1
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Zhang C, Xu M, Yang M, Liao A, Lv P, Liu X, Chen Y, Liu H, He Z. Efficient generation of cloned cats with altered coat colour by editing of the KIT gene. Theriogenology 2024; 222:54-65. [PMID: 38621344 DOI: 10.1016/j.theriogenology.2024.04.001] [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: 11/29/2023] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/17/2024]
Abstract
Coat colour largely determines the market demand for several cat breeds. The KIT proto-oncogene (KIT) gene is a key gene controlling melanoblast differentiation and melanogenesis. KIT mutations usually cause varied changes in coat colour in mammalian species. In this study, we used a pair of single-guide RNAs (sgRNAs) to delete exon 17 of KIT in somatic cells isolated from two different Chinese Li Hua feline foetuses. Edited cells were used as donor nuclei for somatic cell nuclear transfer (SCNT) to generate cloned embryos presenting an average cleavage rate exceeding 85%, and an average blastocyst formation rate exceeding 9.5%. 131 cloned embryos were transplanted into four surrogates, and all surrogates carried their pregnancies to term, and delivered 4.58% (6/131) alive cloned kittens, with 1.53% (2/131) being KIT-edited heterozygotes (KITD17/+). The KITD17/+ cats presented an obvious darkness reduction in the mackerel tabby coat. Immunohistochemical analysis (IHC) of skin tissues indicated impaired proliferation and differentiation of melanoblasts caused by the lack of exon17 in feline KIT. To our knowledge, this is the first report on coat colour modification of cats through gene editing. The findings could facilitate further understanding of the regulatory role of KIT on feline coat colour and provide a basis for the breeding of cats with commercially desired coat colour.
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Affiliation(s)
- Chong Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Meina Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Min Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Alian Liao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Peiru Lv
- Henan Liosio Biotechnology Co., Ltd, PR China
| | - Xiaohong Liu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China
| | - Hongbo Liu
- Henan Liosio Biotechnology Co., Ltd, PR China.
| | - Zuyong He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510006, PR China.
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2
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Wang J, Zhou X, Han T, Zhang H. Epigenetic signatures of trophoblast lineage and their biological functions. Cells Dev 2024:203934. [PMID: 38942294 DOI: 10.1016/j.cdev.2024.203934] [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: 11/15/2023] [Revised: 03/13/2024] [Accepted: 06/13/2024] [Indexed: 06/30/2024]
Abstract
Trophoblasts play a crucial role in embryo implantation and in interacting with the maternal uterus. The trophoblast lineage develops into a substantial part of the placenta, a temporary extra-embryonic organ, capable of undergoing distinctive epigenetic events during development. The critical role of trophoblast-specific epigenetic signatures in regulating placental development has become known, significantly advancing our understanding of trophoblast identity and lineage development. Scientific efforts are revealing how trophoblast-specific epigenetic signatures mediate stage-specific gene regulatory programming during the development of the trophoblast lineage. These epigenetic signatures have a significant impact on blastocyst formation, placental development, as well as the growth and survival of embryos and fetuses. In evolution, DNA hypomethylation in the trophoblast lineage is conserved, and there is a significant disparity in the control of epigenetic dynamics and the landscape of genomic imprinting. Scientists have used murine and human multipotent trophoblast cells as in vitro models to recapitulate the essential epigenetic processes of placental development. Here, we review the epigenetic signatures of the trophoblast lineage and their biological functions to enhance our understanding of placental evolution, development, and function.
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Affiliation(s)
- Jianqi Wang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Xiaobo Zhou
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Reproductive Center, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Tingli Han
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China; The Center for Reproductive Medicine, Obstetrics and Gynecology Department, The Second Affiliated Hospital of Chongqing Medical University, Chongqing 400010, China.
| | - Hua Zhang
- Chongqing Key Laboratory of Maternal and Fetal Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Department of Obstetrics and Gynecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China; Joint International Research Laboratory of Reproduction and Development of Chinese Ministry of Education, Chongqing Medical University, 400016, China.
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3
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Ye DX, Yu JW, Li R, Hao YD, Wang TY, Yang H, Ding H. The Prediction of Recombination Hotspot Based on Automated Machine Learning. J Mol Biol 2024:168653. [PMID: 38871176 DOI: 10.1016/j.jmb.2024.168653] [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: 02/10/2024] [Revised: 05/12/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Meiotic recombination plays a pivotal role in genetic evolution. Genetic variation induced by recombination is a crucial factor in generating biodiversity and a driving force for evolution. At present, the development of recombination hotspot prediction methods has encountered challenges related to insufficient feature extraction and limited generalization capabilities. This paper focused on the research of recombination hotspot prediction methods. We explored deep learning-based recombination hotspot prediction and scrutinized the shortcomings of prevalent models in addressing the challenge of recombination hotspot prediction. To addressing these deficiencies, an automated machine learning approach was utilized to construct recombination hotspot prediction model. The model combined sequence information with physicochemical properties by employing TF-IDF-Kmer and DNA composition components to acquire more effective feature data. Experimental results validate the effectiveness of the feature extraction method and automated machine learning technology used in this study. The final model was validated on three distinct datasets and yielded accuracy rates of 97.14%, 79.71%, and 98.73%, surpassing the current leading models by 2%, 2.56%, and 4%, respectively. In addition, we incorporated tools such as SHAP and AutoGluon to analyze the interpretability of black-box models, delved into the impact of individual features on the results, and investigated the reasons behind misclassification of samples. Finally, an application of recombination hotspot prediction was established to facilitate easy access to necessary information and tools for researchers. The research outcomes of this paper underscore the enormous potential of automated machine learning methods in gene sequence prediction.
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Affiliation(s)
- Dong-Xin Ye
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Jun-Wen Yu
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Rui Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Yu-Duo Hao
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Tian-Yu Wang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hui Yang
- Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou, Zhejiang, China.
| | - Hui Ding
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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4
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Matoba S, Shikata D, Shirai F, Tatebe T, Hirose M, Nakata A, Watanabe N, Hasegawa A, Ito A, Yoshida M, Ogura A. Reduction of H3K9 methylation by G9a inhibitors improves the development of mouse SCNT embryos. Stem Cell Reports 2024; 19:906-921. [PMID: 38729154 DOI: 10.1016/j.stemcr.2024.04.003] [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: 12/01/2023] [Revised: 03/28/2024] [Accepted: 04/04/2024] [Indexed: 05/12/2024] Open
Abstract
Removal of somatic histone H3 lysine 9 trimethylation (H3K9me3) from the embryonic genome can improve the efficiency of mammalian cloning using somatic cell nuclear transfer (SCNT). However, this strategy involves the injection of histone demethylase mRNA into embryos, which is limiting because of its invasive and labor-consuming nature. Here, we report that treatment with an inhibitor of G9a (G9ai), the major histone methyltransferase that introduces H3K9me1/2 in mammals, greatly improved the development of mouse SCNT embryos. Intriguingly, G9ai caused an immediate reduction of H3K9me1/2, a secondary loss of H3K9me3 in SCNT embryos, and increased the birth rate of cloned pups about 5-fold (up to 3.9%). G9ai combined with the histone deacetylase inhibitor trichostatin A further improved this rate to 14.5%. Mechanistically, G9ai and TSA synergistically enhanced H3K9me3 demethylation and boosted zygotic genome activation. Thus, we established an easy, highly effective SCNT protocol that would enhance future cloning research and applications.
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Affiliation(s)
- Shogo Matoba
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.
| | - Daiki Shikata
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Fumiyuki Shirai
- Drug Discovery Chemistry Platform Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Takaki Tatebe
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akiko Nakata
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Naomi Watanabe
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiro Ito
- Laboratory of Cell Signaling, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Minoru Yoshida
- Drug Discovery Seed Compounds Exploratory Unit, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Office of University Professors, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Research Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan; The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan; Bioresource Engineering Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
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5
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Kwon T. Advancing primatology through ethical and scientific perspectives on rhesus monkey (Macaca mulatta) cloning. J Med Primatol 2024; 53:e12704. [PMID: 38812105 DOI: 10.1111/jmp.12704] [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: 03/11/2024] [Revised: 04/24/2024] [Accepted: 05/05/2024] [Indexed: 05/31/2024]
Abstract
A critical turning point was reached in research with the recent success in cloning rhesus monkeys (Macaca mulatta), a major advancement in primatology. This breakthrough marks the beginning of a new age in biomedical research, ushered by improved somatic cell nuclear transfer techniques and creative trophoblast replacement strategies. The successful cloning of rhesus monkeys presents the possibility of producing genetically homogeneous models that are highly advantageous for studying complex biological processes, testing drugs, and researching diseases. However, this achievement raises important ethical questions, particularly regarding animal welfare and the broader ramifications of primate cloning. Approaching the future of primate research with balance is critical, as the scientific world stands on the brink of these revolutionary breakthroughs. This paper aims to summarise the consequences, ethical challenges and possible paths forward in primatology arising from rhesus monkey cloning.
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Affiliation(s)
- Taeho Kwon
- Primate Resources Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Jeongeup-si, Jeonbuk, Korea
- Department of Applied Biological Engineering, KRIBB School of Biotechnology, Korea National University of Science and Technology (UST), Daejeon, Korea
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6
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Oberin R, Petautschnig S, Jarred EG, Qu Z, Tsai T, Youngson NA, Pulsoni G, Truong TT, Fernando D, Bildsoe H, Blücher RO, van den Buuse M, Gardner DK, Sims NA, Adelson DL, Western PS. Fetal growth delay caused by loss of non-canonical imprinting is resolved late in pregnancy and culminates in offspring overgrowth. eLife 2024; 13:e81875. [PMID: 38813868 PMCID: PMC11139480 DOI: 10.7554/elife.81875] [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: 07/14/2022] [Accepted: 05/02/2024] [Indexed: 05/31/2024] Open
Abstract
Germline epigenetic programming, including genomic imprinting, substantially influences offspring development. Polycomb Repressive Complex 2 (PRC2) plays an important role in Histone 3 Lysine 27 trimethylation (H3K27me3)-dependent imprinting, loss of which leads to growth and developmental changes in mouse offspring. In this study, we show that offspring from mouse oocytes lacking the PRC2 protein Embryonic Ectoderm Development (EED) were initially developmentally delayed, characterised by low blastocyst cell counts and substantial growth delay in mid-gestation embryos. This initial developmental delay was resolved as offspring underwent accelerated fetal development and growth in late gestation resulting in offspring that were similar stage and weight to controls at birth. The accelerated development and growth in offspring from Eed-null oocytes was associated with remodelling of the placenta, which involved an increase in fetal and maternal tissue size, conspicuous expansion of the glycogen-enriched cell population, and delayed parturition. Despite placental remodelling and accelerated offspring fetal growth and development, placental efficiency, and fetal blood glucose levels were low, and the fetal blood metabolome was unchanged. Moreover, while expression of the H3K27me3-imprinted gene and amino acid transporter Slc38a4 was increased, fetal blood levels of individual amino acids were similar to controls, indicating that placental amino acid transport was not enhanced. Genome-wide analyses identified extensive transcriptional dysregulation and DNA methylation changes in affected placentas, including a range of imprinted and non-imprinted genes. Together, while deletion of Eed in growing oocytes resulted in fetal growth and developmental delay and placental hyperplasia, our data indicate a remarkable capacity for offspring fetal growth to be normalised despite inefficient placental function and the loss of H3K27me3-dependent genomic imprinting.
