Animal Breeding and Disease Control, Guangxi University, Nanning, 530004, China.
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Liu X, Zhang J, Zhou J, Bu G, Zhu W, He H, Sun Q, Yu Z, Xiong W, Wang L, Wu D, Dou C, Yu L, Zhou K, Wang S, Fan Z, Wang T, Hu R, Hu T, Zhang X, Miao Y. Hierarchical Accumulation of Histone Variant H2A.Z Regulates Transcriptional States and Histone Modifications in Early Mammalian Embryos. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200057. [PMID: 35717671 PMCID: PMC9376818 DOI: 10.1002/advs.202200057] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Indexed: 05/09/2023]
Abstract
Early embryos undergo extensive epigenetic reprogramming to achieve gamete-to-embryo transition, which involves the loading and removal of histone variant H2A.Z on chromatin. However, how does H2A.Z regulate gene expression and histone modifications during preimplantation development remains unrevealed. Here, by using ultra-low-input native chromatin immunoprecipitation and sequencing, the genome-wide distribution of H2A.Z is delineated in mouse oocytes and early embryos. These landscapes indicate that paternal H2A.Z is removed upon fertilization, followed by unbiased accumulation on parental genomes during zygotic genome activation (ZGA). Remarkably, H2A.Z exhibits hierarchical accumulation as different peak types at promoters: promoters with double H2A.Z peaks are colocalized with H3K4me3 and indicate transcriptional activation; promoters with a single H2A.Z peak are more likely to occupy bivalent marks (H3K4me3+H3K27me3) and indicate development gene suppression; promoters with no H2A.Z accumulation exhibit persisting gene silencing in early embryos. Moreover, H2A.Z depletion changes the enrichment of histone modifications and RNA polymerase II binding at promoters, resulting in abnormal gene expression and developmental arrest during lineage commitment. Furthermore, similar transcription and accumulation patterns between mouse and porcine embryos indicate that a dual role of H2A.Z in regulating the epigenome required for proper gene expression is conserved during mammalian preimplantation development.
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Adhikari B, Lee CN, Khadka VS, Deng Y, Fukumoto G, Thorne M, Caires K, Odani J, Mishra B. RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy. BMC Genomics 2022; 23:494. [PMID: 35799127 PMCID: PMC9264496 DOI: 10.1186/s12864-022-08720-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/24/2022] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Maternal recognition is the crucial step for establishing pregnancy in cattle. This study aims to identify endometrial genes and biological pathways involved in the maternal recognition of pregnancy. Caruncular endometrial tissues were collected from Day 15-17 of gestation (pregnant), non-pregnant (absence of conceptus), and cyclic (non-bred) heifers. RESULTS Total RNAs were isolated from the caruncular endometrial tissues of pregnant, non-pregnant, and cyclic heifers, and were subjected to high-throughput RNA-sequencing. The genes with at least two-fold change and Benjamini and Hochberg p-value ≤ 0.05 were considered differentially expressed genes and further confirmed with quantitative real-time PCR. A total of 107 genes (pregnant vs cyclic) and 98 genes (pregnant vs non-pregnant) were differentially expressed in the pregnant endometrium. The most highly up-regulated genes in the pregnant endometrium were MRS2, CST6, FOS, VLDLR, ISG15, IFI6, MX2, C15H11ORF34, EIF3M, PRSS22, MS4A8, and TINAGL1. Interferon signaling, immune response, nutrient transporter, synthesis, and secretion of proteins are crucial pathways during the maternal recognition of pregnancy. CONCLUSIONS The study demonstrated that the presence of conceptus at Day 15-17 of gestation affects the endometrial gene expression related to endometrial remodeling, immune response, nutrients and ion transporters, and relevant signaling pathways in the caruncular region of bovine endometrium during the maternal recognition of pregnancy.
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Affiliation(s)
- Bindu Adhikari
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Chin N Lee
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Vedbar S Khadka
- Department of Quantitative Health Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Glen Fukumoto
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Mark Thorne
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Kyle Caires
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Jenee Odani
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA
| | - Birendra Mishra
- Department of Human Nutrition, Food and Animal Sciences, University of Hawaii at Manoa, Honolulu, HI, 96822, USA.
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Modzelewski AJ, Shao W, Chen J, Lee A, Qi X, Noon M, Tjokro K, Sales G, Biton A, Anand A, Speed TP, Xuan Z, Wang T, Risso D, He L. A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. Cell 2021; 184:5541-5558.e22. [PMID: 34644528 PMCID: PMC8787082 DOI: 10.1016/j.cell.2021.09.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 07/26/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022]
Abstract
Retrotransposons mediate gene regulation in important developmental and pathological processes. Here, we characterized the transient retrotransposon induction during preimplantation development of eight mammals. Induced retrotransposons exhibit similar preimplantation profiles across species, conferring gene regulatory activities, particularly through long terminal repeat (LTR) retrotransposon promoters. A mouse-specific MT2B2 retrotransposon promoter generates an N-terminally truncated Cdk2ap1ΔN that peaks in preimplantation embryos and promotes proliferation. In contrast, the canonical Cdk2ap1 peaks in mid-gestation and represses cell proliferation. This MT2B2 promoter, whose deletion abolishes Cdk2ap1ΔN production, reduces cell proliferation and impairs embryo implantation, is developmentally essential. Intriguingly, Cdk2ap1ΔN is evolutionarily conserved in sequence and function yet is driven by different promoters across mammals. The distinct preimplantation Cdk2ap1ΔN expression in each mammalian species correlates with the duration of its preimplantation development. Hence, species-specific transposon promoters can yield evolutionarily conserved, alternative protein isoforms, bestowing them with new functions and species-specific expression to govern essential biological divergence.
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Affiliation(s)
- Andrew J Modzelewski
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wanqing Shao
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jingqi Chen
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Angus Lee
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xin Qi
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mackenzie Noon
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kristy Tjokro
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Gabriele Sales
- Department of Biology, University of Padova, Padova 35122, Italy
| | - Anne Biton
- Department of Statistics, University of California, Berkeley, Berkeley, CA 94720, USA; Bioinformatics and Biostatistics, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris 75015, France
| | - Aparna Anand
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Terence P Speed
- Bioinformatics Division, WEHI, Parkville, VIC 3052, Australia
| | - Zhenyu Xuan
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - Ting Wang
- Department of Genetics, Edison Family Center for Genome Science and System Biology, McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Davide Risso
- Department of Statistical Sciences, University of Padova, Padova 35122, Italy.
| | - Lin He
- Division of Cellular and Developmental Biology, MCB Department, University of California, Berkeley, Berkeley, CA 94720, USA.
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