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Affiliation(s)
- Ruby Oberin
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Sigrid Petautschnig
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Ellen G Jarred
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, University of AdelaideAdelaideAustralia
| | - Tesha Tsai
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Neil A Youngson
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
- School of Biomedical Sciences, University of New South WalesSydneyAustralia
| | - Gabrielle Pulsoni
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Thi T Truong
- School of BioSciences, University of MelbourneParkvilleAustralia
| | - Dilini Fernando
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Heidi Bildsoe
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | - Rheannon O Blücher
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
| | | | - David K Gardner
- School of BioSciences, University of MelbourneParkvilleAustralia
| | - Natalie A Sims
- Bone Cell Biology and Disease Unit, St. Vincent’s Institute of Medical Research and Department of Medicine at St. Vincent’s Hospital, University of MelbourneFitzroyAustralia
| | - David L Adelson
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, University of AdelaideAdelaideAustralia
| | - Patrick S Western
- Centre for Reproductive Health, Hudson Institute of Medical Research and Department of Molecular and Translational Science, Monash UniversityClaytonAustralia
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7
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Zhang M, Zhai Y, An X, Li Q, Zhang D, Zhou Y, Zhang S, Dai X, Li Z. DNA methylation regulates RNA m 6A modification through transcription factor SP1 during the development of porcine somatic cell nuclear transfer embryos. Cell Prolif 2024; 57:e13581. [PMID: 38095020 PMCID: PMC11056710 DOI: 10.1111/cpr.13581] [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: 10/05/2023] [Revised: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Epigenetic modifications play critical roles during somatic cell nuclear transfer (SCNT) embryo development. Whether RNA N6-methyladenosine (m6A) affects the developmental competency of SCNT embryos remains unclear. Here, we showed that porcine bone marrow mesenchymal stem cells (pBMSCs) presented higher RNA m6A levels than those of porcine embryonic fibroblasts (pEFs). SCNT embryos derived from pBMSCs had higher RNA m6A levels, cleavage, and blastocyst rates than those from pEFs. Compared with pEFs, the promoter region of METTL14 presented a hypomethylation status in pBMSCs. Mechanistically, DNA methylation regulated METTL14 expression by affecting the accessibility of transcription factor SP1 binding, highlighting the role of the DNA methylation/SP1/METTL14 pathway in donor cells. Inhibiting the DNA methylation level in donor cells increased the RNA m6A level and improved the development efficiency of SCNT embryos. Overexpression of METTL14 significantly increased the RNA m6A level in donor cells and the development efficiency of SCNT embryos, whereas knockdown of METTL14 suggested the opposite result. Moreover, we revealed that RNA m6A-regulated TOP2B mRNA stability, translation level, and DNA damage during SCNT embryo development. Collectively, our results highlight the crosstalk between RNA m6A and DNA methylation, and the crucial role of RNA m6A during nuclear reprogramming in SCNT embryo development.
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Affiliation(s)
- Meng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yanhui Zhai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xinglan An
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Qi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Daoyu Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Yongfeng Zhou
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Sheng Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
| | - Ziyi Li
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of EducationThe First Hospital of Jilin UniversityChangchunJilinChina
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8
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Fang S, Chang KW, Lefebvre L. Roles of endogenous retroviral elements in the establishment and maintenance of imprinted gene expression. Front Cell Dev Biol 2024; 12:1369751. [PMID: 38505259 PMCID: PMC10948482 DOI: 10.3389/fcell.2024.1369751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
DNA methylation (DNAme) has long been recognized as a host defense mechanism, both in the restriction modification systems of prokaryotes as well as in the transcriptional silencing of repetitive elements in mammals. When DNAme was shown to be implicated as a key epigenetic mechanism in the regulation of imprinted genes in mammals, a parallel with host defense mechanisms was drawn, suggesting perhaps a common evolutionary origin. Here we review recent work related to this hypothesis on two different aspects of the developmental imprinting cycle in mammals that has revealed unexpected roles for long terminal repeat (LTR) retroelements in imprinting, both canonical and noncanonical. These two different forms of genomic imprinting depend on different epigenetic marks inherited from the mature gametes, DNAme and histone H3 lysine 27 trimethylation (H3K27me3), respectively. DNAme establishment in the maternal germline is guided by transcription during oocyte growth. Specific families of LTRs, evading silencing mechanisms, have been implicated in this process for specific imprinted genes. In noncanonical imprinting, maternally inherited histone marks play transient roles in transcriptional silencing during preimplantation development. These marks are ultimately translated into DNAme, notably over LTR elements, for the maintenance of silencing of the maternal alleles in the extraembryonic trophoblast lineage. Therefore, LTR retroelements play important roles in both establishment and maintenance of different epigenetic pathways leading to imprinted expression during development. Because such elements are mobile and highly polymorphic among different species, they can be coopted for the evolution of new species-specific imprinted genes.
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Affiliation(s)
| | | | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada
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9
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Liao Z, Zhang J, Sun S, Li Y, Xu Y, Li C, Cao J, Nie Y, Niu Z, Liu J, Lu F, Liu Z, Sun Q. Reprogramming mechanism dissection and trophoblast replacement application in monkey somatic cell nuclear transfer. Nat Commun 2024; 15:5. [PMID: 38228612 PMCID: PMC10791636 DOI: 10.1038/s41467-023-43985-7] [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: 03/16/2023] [Accepted: 11/27/2023] [Indexed: 01/18/2024] Open
Abstract
Somatic cell nuclear transfer (SCNT) successfully clones cynomolgus monkeys, but the efficiency remains low due to a limited understanding of the reprogramming mechanism. Notably, no rhesus monkey has been cloned through SCNT so far. Our study conducts a comparative analysis of multi-omics datasets, comparing embryos resulting from intracytoplasmic sperm injection (ICSI) with those from SCNT. Our findings reveal a widespread decrease in DNA methylation and the loss of imprinting in maternally imprinted genes within SCNT monkey blastocysts. This loss of imprinting persists in SCNT embryos cultured in-vitro until E17 and in full-term SCNT placentas. Additionally, histological examination of SCNT placentas shows noticeable hyperplasia and calcification. To address these defects, we develop a trophoblast replacement method, ultimately leading to the successful cloning of a healthy male rhesus monkey. These discoveries provide valuable insights into the reprogramming mechanism of monkey SCNT and introduce a promising strategy for primate cloning.
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Affiliation(s)
- Zhaodi Liao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jixiang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shiyu Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuzhuo Li
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Yuting Xu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Chunyang Li
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Jing Cao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Yanhong Nie
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China
| | - Zhuoyue Niu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jingwen Liu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Falong Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Liu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China.
| | - Qiang Sun
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- Shanghai Center for Brain Science and Brain-Inspired Technology, Shanghai, 201210, China.
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10
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Liu Z, Wang W, Xia Y, Gao Y, Wang Z, Li M, Presicce GA, An L, Du F. Overcoming the H4K20me3 epigenetic barrier improves somatic cell nuclear transfer reprogramming efficiency in mice. Cell Prolif 2024; 57:e13519. [PMID: 37322828 PMCID: PMC10771106 DOI: 10.1111/cpr.13519] [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: 03/31/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Epigenetic reprogramming during fertilization and somatic cell nuclear transfer (NT) is required for cell plasticity and competent development. Here, we characterize the epigenetic modification pattern of H4K20me3, a repressive histone signature in heterochromatin, during fertilization and NT reprogramming. Importantly, the dynamic H4K20me3 signature identified during preimplantation development in fertilized embryos differed from NT and parthenogenetic activation (PA) embryos. In fertilized embryos, only maternal pronuclei carried the canonical H4K20me3 peripheral nucleolar ring-like signature. H4K20me3 disappeared at the 2-cell stage and reappeared in fertilized embryos at the 8-cell stage and in NT and PA embryos at the 4-cell stage. H4K20me3 intensity in 4-cell, 8-cell, and morula stages of fertilized embryos was significantly lower than in NT and PA embryos, suggesting aberrant regulation of H4K20me3 in PA and NT embryos. Indeed, RNA expression of the H4K20 methyltransferase Suv4-20h2 in 4-cell fertilized embryos was significantly lower than NT embryos. Knockdown of Suv4-20h2 in NT embryos rescued the H4K20me3 pattern similar to fertilized embryos. Compared to control NT embryos, knockdown of Suv4-20h2 in NT embryos improved blastocyst development ratios (11.1% vs. 30.5%) and full-term cloning efficiencies (0.8% vs. 5.9%). Upregulation of reprogramming factors, including Kdm4b, Kdm4d, Kdm6a, and Kdm6b, as well as ZGA-related factors, including Dux, Zscan4, and Hmgpi, was observed with Suv4-20h2 knockdown in NT embryos. Collectively, these are the first findings to demonstrate that H4K20me3 is an epigenetic barrier of NT reprogramming and begin to unravel the epigenetic mechanisms of H4K20 trimethylation in cell plasticity during natural reproduction and NT reprogramming in mice.
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Affiliation(s)
- Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Weiguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yuhan Xia
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yuan Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhisong Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Mingyang Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | | | - Liyou An
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and TechnologyXinjiang UniversityUrumqiChina
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
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11
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Jiang L, Wang X, Wang L, Ma S, Ding Y, Liu C, Wang S, Shao X, Zhang Y, Li Z, Li W, Feng G, Zhou Q. Deciphering the placental abnormalities associated with somatic cell nuclear transfer at single-nucleus resolution. Protein Cell 2023; 14:924-928. [PMID: 37208440 PMCID: PMC10691845 DOI: 10.1093/procel/pwad030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023] Open
Affiliation(s)
- Liyuan Jiang
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Leyun Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Sinan Ma
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
| | - Yali Ding
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Siqi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xuan Shao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Zhikun Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Qi Zhou
- College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
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12
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Li Y, Zheng C, Liu Y, He J, Zhang Q, Zhang Y, Kou X, Zhao Y, Liu K, Bai D, Jia Y, Han X, Sheng Y, Yin J, Wang H, Gao S, Liu W, Gao S. Inhibition of Wnt activity improves peri-implantation development of somatic cell nuclear transfer embryos. Natl Sci Rev 2023; 10:nwad173. [PMID: 37593113 PMCID: PMC10430793 DOI: 10.1093/nsr/nwad173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 06/02/2023] [Indexed: 08/19/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram differentiated somatic cells into totipotency. Although pre-implantation development of SCNT embryos has greatly improved, most SCNT blastocysts are still arrested at the peri-implantation stage, and the underlying mechanism remains elusive. Here, we develop a 3D in vitro culture system for SCNT peri-implantation embryos and discover that persistent Wnt signals block the naïve-to-primed pluripotency transition of epiblasts with aberrant H3K27me3 occupancy, which in turn leads to defects in epiblast transformation events and subsequent implantation failure. Strikingly, manipulating Wnt signals can attenuate the pluripotency transition and H3K27me3 deposition defects in epiblasts and achieve up to a 9-fold increase in cloning efficiency. Finally, single-cell RNA-seq analysis reveals that Wnt inhibition markedly enhances the lineage developmental trajectories of SCNT blastocysts during peri-implantation development. Overall, these findings reveal diminished potentials of SCNT blastocysts for lineage specification and validate a critical peri-implantation barrier for SCNT embryos.
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Affiliation(s)
- Yanhe Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Caihong Zheng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Yingdong Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jincan He
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Qiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalin Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaochen Kou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanhong Zhao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Kuisheng Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dandan Bai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yanping Jia
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Xiaoxiao Han
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Yifan Sheng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Jiqing Yin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Hong Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenqiang Liu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
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13
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Xu R, Zhu Q, Zhao Y, Chen M, Yang L, Shen S, Yang G, Shi Z, Zhang X, Shi Q, Kou X, Zhao Y, Wang H, Jiang C, Li C, Gao S, Liu X. Unreprogrammed H3K9me3 prevents minor zygotic genome activation and lineage commitment in SCNT embryos. Nat Commun 2023; 14:4807. [PMID: 37558707 PMCID: PMC10412629 DOI: 10.1038/s41467-023-40496-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 07/27/2023] [Indexed: 08/11/2023] Open
Abstract
Somatic cell nuclear transfer (SCNT) can be used to reprogram differentiated somatic cells to a totipotent state but has poor efficiency in supporting full-term development. H3K9me3 is considered to be an epigenetic barrier to zygotic genomic activation in 2-cell SCNT embryos. However, the mechanism underlying the failure of H3K9me3 reprogramming during SCNT embryo development remains elusive. Here, we perform genome-wide profiling of H3K9me3 in cumulus cell-derived SCNT embryos. We find redundant H3K9me3 marks are closely related to defective minor zygotic genome activation. Moreover, SCNT blastocysts show severely indistinct lineage-specific H3K9me3 deposition. We identify MAX and MCRS1 as potential H3K9me3-related transcription factors and are essential for early embryogenesis. Overexpression of Max and Mcrs1 significantly benefits SCNT embryo development. Notably, MCRS1 partially rescues lineage-specific H3K9me3 allocation, and further improves the efficiency of full-term development. Importantly, our data confirm the conservation of deficient H3K9me3 differentiation in Sertoli cell-derived SCNT embryos, which may be regulated by alternative mechanisms.
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Affiliation(s)
- Ruimin Xu
- 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
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Qianshu Zhu
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Yuyan Zhao
- 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
| | - Mo Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, 400013, Chongqing, China
| | - Lingyue Yang
- 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
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Shijun Shen
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Guang Yang
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Zhifei Shi
- 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
| | - Xiaolei 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
| | - Qi Shi
- 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
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China
| | - Cizhong Jiang
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Chong Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China.
- Frontier Science Center for Stem Cell Research, 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.
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translation Research Center, Shanghai First Maternity and Infant Hospital, School of Life Science and Technology, Tongji University, 200092, Shanghai, China.
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
| | - Xiaoyu 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.
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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14
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Bi S, Tu Z, Chen D, Zhang S. Histone modifications in embryo implantation and placentation: insights from mouse models. Front Endocrinol (Lausanne) 2023; 14:1229862. [PMID: 37600694 PMCID: PMC10436591 DOI: 10.3389/fendo.2023.1229862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023] Open
Abstract
Embryo implantation and placentation play pivotal roles in pregnancy by facilitating crucial maternal-fetal interactions. These dynamic processes involve significant alterations in gene expression profiles within the endometrium and trophoblast lineages. Epigenetics regulatory mechanisms, such as DNA methylation, histone modification, chromatin remodeling, and microRNA expression, act as regulatory switches to modulate gene activity, and have been implicated in establishing a successful pregnancy. Exploring the alterations in these epigenetic modifications can provide valuable insights for the development of therapeutic strategies targeting complications related to pregnancy. However, our current understanding of these mechanisms during key gestational stages remains incomplete. This review focuses on recent advancements in the study of histone modifications during embryo implantation and placentation, while also highlighting future research directions in this field.
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Affiliation(s)
- Shilei Bi
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Zhaowei Tu
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Dunjin Chen
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
| | - Shuang Zhang
- Key Laboratory for Major Obstetric Diseases of Guangdong, Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine, Guangzhou, China
- Guangdong Engineering and Technology Research Center of Maternal-Fetal Medicine, Guangzhou, China
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15
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Zhang W, Wang M, Song Z, Fu Q, Chen J, Zhang W, Gao S, Sun X, Yang G, Zhang Q, Yang J, Tang H, Wang H, Kou X, Wang H, Mao Z, Xu X, Gao S, Jiang Y. Farrerol directly activates the deubiqutinase UCHL3 to promote DNA repair and reprogramming when mediated by somatic cell nuclear transfer. Nat Commun 2023; 14:1838. [PMID: 37012254 PMCID: PMC10070447 DOI: 10.1038/s41467-023-37576-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 04/05/2023] Open
Abstract
Farrerol, a natural flavanone, promotes homologous recombination (HR) repair to improve genome-editing efficiency, but the specific protein that farrerol directly targets to regulate HR repair and the underlying molecular mechanisms have not been determined. Here, we find that the deubiquitinase UCHL3 is the direct target of farrerol. Mechanistically, farrerol enhanced the deubiquitinase activity of UCHL3 to promote RAD51 deubiquitination, thereby improving HR repair. Importantly, we find that embryos of somatic cell nuclear transfer (SCNT) exhibited defective HR repair, increased genomic instability and aneuploidy, and that the farrerol treatment post nuclear transfer enhances HR repair, restores transcriptional and epigenetic network, and promotes SCNT embryo development. Ablating UCHL3 significantly attenuates farrerol-mediated stimulation in HR and SCNT embryo development. In summary, we identify farrerol as an activator of the deubiquitinase UCHL3, highlighted the importance of HR and epigenetic changes in SCNT reprogramming and provide a feasible method to promote SCNT efficiency.
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Affiliation(s)
- Weina Zhang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Tsingtao Advanced Research Institute, Tongji University, 266071, Qingdao, China
| | - Mingzhu Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Jiaxing University Affiliated Women and Children Hospital, 314000, Jiaxing, China
| | - Zhiwei Song
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Qianzheng Fu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Jiayu Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Weitao Zhang
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Xiaoxiang Sun
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Guang Yang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Qiang Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China
| | - Jiaqing Yang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Huanyin Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Haiyan Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
- Tsingtao Advanced Research Institute, Tongji University, 266071, Qingdao, China.
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, China.
| | - Xiaojun Xu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, 210009, Nanjing, China.
| | - Shaorong Gao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Ying Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
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16
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Inoue A. Noncanonical imprinting: intergenerational epigenetic inheritance mediated by Polycomb complexes. Curr Opin Genet Dev 2023; 78:102015. [PMID: 36577293 DOI: 10.1016/j.gde.2022.102015] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/06/2022] [Accepted: 11/22/2022] [Indexed: 12/27/2022]
Abstract
Genomic imprinting is illustrative of intergenerational epigenetic inheritance. The passage of parental genomes into the embryo is accompanied by epigenetic modifications, resulting in imprinted monoallelic gene expression in mammals. Some imprinted genes are regulated by maternal inheritance of H3K27me3, which is termed noncanonical imprinting. Noncanonical imprinting is established by Polycomb repressive complexes during oogenesis and maintained in preimplantation embryos and extraembryonic tissues, including the placenta. Recent studies of noncanonical imprinting have contributed to our understanding of chromatin regulation in oocytes and early embryos, imprinted X-chromosome inactivation, secondary differentially DNA-methylated regions, and the anomalies of cloned mice. Here, I summarize the current knowledge of noncanonical imprinting and remark on analogous mechanisms in invertebrates and plants.
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Affiliation(s)
- Azusa Inoue
- Laboratory for Epigenome Inheritance, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan; Tokyo Metropolitan University, Hachioji 192-0397, Japan.
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17
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Vargas LN, Silveira MM, Franco MM. Epigenetic Reprogramming and Somatic Cell Nuclear Transfer. Methods Mol Biol 2023; 2647:37-58. [PMID: 37041328 DOI: 10.1007/978-1-0716-3064-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Epigenetics is an area of genetics that studies the heritable modifications in gene expression and phenotype that are not controlled by the primary sequence of DNA. The main epigenetic mechanisms are DNA methylation, post-translational covalent modifications in histone tails, and non-coding RNAs. During mammalian development, there are two global waves of epigenetic reprogramming. The first one occurs during gametogenesis and the second one begins immediately after fertilization. Environmental factors such as exposure to pollutants, unbalanced nutrition, behavioral factors, stress, in vitro culture conditions can negatively affect epigenetic reprogramming events. In this review, we describe the main epigenetic mechanisms found during mammalian preimplantation development (e.g., genomic imprinting, X chromosome inactivation). Moreover, we discuss the detrimental effects of cloning by somatic cell nuclear transfer on the reprogramming of epigenetic patterns and some molecular alternatives to minimize these negative impacts.
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Affiliation(s)
- Luna N Vargas
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Márcia M Silveira
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | - Maurício M Franco
- Laboratory of Animal Reproduction, Embrapa Genetic Resources and Biotechnology, Brasília, Distrito Federal, Brazil.
- Institute of Biotechnology, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
- School of Veterinary Medicine, Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil.
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18
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Goissis MD, Cibelli JB. Early Cell Specification in Mammalian Fertilized and Somatic Cell Nuclear Transfer Embryos. Methods Mol Biol 2023; 2647:59-81. [PMID: 37041329 DOI: 10.1007/978-1-0716-3064-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Early cell specification in mammalian preimplantation embryos is an intricate cellular process that leads to coordinated spatial and temporal expression of specific genes. Proper segregation into the first two cell lineages, the inner cell mass (ICM) and the trophectoderm (TE), is imperative for developing the embryo proper and the placenta, respectively. Somatic cell nuclear transfer (SCNT) allows the formation of a blastocyst containing both ICM and TE from a differentiated cell nucleus, which means that this differentiated genome must be reprogrammed to a totipotent state. Although blastocysts can be generated efficiently through SCNT, the full-term development of SCNT embryos is impaired mostly due to placental defects. In this review, we examine the early cell fate decisions in fertilized embryos and compare them to observations in SCNT-derived embryos, in order to understand if these processes are affected by SCNT and could be responsible for the low success of reproductive cloning.
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Affiliation(s)
- Marcelo D Goissis
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Jose B Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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19
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Ikeda S. Current status of genome-wide epigenetic profiling of mammalian preimplantation embryos. Reprod Med Biol 2023; 22:e12521. [PMID: 37351110 PMCID: PMC10283350 DOI: 10.1002/rmb2.12521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/25/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
Background Genome-wide information on epigenetic modifications in mammalian preimplantation embryos was an unexplored sanctuary of valuable research insights protected by the difficulty of its analysis. However, that is no longer the case, and many epigenome maps are now available for sightseeing there. Methods This review overviews the current status of genome-wide epigenetic profiling in terms of DNA methylome and histone modifications in mammalian preimplantation embryos. Main findings As the sensitivity of methods for analyzing epigenetic modifications increased, pioneering work began to explore the genome-wide epigenetic landscape in the mid-2010s, first for DNA methylation and then for histone modifications. Since then, a huge amount of data has accumulated, revealing typical epigenetic profiles in preimplantation development and, more recently, changes in response to environmental interventions. Conclusions These accumulating data may be used to improve the quality of preimplantation embryos, both in terms of their short-term developmental competence and their subsequent long-term health implications.
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Affiliation(s)
- Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of AgricultureKyoto UniversityKyotoJapan
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20
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Moura MT. Cloning by SCNT: Integrating Technical and Biology-Driven Advances. Methods Mol Biol 2023; 2647:1-35. [PMID: 37041327 DOI: 10.1007/978-1-0716-3064-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Somatic cell nuclear transfer (SCNT) into enucleated oocytes initiates nuclear reprogramming of lineage-committed cells to totipotency. Pioneer SCNT work culminated with cloned amphibians from tadpoles, while technical and biology-driven advances led to cloned mammals from adult animals. Cloning technology has been addressing fundamental questions in biology, propagating desired genomes, and contributing to the generation of transgenic animals or patient-specific stem cells. Nonetheless, SCNT remains technically complex and cloning efficiency relatively low. Genome-wide technologies revealed barriers to nuclear reprogramming, such as persistent epigenetic marks of somatic origin and reprogramming resistant regions of the genome. To decipher the rare reprogramming events that are compatible with full-term cloned development, it will likely require technical advances for large-scale production of SCNT embryos alongside extensive profiling by single-cell multi-omics. Altogether, cloning by SCNT remains a versatile technology, while further advances should continuously refresh the excitement of its applications.
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Affiliation(s)
- Marcelo Tigre Moura
- Chemical Biology Graduate Program, Federal University of São Paulo - UNIFESP, Campus Diadema, Diadema - SP, Brazil
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21
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The influence of high-order chromatin state in the regulation of stem cell fate. Biochem Soc Trans 2022; 50:1809-1822. [DOI: 10.1042/bst20220763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
In eukaryotic cells, genomic DNA is hierarchically compacted by histones into chromatin, which is initially assembled by the nucleosome and further folded into orderly and flexible structures that include chromatin fiber, chromatin looping, topologically associated domains (TADs), chromosome compartments, and chromosome territories. These distinct structures and motifs build the three-dimensional (3D) genome architecture, which precisely controls spatial and temporal gene expression in the nucleus. Given that each type of cell is characterized by its own unique gene expression profile, the state of high-order chromatin plays an essential role in the cell fate decision. Accumulating evidence suggests that the plasticity of high-order chromatin is closely associated with stem cell fate. In this review, we summarize the biological roles of the state of high-order chromatin in embryogenesis, stem cell differentiation, the maintenance of stem cell identity, and somatic cell reprogramming. In addition, we highlight the roles of epigenetic factors and pioneer transcription factors (TFs) involved in regulating the state of high-order chromatin during the determination of stem cell fate and discuss how H3K9me3-heterochromatin restricts stem cell fate. In summary, we review the most recent progress in research on the regulatory functions of high-order chromatin dynamics in the determination and maintenance of stem cell fate.
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22
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Shikata D, Matoba S, Hada M, Sakashita A, Inoue K, Ogura A. Suppression of endogenous retroviral enhancers in mouse embryos derived from somatic cell nuclear transfer. Front Genet 2022; 13:1032760. [PMID: 36425066 PMCID: PMC9681155 DOI: 10.3389/fgene.2022.1032760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022] Open
Abstract
Endogenous retroviruses (ERVs) in the mammalian genome play diverse roles in embryonic development. These developmentally related ERVs are generally repressed in somatic cells and therefore are likely repressed in embryos derived from somatic cell nuclear transfer (SCNT). In this study, we sought to identify ERVs that are repressed in SCNT-derived morulae, which might cause previously unexplained embryonic deaths shortly after implantation. Our transcriptome analysis revealed that, amongst ERV families, ERVK was specifically, and strongly downregulated in SCNT-derived embryos while other transposable elements including LINE and ERVL were unchanged. Among the subfamilies of ERVK, RLTR45-int was most repressed in SCNT-derived embryos despite its highest expression in control fertilized embryos. Interestingly, the nearby genes (within 5–50 kb, n = 18; 50–200 kb, n = 63) of the repressed RLTR45-int loci were also repressed in SCNT-derived embryos, with a significant correlation between them. Furthermore, lysine H3K27 acetylation was enriched around the RLTR45-int loci. These findings indicate that RLTR45-int elements function as enhancers of nearby genes. Indeed, deletion of two sequential RLTR45-int loci on chromosome 4 or 18 resulted in downregulations of nearby genes at the morula stage. We also found that RLTR45-int loci, especially SCNT-low, enhancer-like loci, were strongly enriched with H3K9me3, a repressive histone mark. Importantly, these H3K9me3-enriched regions were not activated by overexpression of H3K9me3 demethylase Kdm4d in SCNT-derived embryos, suggesting the presence of another epigenetic barrier repressing their expressions and enhancer activities in SCNT embryos. Thus, we identified ERVK subfamily RLTR45-int, putative enhancer elements, as a strong reprogramming barrier for SCNT (253 words).
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Affiliation(s)
- Daiki Shikata
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Masashi Hada
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Laboratory of Pathology and Development, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Shinjuku-ku, Tokyo, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN BioResource Research Center, Tsukuba, Ibaraki, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
- RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- *Correspondence: Atsuo Ogura,
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23
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Yu T, Meng R, Song W, Sun H, An Q, Zhang C, Zhang Y, Su J. ZFP57 regulates DNA methylation of imprinted genes to facilitate embryonic development of somatic cell nuclear transfer embryos in Holstein cows. J Dairy Sci 2022; 106:769-782. [DOI: 10.3168/jds.2022-22427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/17/2022] [Indexed: 11/17/2022]
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24
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Navarro M, Halstead MM, Rincon G, Mutto AA, Ross PJ. bESC from cloned embryos do not retain transcriptomic or epigenetic memory from somatic donor cells. Reproduction 2022; 164:243-257. [PMID: 35951478 DOI: 10.1530/rep-22-0063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 08/11/2022] [Indexed: 11/08/2022]
Abstract
In brief Epigenetic reprogramming after mammalian somatic cell nuclear transfer is often incomplete, resulting in low efficiency of cloning. However, gene expression and histone modification analysis indicated high similarities in transcriptome and epigenomes of bovine embryonic stem cells from in vitro fertilized and somatic cell nuclear transfer embryos. Abstract Embryonic stem cells (ESC) indefinitely maintain the pluripotent state of the blastocyst epiblast. Stem cells are invaluable for studying development and lineage commitment, and in livestock, they constitute a useful tool for genomic improvement and in vitro breeding programs. Although these cells have been recently derived from bovine blastocysts, a detailed characterization of their molecular state is lacking. Here, we apply cutting-edge technologies to analyze the transcriptomic and epigenomic landscape of bovine ESC (bESC) obtained from in vitro fertilized (IVF) and somatic cell nuclear transfer (SCNT) embryos. bESC were efficiently derived from SCNT and IVF embryos and expressed pluripotency markers while retaining genome stability. Transcriptome analysis revealed that only 46 genes were differentially expressed between IVF- and SCNT-derived bESC, which did not reflect significant deviation in cellular function. Interrogating histone 3 lysine 4 trimethylation, histone 3 lysine 9 trimethylation, and histone 3 lysine 27 trimethylation with cleavage under targets and tagmentation, we found that the epigenomes of both bESC groups were virtually indistinguishable. Minor epigenetic differences were randomly distributed throughout the genome and were not associated with differentially expressed or developmentally important genes. Finally, the categorization of genomic regions according to their combined histone mark signal demonstrated that all bESC shared the same epigenomic signatures, especially at gene promoters. Overall, we conclude that bESC derived from SCNT and IVF embryos are transcriptomically and epigenetically analogous, allowing for the production of an unlimited source of pluripotent cells from high genetic merit organisms without resorting to transgene-based techniques.
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Affiliation(s)
- M Navarro
- Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde', UNSAM-CONICET, Buenos Aires, Argentina.,Department of Animal Science, University of California, Davis, California, USA
| | - M M Halstead
- Department of Animal Science, University of California, Davis, California, USA
| | | | - A A Mutto
- Instituto de Investigaciones Biotecnológicas 'Dr Rodolfo Ugalde', UNSAM-CONICET, Buenos Aires, Argentina
| | - P J Ross
- Department of Animal Science, University of California, Davis, California, USA
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25
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Dynamic and aberrant patterns of H3K4me3, H3K9me3, and H3K27me3 during early zygotic genome activation in cloned mouse embryos. ZYGOTE 2022; 30:903-909. [DOI: 10.1017/s0967199422000454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Summary
Somatic cell nuclear transfer (NT) is associated with aberrant changes in epigenetic reprogramming that impede the development of embryos, particularly during zygotic genome activation. Here, we characterized epigenetic patterns of H3K4me3, H3K9me3, and H3K27me3 in mouse NT embryos up to the second cell cycle (i.e. four-celled stage) during zygotic genome activation. In vivo fertilized and parthenogenetically activated (PA) embryos served as controls. In fertilized embryos, maternal and paternal pronuclei exhibited asymmetric H3K4me3, H3K9me3, and H3K27me3 modifications, with the paternal pronucleus showing delayed epigenetic modifications. Higher levels of H3K4me3 and H3K9me3 were observed in NT and PA embryos than in fertilized embryos. However, NT embryos exhibited a lower level of H3K27me3 than PA and fertilized embryos from pronuclear stage 3 to the four-celled stage. Our finding that NT embryos exhibited aberrant H3K4me3, H3K9me3, and H3K27me3 modifications in comparison with fertilized embryos during early zygotic genome activation help to unravel the epigenetic mechanisms of methylation changes in early NT reprogramming and provide an insight into the role of histone H3 in the regulation of cell plasticity during natural reproduction and somatic cell NT.
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26
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Li Y, Sun Q. Epigenetic manipulation to improve mouse SCNT embryonic development. Front Genet 2022; 13:932867. [PMID: 36110221 PMCID: PMC9468881 DOI: 10.3389/fgene.2022.932867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 07/29/2022] [Indexed: 11/29/2022] Open
Abstract
Cloned mammals can be achieved through somatic cell nuclear transfer (SCNT), which involves reprogramming of differentiated somatic cells into a totipotent state. However, low cloning efficiency hampers its application severely. Cloned embryos have the same DNA as donor somatic cells. Therefore, incomplete epigenetic reprogramming accounts for low development of cloned embryos. In this review, we describe recent epigenetic barriers in SCNT embryos and strategies to correct these epigenetic defects and avoid the occurrence of abnormalities in cloned animals.
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Affiliation(s)
- Yamei Li
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Qiang Sun
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Neuroscience, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
- *Correspondence: Qiang Sun,
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27
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Liu Z, Li M, Sun Y, Wang W, Wang Z, Presicce GA, An L, Du F. Epigenetic dynamics of H4K20me3 modification during oocyte maturation and early reprogramming of somatic cell nuclear transfer goat embryos. Am J Transl Res 2022; 14:5941-5951. [PMID: 36105059 PMCID: PMC9452338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/22/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE We examined the epigenetic dynamics of histone H4K20 trimethylation (H4K20me3), a repressive signature in heterochromatin, during goat oocyte meiosis and the reprogramming of somatic cell nuclear transfer (NT) embryos through the first three cell divisions. METHODS Following NT, oocytes were treated with parthenogenetic activation (PA), by 5 µM calcium ionophore A23187 for 5 min followed by incubation in 2.0 mM 6-dimethylaminopurine with 5 µg/mL cycloheximide for 4 h. NT embryos up to 8-celled stage were incubated with H4K20me3 antibody. RESULTS Immunofluorescence microscopy revealed the existence of a persistent H4K20me3 signature during oocyte maturation from germinal vesicle phase to metaphase I, anaphase I, telophase I, and metaphase II, with a gradual reduction in staining intensity. NT embryos at the 2-, 4- and 8-celled stage showed lower H4K20me3 intensity than PA and IVF embryos (P < 0.05). CONCLUSION These results indicate that NT embryos exhibit insufficient H4K20me3 modification compared with IVF and PA embryos during early reprogramming, suggesting the existence of a resistant memory of differentiated cell nuclear architecture. These findings help unravel the epigenetic mechanism of histone H4K20me3 in goat nuclear transfer reprogramming.
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Affiliation(s)
- Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
| | - Mingyang Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
| | - Yu Sun
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
| | - Weiguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
| | - Zhisong Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
| | | | - Liyou An
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang UniversityUrumqi 830046, Xinjiang, PR China
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal UniversityNanjing 210046, Jiangsu, PR China
- Renova Life Inc., College ParkMaryland 20742, USA
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28
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Wang J, Zhou C, Gao S, Song X, Yang X, Fan J, Ren S, Ma L, Zhao J, Cui M, Song K, Wang M, Li C, Zheng Y, Luo F, Miao K, Bai X, Hutchins AP, Li L, Chang G, Zhao XY. Single-cell multiomics sequencing reveals the reprogramming defects in embryos generated by round spermatid injection. SCIENCE ADVANCES 2022; 8:eabm3976. [PMID: 35947654 PMCID: PMC9365279 DOI: 10.1126/sciadv.abm3976] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/23/2022] [Indexed: 06/15/2023]
Abstract
Round spermatid injection (ROSI) technique holds great promise for clinical treatment of a proportion of infertile men. However, the compromised developmental potential of ROSI embryos largely limits the clinical application, and the mechanisms are not fully understood. Here, we describe the transcriptome, chromatin accessibility, and DNA methylation landscapes of mouse ROSI embryos derived from early-stage round spermatids using a single-cell multiomics sequencing approach. By interrogating these data, we identify the reprogramming defects in ROSI embryos at the pronuclear stages, which are mainly associated with the misexpression of a cohort of minor zygotic genome activation genes. We screen a small compound, A366, that can significantly increase the developmental potential of ROSI embryos, in which A366 can partially overcome the reprogramming defects by amending the epigenetic and transcriptomic states. Collectively, our study uncovers the reprogramming defects in ROSI embryos for understanding the mechanisms underlying compromised developmental potential and offers an avenue for ROSI technique optimization.
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Affiliation(s)
- Jing Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Cai Zhou
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Shuai Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of the MARA, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, P. R. China
| | - Xiuling Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Xinyan Yang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Jiaqi Fan
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Shaofang Ren
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Linzi Ma
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Jiexiang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Manman Cui
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Ke Song
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Mei Wang
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Chaohui Li
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Yi Zheng
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Fang Luo
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Kai Miao
- Center for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau, SAR, China
| | - Xiaochun Bai
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
| | - Andrew P. Hutchins
- Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518060, P. R. China
| | - Lin Li
- Guangdong Provincial Key Laboratory of Proteomics, Department of Pathophysiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Gang Chang
- Department of Biochemistry and Molecular Biology, Shenzhen University Health Science Center, Shenzhen, Guangdong 518060, P. R. China
| | - Xiao-Yang Zhao
- State Key Laboratory of Organ Failure Research, Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
- Guangdong Key Laboratory of Construction and Detection in Tissue Engineering, Southern Medical University, Guangzhou, Guangdong 510515, P. R. China
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou, Guangdong 510700, P. R. China
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29
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Zhao Y, Bai D, Wu Y, Zhang D, Liu M, Tian Y, Lu J, Wang H, Gao S, Lu Z. Maternal Ezh1/2 deficiency in oocyte delays H3K27me2/3 restoration and impairs epiblast development responsible for embryonic sub-lethality in mouse. Development 2022; 149:dev200316. [PMID: 38771308 DOI: 10.1242/dev.200316] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 06/23/2022] [Indexed: 05/22/2024]
Abstract
How maternal Ezh1 and Ezh2 function in H3K27 methylation in vivo in pre-implantation embryos and during embryonic development is not clear. Here, we have deleted Ezh1 and Ezh2 alone or simultaneously from mouse oocytes. H3K27me3 was absent in oocytes without Ezh2 alone, while both H3K27me2 and H3K27me3 were absent in Ezh1/Ezh2 (Ezh1/2) double knockout (KO) oocytes. The effects of Ezh1/2 maternal KO were inherited in zygotes and early embryos, in which restoration of H3K27me3 and H3K27me2 was delayed by the loss of Ezh2 alone or of both Ezh1 and Ezh2. However, the ablation of both Ezh1 and Ezh2, but not Ezh1 or Ezh2 alone, led to significantly decreased litter size due to growth retardation post-implantation. Maternal Ezh1/2 deficiency caused compromised H3K27me3 and pluripotent epiblast cells in late blastocysts, followed by defective embryonic development. By using RNA-seq, we examined crucial developmental genes in maternal Ezh1/2 KO embryos and identified 80 putatively imprinted genes. Maternal Ezh1/2-H3K27 methylation is inherited in offspring embryos and has a critical effect on fetal and placental development. Thus, this work sheds light on maternal epigenetic modifications during embryonic development.
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Affiliation(s)
- Yinan Zhao
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Dandan Bai
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - You Wu
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Dan Zhang
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Mengying Liu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Yingpu Tian
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian 361005, China
| | - Jinhua Lu
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, Fujian 361102, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, Fujian 361102, China
| | - Shaorong Gao
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Zhongxian Lu
- School of Pharmaceutical Sciences, State Key Laboratory of Cellular Stress Biology, Xiamen University, Xiamen, Fujian 361005, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Medical College of Xiamen University, Xiamen, Fujian 361102, China
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30
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Bu G, Zhu W, Liu X, Zhang J, Yu L, Zhou K, Wang S, Li Z, Fan Z, Wang T, Hu T, Hu R, Liu Z, Wang T, Wu L, Zhang X, Zhao S, Miao YL. Coordination of zygotic genome activation entry and exit by H3K4me3 and H3K27me3 in porcine early embryos. Genome Res 2022; 32:gr.276207.121. [PMID: 35868641 PMCID: PMC9435746 DOI: 10.1101/gr.276207.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/19/2022] [Indexed: 02/03/2023]
Abstract
Histone modifications are critical epigenetic indicators of chromatin state associated with gene expression. Although the reprogramming patterns of H3K4me3 and H3K27me3 have been elucidated in mouse and human preimplantation embryos, the relationship between these marks and zygotic genome activation (ZGA) remains poorly understood. By ultra-low-input native chromatin immunoprecipitation and sequencing, we profiled global H3K4me3 and H3K27me3 in porcine oocytes and in vitro fertilized (IVF) embryos. We found that promoters of ZGA genes occupied sharp H3K4me3 peaks in oocytes, and these peaks became broader after fertilization, and reshaped into sharp again during ZGA. By simultaneous depletion of H3K4me3 demethylase KDM5B and KDM5C, we determined that broad H3K4me3 domain maintenance impaired ZGA gene expression, suggesting its function to prevent premature ZGA entry. By contrast, broad H3K27me3 domains underwent global removal upon fertilization, followed by a re-establishment for H3K4me3/H3K27me3 bivalency in morulae. We also found that bivalent marks were deposited at promoters of ZGA genes, and inhibiting this deposition was correlated with the activation of ZGA genes. It suggests that promoter bivalency contributes to ZGA exit in porcine embryos. Moreover, we demonstrated that aberrant reprogramming of H3K4me3 and H3K27me3 triggered ZGA dysregulation in somatic cell nuclear transfer (SCNT) embryos, whereas H3K27me3-mediated imprinting did not exist in porcine IVF and SCNT embryos. Our findings highlight two previously unknown epigenetic reprogramming modes coordinated with ZGA in porcine preimplantation embryos. Finally, the similarities observed between porcine and human histone modification dynamics suggest that the porcine embryo may also be a useful model for human embryo research.
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Affiliation(s)
| | - Wei Zhu
- Huazhong Agricultural University
| | - Xin Liu
- Huazhong Agricultural University
| | | | | | - Kai Zhou
- Huazhong Agricultural University
| | | | | | | | | | | | | | | | - Tao Wang
- Huazhong Agricultural University
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31
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Liu Z, Chen Q, You X, Wu X, Liu R, Li T, Gao L, Chen X, Lei A, Zeng W, Zheng Y. Sperm-derived RNAs improve the efficiency of somatic cell nuclear transfer (SCNT) through promoting R-loop formation. Mol Reprod Dev 2022; 89:325-336. [PMID: 35734898 DOI: 10.1002/mrd.23627] [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: 01/19/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/10/2022]
Abstract
Mammalian sperm and oocytes are haploid cells that carry parental genetic and epigenetic information for their progeny. The cytoplasm of oocytes is also capable of reprograming somatic cells to establish totipotency through somatic cell nuclear transfer (SCNT). However, epigenetic barriers seriously counteract SCNT reprogramming. Here, we found that sperm-derived RNAs elevated chromatin accessibility of nuclear donor cells concurrent with the appearance of increased RNA amount and decreased cell proliferation, instead of activating DNA damage response. Additionally, tri-methylation of lysine 9 on histone H3 (H3K9me3) and the H3K9 methyltransferase SUV39H2 were significantly downregulated by the sperm-derived RNA treatment. Our findings thus raise a fascinating possibility that sperm RNA-induced R-loops may activate gene expression and chromatin structure, thereby promoting SCNT reprogramming.
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Affiliation(s)
- Zidong Liu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Qiang Chen
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xueni You
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xiaodong Wu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Ruifang Liu
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Tao Li
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Leilei Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Xiaoxu Chen
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Anmin Lei
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, Shaanxi Stem Cell Engineering and Technology Center, Northwest A&F University, Xianyang, Shaanxi, China
| | - Wenxian Zeng
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
| | - Yi Zheng
- Department of Animal Science, Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Xianyang, Shaanxi, China
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32
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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33
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Ren X, She C, Huang S, Yang T, Tong Y, Yuan X, Shi D, Li X. Chromatin openness of donor cells is directly correlated with the in vitro developmental capabilities of cloned buffalo embryos. Reprod Domest Anim 2022; 57:1113-1124. [PMID: 35689464 DOI: 10.1111/rda.14177] [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: 04/28/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
The Switch/sucrose nonfermentable (SWI/SNF) chromatin remodelling complex is closely related to chromatin openness and gene transcriptional activity. To understand if the chromatin openness of donor cells was related to the development efficiency of somatic cell cloning embryos, two buffalo fetal fibroblasts (BFF), BFF1 and BFF3, with significantly different cloned blastocyst development rates (18.4% and 30.9% respectively), were selected in this study. The expression of SWI/SNF complex genes, chromatin openness, and transcript level of these two cell lines were analysed, and the effect of ATP on the expression of the SWI/SNF complex genes was further explored. The results showed that compared with BFF1, the expression of SWI/SNF complex family genes was higher in BFF3 at the G0/G1 phase, where SMARCC1, SMARCC2 and SMARCE1 were significantly different (p < .05). Assay of Transposase Accessible Chromatin sequencing (ATAC-seq) results showed that, at the genome-wide level, BFF3 had more open chromatin, especially which having more open chromatin peaks at SMARCA4, SMARCA2, and RBPMS2 (RNA Binding Protein, mRNA Processing Factor 2) sites. In total, 2,712 differentially expressed genes (DEGs) were identified by the RNA-Seq method, with 1380 up- and 1332 down-regulated genes in BFF3. Interestingly, the ATPase-related genes ATP1B1 and ATP11A were extreme significantly up-regulated in BFF3 (p < .01). The ATP content and the expression of SWI/SNF complex genes in both BFF1 and BFF3 decreased when treated with rotenone. The above results demonstrated that the SWI/SNF complex contributed to chromatin opening, and chromatin opening of donor cells was essential for cloned embryo development.
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Affiliation(s)
- Xuan Ren
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Chun She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Shihai Huang
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Ting Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Yi Tong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Xi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
| | - Xiangping Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
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34
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Rong Y, Zhu YZ, Yu JL, Wu YW, Ji SY, Zhou Y, Jiang Y, Jin J, Fan HY, Shen L, Sha QQ. USP16-mediated histone H2A lysine-119 deubiquitination during oocyte maturation is a prerequisite for zygotic genome activation. Nucleic Acids Res 2022; 50:5599-5616. [PMID: 35640597 PMCID: PMC9178006 DOI: 10.1093/nar/gkac468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/12/2022] [Accepted: 05/17/2022] [Indexed: 12/12/2022] Open
Abstract
Maternal-to-zygotic transition (MZT) is the first and key step in the control of animal development and intimately related to changes in chromatin structure and histone modifications. H2AK119ub1, an important epigenetic modification in regulating chromatin configuration and function, is primarily catalyzed by PRC1 and contributes to resistance to transcriptional reprogramming in mouse embryos. In this study, the genome-wide dynamic distribution of H2AK119ub1 during MZT in mice was investigated using chromosome immunoprecipitation and sequencing. The results indicated that H2AK119ub1 accumulated in fully grown oocytes and was enriched at the TSSs of maternal genes, but was promptly declined after meiotic resumption at genome-wide including the TSSs of early zygotic genes, by a previously unidentified mechanism. Genetic evidences indicated that ubiquitin-specific peptidase 16 (USP16) is the major deubiquitinase for H2AK119ub1 in mouse oocytes. Conditional knockout of Usp16 in oocytes did not impair their survival, growth, or meiotic maturation. However, oocytes lacking USP16 have defects when undergoing zygotic genome activation or gaining developmental competence after fertilization, potentially associated with high levels of maternal H2AK119ub1 deposition on the zygotic genomes. Taken together, H2AK119ub1 level is declined during oocyte maturation by an USP16-dependent mechanism, which ensures zygotic genome reprogramming and transcriptional activation of essential early zygotic genes.
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Affiliation(s)
- Yan Rong
- Key Laboratory of Reproductive Dysfunction Management of Zhejiang Province; Assisted Reproduction Unit, Department of Obstetrics and Gynecology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China.,MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ye-Zhang Zhu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jia-Li Yu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Shu-Yan Ji
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yong Zhou
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
| | - Yu Jiang
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jin Jin
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- MOE Key Laboratory for Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Qian-Qian Sha
- Fertility Preservation Laboratory, Reproductive Medicine Center, Guangdong Second Provincial General Hospital, Guangzhou 510317, China
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35
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Liu C, Li W. Advances in haploid embryonic stem cell research. Biol Reprod 2022; 107:250-260. [PMID: 35639627 DOI: 10.1093/biolre/ioac110] [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: 01/25/2022] [Revised: 05/12/2022] [Accepted: 05/25/2022] [Indexed: 11/14/2022] Open
Abstract
Haploid embryonic stem cells are embryonic stem cells of a special type. Their nuclei contain one complete set of genetic material, and they are capable of self-renewal and differentiation. The emergence of haploid embryonic stem cells has aided research in functional genomics, genetic imprinting, parthenogenesis, genetic screening, and somatic cell nuclear transfer. This article reviews current issues in haploid stem cell research based on reports published in recent years and assesses the potential applications of these cells in somatic cell nuclear transfer, genome imprinting, and parthenogenesis.
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Affiliation(s)
- Chao Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.,Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing 100101, China.,Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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36
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Matoba S, Kozuka C, Miura K, Inoue K, Kumon M, Hayashi R, Ohhata T, Ogura A, Inoue A. Noncanonical imprinting sustains embryonic development and restrains placental overgrowth. Genes Dev 2022; 36:483-494. [PMID: 35483741 PMCID: PMC9067403 DOI: 10.1101/gad.349390.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/08/2022] [Indexed: 01/23/2023]
Abstract
In this study, Matoba et al. use a combinatorial maternal KO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, and show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Their findings provide evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth. Genomic imprinting regulates parental origin-dependent monoallelic gene expression. It is mediated by either germline differential methylation of DNA (canonical imprinting) or oocyte-derived H3K27me3 (noncanonical imprinting) in mice. Depletion of Eed, an essential component of Polycomb repressive complex 2, results in genome-wide loss of H3K27me3 in oocytes, which causes loss of noncanonical imprinting (LOI) in embryos. Although Eed maternal KO (matKO) embryos show partial lethality after implantation, it is unknown whether LOI itself contributes to the developmental phenotypes of these embryos, which makes it unclear whether noncanonical imprinting is developmentally relevant. Here, by combinatorial matKO of Xist, a noncanonical imprinted gene whose LOI causes aberrant transient maternal X-chromosome inactivation (XCI) at preimplantation, we show that prevention of the transient maternal XCI greatly restores the development of Eed matKO embryos. Moreover, we found that the placentae of Eed matKO embryos are remarkably enlarged in a manner independent of Xist LOI. Heterozygous deletion screening of individual autosomal noncanonical imprinted genes suggests that LOI of the Sfmbt2 miRNA cluster chromosome 2 miRNA cluster (C2MC), solute carrier family 38 member 4 (Slc38a4), and Gm32885 contributes to the placental enlargement. Taken together, our study provides evidence that Xist imprinting sustains embryonic development and that autosomal noncanonical imprinting restrains placental overgrowth.
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Affiliation(s)
- Shogo Matoba
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu 183-8509, Japan
| | - Chisayo Kozuka
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Kento Miura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan
| | - Mami Kumon
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Ryoya Hayashi
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu 431-3192, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, RIKEN Bioresource Research Center, Tsukuba 305-0074, Japan.,Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan.,The Center for Disease Biology and Integrative Medicine, Faculty of Medicine, University of Tokyo, Tokyo 113-0033, Japan.,RIKEN Cluster for Pioneering Research, Wako 351-0198, Japan
| | - Azusa Inoue
- Young Chief Investigator (YCI) Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Tokyo Metropolitan University, Hachioji 192-0397, Japan
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37
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Xie Z, Zhang W, Zhang Y. Loss of Slc38a4 imprinting is a major cause of mouse placenta hyperplasia in somatic cell nuclear transferred embryos at late gestation. Cell Rep 2022; 38:110407. [PMID: 35196486 PMCID: PMC8919768 DOI: 10.1016/j.celrep.2022.110407] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 11/02/2021] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Placenta hyperplasia is commonly observed in cloned animals and is believed to impede the proper development of cloned embryos. However, the mechanism underlying this phenomenon is largely unknown. Here, we show that placenta hyperplasia of cloned mouse embryos occurs in both middle and late gestation. Interestingly, restoring paternal-specific expression of an amino acid transporter Slc38a4, which loses maternal H3K27me3-dependent imprinting and becomes biallelically expressed in cloned placentae, rescues the overgrowth of cloned placentae at late gestation. Molecular analyses reveal that loss of Slc38a4 imprinting leads to over-activation of the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway in cloned placentae, which is likely due to the increased amino acids transport by SLC38A4. Collectively, our study not only reveals loss of Slc38a4 imprinting is responsible for overgrowth of cloned placentae at late gestation but also suggests the underlying mechanism involves increased amino acid transport and over-activation of mTORC1.
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Affiliation(s)
- Zhenfei Xie
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; The Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA 02139, USA
| | - Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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38
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Cao W, Zhao J, Qu P, Liu E. Current Progress and Prospects in Rabbit Cloning. Cell Reprogram 2022; 24:63-70. [PMID: 35167365 DOI: 10.1089/cell.2021.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) shows great value in the generation of transgenic animals, protection of endangered animals, and stem cell therapy. The combination of SCNT and gene editing has produced a variety of genetically modified animals for life science and medical research. Rabbits have unique advantages as transgenic bioreactors and human disease models; however, the low SCNT efficiency severely impedes the application of this technology. The difficulty in SCNT may be attributable to the abnormal reprogramming of somatic cells in rabbits. This review focuses on the abnormal reprogramming of cloned mammalian embryos and evaluates the progress and prospects of rabbit somatic cell cloning.
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Affiliation(s)
- Wenbin Cao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jinpeng Zhao
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Pengxiang Qu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Enqi Liu
- Laboratory Animal Center, Xi'an Jiaotong University Health Science Center, Xi'an, China
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Strategies to Improve the Efficiency of Somatic Cell Nuclear Transfer. Int J Mol Sci 2022; 23:ijms23041969. [PMID: 35216087 PMCID: PMC8879641 DOI: 10.3390/ijms23041969] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/07/2022] [Accepted: 02/08/2022] [Indexed: 01/04/2023] Open
Abstract
Mammalian oocytes can reprogram differentiated somatic cells into a totipotent state through somatic cell nuclear transfer (SCNT), which is known as cloning. Although many mammalian species have been successfully cloned, the majority of cloned embryos failed to develop to term, resulting in the overall cloning efficiency being still low. There are many factors contributing to the cloning success. Aberrant epigenetic reprogramming is a major cause for the developmental failure of cloned embryos and abnormalities in the cloned offspring. Numerous research groups attempted multiple strategies to technically improve each step of the SCNT procedure and rescue abnormal epigenetic reprogramming by modulating DNA methylation and histone modifications, overexpression or repression of embryonic-related genes, etc. Here, we review the recent approaches for technical SCNT improvement and ameliorating epigenetic modifications in donor cells, oocytes, and cloned embryos in order to enhance cloning efficiency.
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Hada M, Miura H, Tanigawa A, Matoba S, Inoue K, Ogonuki N, Hirose M, Watanabe N, Nakato R, Fujiki K, Hasegawa A, Sakashita A, Okae H, Miura K, Shikata D, Arima T, Shirahige K, Hiratani I, Ogura A. Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells. Genes Dev 2022; 36:84-102. [PMID: 34992147 PMCID: PMC8763053 DOI: 10.1101/gad.348782.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 12/21/2021] [Indexed: 01/22/2023]
Abstract
Here, Hada et al. comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). They used genome-wide, high-throughput analyses to show that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures that have a high degree of histone H3.1/3.2–H3K9me3 accumulation, termed TSC-defined highly heterochromatinized domains (THDs), and are uniquely developed in placental lineage cells that serve to protect them from fate reprogramming to stably maintain placental function. The placenta is a highly evolved, specialized organ in mammals. It differs from other organs in that it functions only for fetal maintenance during gestation. Therefore, there must be intrinsic mechanisms that guarantee its unique functions. To address this question, we comprehensively analyzed epigenomic features of mouse trophoblast stem cells (TSCs). Our genome-wide, high-throughput analyses revealed that the TSC genome contains large-scale (>1-Mb) rigid heterochromatin architectures with a high degree of histone H3.1/3.2–H3K9me3 accumulation, which we termed TSC-defined highly heterochromatinized domains (THDs). Importantly, depletion of THDs by knockdown of CAF1, an H3.1/3.2 chaperone, resulted in down-regulation of TSC markers, such as Cdx2 and Elf5, and up-regulation of the pluripotent marker Oct3/4, indicating that THDs maintain the trophoblastic nature of TSCs. Furthermore, our nuclear transfer technique revealed that THDs are highly resistant to genomic reprogramming. However, when H3K9me3 was removed, the TSC genome was fully reprogrammed, giving rise to the first TSC cloned offspring. Interestingly, THD-like domains are also present in mouse and human placental cells in vivo, but not in other cell types. Thus, THDs are genomic architectures uniquely developed in placental lineage cells, which serve to protect them from fate reprogramming to stably maintain placental function.
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Affiliation(s)
- Masashi Hada
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Hisashi Miura
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Akie Tanigawa
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan
| | - Shogo Matoba
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Cooperative Division of Veterinary Sciences, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan
| | - Kimiko Inoue
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan
| | - Narumi Ogonuki
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Michiko Hirose
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Naomi Watanabe
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Ryuichiro Nakato
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Katsunori Fujiki
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ayumi Hasegawa
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Akihiko Sakashita
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hiroaki Okae
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Kento Miura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Department of Disease Model, Research Institute of Radiation Biology and Medicine, Hiroshima University, Hiroshima 734-8553, Japan
| | - Daiki Shikata
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan
| | - Takahiro Arima
- Department of Informative Genetics, Environment and Genome Research Center, Tohoku University Graduate School of Medicine, Aoba-ku, Sendai 980-8575, Japan
| | - Katsuhiko Shirahige
- Institute of Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Ichiro Hiratani
- Laboratory for Developmental Epigenetics, RIKEN Center for Developmental Biology, Center for Biosystems Dynamics Research, Kobe 650-0047, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsuo Ogura
- Bioresource Engineering Division, Bioresource Center, RIKEN, Tsukuba, Ibaraki 305-0074, Japan.,Graduate school of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8577, Japan.,RIKEN Cluster for Pioneering Research, Hirosawa, Wako, Saitama 351-0198, Japan
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41
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Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:111-136. [PMID: 36350508 PMCID: PMC9815518 DOI: 10.1007/978-3-031-11454-0_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Cytosine methylation at the C5-position-generating 5-methylcytosine (5mC)-is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80%) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation and genetic alterations in enzymes and regulators involved in DNA methylation are associated with various human diseases, including cancer and developmental disorders. In mammals, DNA methylation is mediated by two families of DNA methyltransferases (Dnmts), namely Dnmt1 and Dnmt3 proteins. Over the last three decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and human diseases.
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Zhu Y, Yu J, Rong Y, Wu YW, Li Y, Zhang L, Pan Y, Fan HY, Shen L. Genomewide decoupling of H2AK119ub1 and H3K27me3 in early mouse development. Sci Bull (Beijing) 2021; 66:2489-2497. [PMID: 36654208 DOI: 10.1016/j.scib.2021.06.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/10/2021] [Accepted: 06/03/2021] [Indexed: 02/03/2023]
Abstract
Polycomb group (PcG) proteins are crucial chromatin regulators during development. H2AK119ub1 (H2Aub) and H3K27me3 are catalyzed by Polycomb-repressive complex 1 and 2 (PRC1/2) respectively, and they largely overlap in the genome due to mutual recruitment of the two complexes. However, it is unclear whether PRC1/H2Aub and PRC2/H3K27me3 can also function independently. By developing an ultra-sensitive carrier-DNA-assisted chromatin immunoprecipitation sequencing method termed CATCH-Seq, we generated allelic H2Aub profiles in mouse gametes and early embryos. Our results revealed an unexpected genomewide decoupling of H2Aub and H3K27me3 in mouse preimplantation embryos, where H2Aub but not H3K27me3 was enriched at PcG targets while only H3K27me3 was deposited in the broad distal domains associated with DNA methylation-independent non-canonical imprinting. These observations suggest that H2Aub represses future bivalent genes during early embryogenesis without H3K27me3, but it is not required for the maintenance of non-canonical imprinting, which is mediated by maternal H3K27me3. Thus, our study reveals the distinct depositions and independent functions of H2Aub and H3K27me3 during early mammalian development.
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Affiliation(s)
- Yezhang Zhu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Jiali Yu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yan Rong
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yun-Wen Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yang Li
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Lejiao Zhang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yinghao Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Heng-Yu Fan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Li Shen
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; Department of Orthopedics Surgery, the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China; Hangzhou Innovation Center, Zhejiang University, Hangzhou 311215, China.
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43
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de Macedo MP, Glanzner WG, Gutierrez K, Bordignon V. Chromatin role in early programming of embryos. Anim Front 2021; 11:57-65. [PMID: 34934530 PMCID: PMC8683133 DOI: 10.1093/af/vfab054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
| | - Werner Giehl Glanzner
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Karina Gutierrez
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, QC, Canada
| | - Vilceu Bordignon
- Department of Animal Science, McGill University, Sainte Anne de Bellevue, QC, Canada
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Defective chromatin architectures in embryonic stem cells derived from somatic cell nuclear transfer impair their differentiation potentials. Cell Death Dis 2021; 12:1085. [PMID: 34785659 PMCID: PMC8595669 DOI: 10.1038/s41419-021-04384-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/26/2021] [Accepted: 10/29/2021] [Indexed: 11/08/2022]
Abstract
Nuclear transfer embryonic stem cells (ntESCs) hold enormous promise for individual-specific regenerative medicine. However, the chromatin states of ntESCs remain poorly characterized. In this study, we employed ATAC-seq and Hi-C techniques to explore the chromatin accessibility and three-dimensional (3D) genome organization of ntESCs. The results show that the chromatin accessibility and genome structures of somatic cells are re-arranged to ESC-like states overall in ntESCs, including compartments, topologically associating domains (TADs) and chromatin loops. However, compared to fertilized ESCs (fESCs), ntESCs show some abnormal openness and structures that have not been reprogrammed completely, which impair the differentiation potential of ntESCs. The histone modification H3K9me3 may be involved in abnormal structures in ntESCs, including incorrect compartment switches and incomplete TAD rebuilding. Moreover, ntESCs and iPSCs show high similarity in 3D genome structures, while a few differences are detected due to different somatic cell origins and reprogramming mechanisms. Through systematic analyses, our study provides a global view of chromatin accessibility and 3D genome organization in ntESCs, which can further facilitate the understanding of the similarities and differences between ntESCs and fESCs.
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Andergassen D, Smith ZD, Kretzmer H, Rinn JL, Meissner A. Diverse epigenetic mechanisms maintain parental imprints within the embryonic and extraembryonic lineages. Dev Cell 2021; 56:2995-3005.e4. [PMID: 34752748 DOI: 10.1016/j.devcel.2021.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 08/06/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022]
Abstract
Genomic imprinting and X chromosome inactivation (XCI) require epigenetic mechanisms to encode allele-specific expression, but how these specific tasks are accomplished at single loci or across chromosomal scales remains incompletely understood. Here, we systematically disrupt essential epigenetic pathways within polymorphic embryos in order to examine canonical and non-canonical genomic imprinting as well as XCI. We find that DNA methylation and Polycomb group repressors are indispensable for autosomal imprinting, albeit at distinct gene sets. Moreover, the extraembryonic ectoderm relies on a broader spectrum of imprinting mechanisms, including non-canonical targeting of maternal endogenous retrovirus (ERV)-driven promoters by the H3K9 methyltransferase G9a. We further identify Polycomb-dependent and -independent gene clusters on the imprinted X chromosome, which appear to reflect distinct domains of Xist-mediated suppression. From our data, we assemble a comprehensive inventory of the epigenetic pathways that maintain parent-specific imprinting in eutherian mammals, including an expanded view of the placental lineage.
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Affiliation(s)
- Daniel Andergassen
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Institute of Pharmacology and Toxicology, Technical University Munich (TUM), Munich 80802, Germany
| | - Zachary D Smith
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Yale Stem Cell Center, Department of Genetics, Yale School of Medicine, New Haven, CT 06519, USA
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder 80303, USA
| | - Alexander Meissner
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin 14195, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin 14195, Germany.
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46
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Chu C, Zhang W, Kang Y, Si C, Ji W, Niu Y, Zhang Y. Analysis of developmental imprinting dynamics in primates using SNP-free methods to identify imprinting defects in cloned placenta. Dev Cell 2021; 56:2826-2840.e7. [PMID: 34619096 DOI: 10.1016/j.devcel.2021.09.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 08/25/2021] [Accepted: 09/10/2021] [Indexed: 12/30/2022]
Abstract
Our knowledge of genomic imprinting in primates is lagging behind that of mice largely because of the difficulties of allelic analyses in outbred animals. To understand imprinting dynamics in primates, we profiled transcriptomes, DNA methylomes, and H3K27me3 in uniparental monkey embryos. We further developed single-nucleotide-polymorphism (SNP)-free methods, TARSII and CARSII, to identify germline differentially methylated regions (DMRs) in somatic tissues. Our comprehensive analyses showed that allelic DNA methylation, but not H3K27me3, is a major mark that correlates with paternal-biasedly expressed genes (PEGs) in uniparental monkey embryos. Interestingly, primate germline DMRs are different from PEG-associated DMRs in early embryos and are enriched in placenta. Strikingly, most placenta-specific germline DMRs are lost in placenta of cloned monkeys. Collectively, our study establishes SNP-free germline DMR identification methods, defines developmental imprinting dynamics in primates, and demonstrates imprinting defects in cloned monkey placenta, which provides important clues for improving primate cloning.
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Affiliation(s)
- Chu Chu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Wenhao Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA.
| | - Yu Kang
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Chenyang Si
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Weizhi Ji
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China.
| | - Yuyu Niu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Yunnan Key Laboratory of Primate Biomedical Research, Kunming, Yunnan 650500, China; Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan 650500, China.
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA 02115, USA; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Division of Hematology/Oncology, Department of Pediatrics, Boston Children's Hospital, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, WAB-149G, 200 Longwood Avenue, Boston, MA 02115, USA.
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Flook M, Escalera-Balsera A, Gallego-Martinez A, Espinosa-Sanchez JM, Aran I, Soto-Varela A, Lopez-Escamez JA. DNA Methylation Signature in Mononuclear Cells and Proinflammatory Cytokines May Define Molecular Subtypes in Sporadic Meniere Disease. Biomedicines 2021; 9:1530. [PMID: 34829759 PMCID: PMC8615058 DOI: 10.3390/biomedicines9111530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Meniere Disease (MD) is a multifactorial disorder of the inner ear characterized by vertigo attacks associated with sensorineural hearing loss and tinnitus with a significant heritability. Although MD has been associated with several genes, no epigenetic studies have been performed on MD. Here we performed whole-genome bisulfite sequencing in 14 MD patients and six healthy controls, with the aim of identifying an MD methylation signature and potential disease mechanisms. We observed a high number of differentially methylated CpGs (DMC) when comparing MD patients to controls (n= 9545), several of them in hearing loss genes, such as PCDH15, ADGRV1 and CDH23. Bioinformatic analyses of DMCs and cis-regulatory regions predicted phenotypes related to abnormal excitatory postsynaptic currents, abnormal NMDA-mediated receptor currents and abnormal glutamate-mediated receptor currents when comparing MD to controls. Moreover, we identified various DMCs in genes previously associated with cochleovestibular phenotypes in mice. We have also found 12 undermethylated regions (UMR) that were exclusive to MD, including two UMR in an inter CpG island in the PHB gene. We suggest that the DNA methylation signature allows distinguishing between MD patients and controls. The enrichment analysis confirms previous findings of a chronic inflammatory process underlying MD.
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Affiliation(s)
- Marisa Flook
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer University of Granada Andalusian Regional Government, PTS, 18016 Granada, Spain; (M.F.); (A.E.-B.); (A.G.-M.); (J.M.E.-S.)
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.Granada, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18014 Granada, Spain
| | - Alba Escalera-Balsera
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer University of Granada Andalusian Regional Government, PTS, 18016 Granada, Spain; (M.F.); (A.E.-B.); (A.G.-M.); (J.M.E.-S.)
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.Granada, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18014 Granada, Spain
| | - Alvaro Gallego-Martinez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer University of Granada Andalusian Regional Government, PTS, 18016 Granada, Spain; (M.F.); (A.E.-B.); (A.G.-M.); (J.M.E.-S.)
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.Granada, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18014 Granada, Spain
| | - Juan Manuel Espinosa-Sanchez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer University of Granada Andalusian Regional Government, PTS, 18016 Granada, Spain; (M.F.); (A.E.-B.); (A.G.-M.); (J.M.E.-S.)
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.Granada, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18014 Granada, Spain
| | - Ismael Aran
- Department of Otolaryngology, Complexo Hospitalario de Pontevedra, 36071 Pontevedra, Spain;
| | - Andres Soto-Varela
- Division of Otoneurology, Department of Otorhinolaryngology, Complexo Hospitalario Universitario, 15706 Santiago de Compostela, Spain;
| | - Jose Antonio Lopez-Escamez
- Otology & Neurotology Group CTS495, Department of Genomic Medicine, GENYO, Centre for Genomics and Oncological Research, Pfizer University of Granada Andalusian Regional Government, PTS, 18016 Granada, Spain; (M.F.); (A.E.-B.); (A.G.-M.); (J.M.E.-S.)
- Sensorineural Pathology Programme, Centro de Investigación Biomédica en Red en Enfermedades Raras, CIBERER, 28029 Madrid, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria ibs.Granada, Hospital Universitario Virgen de las Nieves, Universidad de Granada, 18014 Granada, Spain
- Division of Otolaryngology, Department of Surgery, University of Granada, 18011 Granada, Spain
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Jiao D, Cheng W, Zhang X, Zhang Y, Guo J, Li Z, Shi D, Xiong Z, Qing Y, Jamal MA, Xu K, Zhao HY, Wei HJ. Improving porcine SCNT efficiency by selecting donor cells size. Cell Cycle 2021; 20:2264-2277. [PMID: 34583621 DOI: 10.1080/15384101.2021.1980983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Considerable advancements have recently been achieved in porcine somatic cell nuclear transfer (SCNT), but the efficiency remains low. Donor cell size might play an important role in SCNT, but its effects in pigs remain unclear. This study aimed to evaluate the efficiency of porcine SCNT by selecting donor cells of suitable size. Porcine fetal fibroblasts (PFFs) were divided into three groups, group S (small, d ≤ 13 μm), group M (medium, 13 μm<d ≤ 18 μm), and group L (large, d > 18 μm), and their biological characteristics were analyzed. Next, SCNT was performed using PFFs of different sizes to evaluate the developmental potential of reconstructed embryos. The data showed that PFFs in groups S, M and L accounted for 17.5%, 47.7% and 34.8% of cells, respectively. Morphologically, cells in group S exhibited clear and regular cell membranes and nuclei, whereas cells in groups M and L displayed varying degrees of cell membrane protuberance, karyo-pyknosis, autophagy and mitochondrial abnormalities. In addition, the growth status and proliferation capabilities of cells in group S were significantly better than those of group M and group L. The percentage of cells at G0/G1 in group S and M were significantly greater than group L. The senescence rate of group S was lower than group M and group L. The apoptosis rate of group S was significantly lower than that of group L but comparable to that of group M . The cleavage rate of group S was also significantly greater than that of group M but comparable to that of group L . The blastocyst rate of group S was significantly greater than that of group M and group L. The blastocyst cell numbers of group S were also significantly greater than those of group M and group L. These findings suggested that small PFFs with a diameter of less than 13 μm are more suitable donor cells for SCNT in pigs.Abbreviations: DMEM: Dulbecco's modified Eagle's medium; FBS: Fetal bovine serum; PBS: Phosphate buffer saline; PFFs: Porcine fetal fibroblast cells; SCNT: Somatic cell nuclear transfer.
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Affiliation(s)
- Deling Jiao
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wenmin Cheng
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xiaolin Zhang
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yifan Zhang
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Jianxiong Guo
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhuo Li
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Dejia Shi
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhe Xiong
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yubo Qing
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China.,College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Muhammad Ameen Jamal
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Kaixiang Xu
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hong-Ye Zhao
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Hong-Jiang Wei
- Key laboratory for porcine gene editing and xenotransplantation in Yunnan Province, Yunnan Agricultural University, Kunming, China.,Xenotransplantation Research Engineering Center in Yunnan Province, Yunnan Agricultural University, Kunming, China.,College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
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Zhao K, Wang M, Gao S, Chen J. Chromatin architecture reorganization during somatic cell reprogramming. Curr Opin Genet Dev 2021; 70:104-114. [PMID: 34530248 DOI: 10.1016/j.gde.2021.07.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 01/14/2023]
Abstract
It has been nearly 60 years since Dr John Gurdon achieved the first cloning of Xenopus by somatic cell nuclear transfer (SCNT). Later, in 2006, Takahashi and Yamanaka published their landmark study demonstrating the application of four transcription factors to induce pluripotency. These two amazing discoveries both clearly established that cell identity can be reprogrammed and that mature cells still contain the information required for lineage specification. Considering that different cell types possess identical genomes, what orchestrates reprogramming has attracted wide interest. Epigenetics, including high-level chromatin structure, might provide some answers. Benefitting from the tremendous progress in high-throughput and multi-omics techniques, we here address the roles and interactions of genome architecture, chromatin modifications, and transcription regulation during somatic cell reprogramming that were previously beyond reach. In addition, we provide perspectives on recent technical advances that might help to overcome certain barriers in the field.
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Affiliation(s)
- Kun Zhao
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Mingzhu Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China
| | - Shaorong Gao
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
| | - Jiayu Chen
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China; Frontier Science Center for Stem Cell Research, Tongji University, Shanghai 200092, China.
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50
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Long C, Li H, Li X, Yang W, Zuo Y. Nuclear Transfer Arrest Embryos Show Massive Dysregulation of Genes Involved in Transcription Pathways. Int J Mol Sci 2021; 22:ijms22158187. [PMID: 34360962 PMCID: PMC8347363 DOI: 10.3390/ijms22158187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 11/28/2022] Open
Abstract
Somatic cell nuclear transfer (SCNT) technology can reprogram terminally differentiated cell nuclei into a totipotent state. However, the underlying molecular barriers of SCNT embryo development remain incompletely elucidated. Here, we observed that transcription-related pathways were incompletely activated in nuclear transfer arrest (NTA) embryos compared to normal SCNT embryos and in vivo fertilized (WT) embryos, which hinders the development of SCNT embryos. We further revealed the transcription pathway associated gene regulatory networks (GRNs) and found the aberrant transcription pathways can lead to the massive dysregulation of genes in NTA embryos. The predicted target genes of transcription pathways contain a series of crucial factors in WT embryos, which play an important role in catabolic process, pluripotency regulation, epigenetic modification and signal transduction. In NTA embryos, however, these genes were varying degrees of inhibition and show a defect in synergy. Overall, our research found that the incomplete activation of transcription pathways is another potential molecular barrier for SCNT embryos besides the incomplete reprogramming of epigenetic modifications, broadening the understanding of molecular mechanism of SCNT embryonic development.
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