1
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Tang C, Hu W. Epigenetic modifications during embryonic development: Gene reprogramming and regulatory networks. J Reprod Immunol 2024; 165:104311. [PMID: 39047672 DOI: 10.1016/j.jri.2024.104311] [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: 11/04/2023] [Revised: 06/02/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
The maintenance of normal pregnancy requires appropriate maturation and transformation of various cells, which constitute the microenvironmental regulatory network at the maternal-fetal interface. Interestingly, changes in the cellular components of the maternal-fetal immune microenvironment and the regulation of epigenetic modifications of the genome have attracted much attention. With the development of epigenetics (DNA and RNA methylation, histone modifications, etc.), new insights have been gained into early embryonic developmental stages (e.g., maternal-to-zygotic transition, MZT). Understanding the various appropriate modes of transcriptional regulation required for the early embryonic developmental process from the perspective of epigenetic modifications will help us to provide new targets and insights into the pathogenesis of embryonic failure during further natural fertilization. This review focuses on the loci of action of epigenetic modifications from the perspectives of female germ cell development and embryo development to provide new insights for personalized diagnosis and treatment of abortion.
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Affiliation(s)
- Cen Tang
- Kunming Medical University Second Affiliated Hospital, Obstetrics Department, Kunming, Yunnan 650106, China
| | - Wanqin Hu
- Kunming Medical University Second Affiliated Hospital, Obstetrics Department, Kunming, Yunnan 650106, China.
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2
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Zou Z, Wang Q, Wu X, Schultz RM, Xie W. Kick-starting the zygotic genome: licensors, specifiers, and beyond. EMBO Rep 2024:10.1038/s44319-024-00223-5. [PMID: 39160344 DOI: 10.1038/s44319-024-00223-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 06/14/2024] [Accepted: 07/24/2024] [Indexed: 08/21/2024] Open
Abstract
Zygotic genome activation (ZGA), the first transcription event following fertilization, kickstarts the embryonic program that takes over the control of early development from the maternal products. How ZGA occurs, especially in mammals, is poorly understood due to the limited amount of research materials. With the rapid development of single-cell and low-input technologies, remarkable progress made in the past decade has unveiled dramatic transitions of the epigenomes, transcriptomes, proteomes, and metabolomes associated with ZGA. Moreover, functional investigations are yielding insights into the key regulators of ZGA, among which two major classes of players are emerging: licensors and specifiers. Licensors would control the permission of transcription and its timing during ZGA. Accumulating evidence suggests that such licensors of ZGA include regulators of the transcription apparatus and nuclear gatekeepers. Specifiers would instruct the activation of specific genes during ZGA. These specifiers include key transcription factors present at this stage, often facilitated by epigenetic regulators. Based on data primarily from mammals but also results from other species, we discuss in this review how recent research sheds light on the molecular regulation of ZGA and its executors, including the licensors and specifiers.
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Affiliation(s)
- Zhuoning Zou
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Qiuyan Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Xi Wu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China
- Peking University-Tsinghua University-National Institute of Biological Sciences (PTN) Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, China
| | - Richard M Schultz
- Department of Biology, University of Pennsylvania, Philadelphia, PA, USA
- Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 100084, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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3
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Ouyang Z, Liu F, Li W, Wang J, Chen B, Zheng Y, Li Y, Tao H, Xu X, Li C, Cong Y, Li H, Bo X, Chen H. The developmental and evolutionary characteristics of transcription factor binding site clustered regions based on an explainable machine learning model. Nucleic Acids Res 2024; 52:7610-7626. [PMID: 38813828 PMCID: PMC11260490 DOI: 10.1093/nar/gkae441] [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: 01/22/2024] [Revised: 04/26/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024] Open
Abstract
Gene expression is temporally and spatially regulated by the interaction of transcription factors (TFs) and cis-regulatory elements (CREs). The uneven distribution of TF binding sites across the genome poses challenges in understanding how this distribution evolves to regulate spatio-temporal gene expression and consequent heritable phenotypic variation. In this study, chromatin accessibility profiles and gene expression profiles were collected from several species including mammals (human, mouse, bovine), fish (zebrafish and medaka), and chicken. Transcription factor binding sites clustered regions (TFCRs) at different embryonic stages were characterized to investigate regulatory evolution. The study revealed dynamic changes in TFCR distribution during embryonic development and species evolution. The synchronization between TFCR complexity and gene expression was assessed across species using RegulatoryScore. Additionally, an explainable machine learning model highlighted the importance of the distance between TFCR and promoter in the coordinated regulation of TFCRs on gene expression. Our results revealed the developmental and evolutionary dynamics of TFCRs during embryonic development from fish, chicken to mammals. These data provide valuable resources for exploring the relationship between transcriptional regulation and phenotypic differences during embryonic development.
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Affiliation(s)
- Zhangyi Ouyang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Feng Liu
- College of Medical Informatics, Chongqing Medical University, Chongqing 400016, China
| | - Wanying Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Junting Wang
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Bijia Chen
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yang Zheng
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Yaru Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Huan Tao
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiang Xu
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Cheng Li
- Center for Bioinformatics, School of Life Sciences, Center for Statistical Science, Peking University, Beijing 100871, China
| | - Yuwen Cong
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hao Li
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Xiaochen Bo
- Academy of Military Medical Sciences, Beijing 100850, China
| | - Hebing Chen
- Academy of Military Medical Sciences, Beijing 100850, China
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4
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Zhou K, Wang T, Zhang J, Zhang J, Liu X, Guan J, Su P, Wu L, Yang X, Hu R, Sun Q, Fan Z, Yang S, Chu X, Song W, Shang Y, Zhou S, Hao X, Zhang X, Sun Q, Liu X, Miao YL. LEUTX regulates porcine embryonic genome activation in somatic cell nuclear transfer embryos. Cell Rep 2024; 43:114372. [PMID: 38878289 DOI: 10.1016/j.celrep.2024.114372] [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: 02/28/2024] [Revised: 05/06/2024] [Accepted: 05/31/2024] [Indexed: 07/02/2024] Open
Abstract
Emerging evidence highlights the regulatory role of paired-like (PRD-like) homeobox transcription factors (TFs) in embryonic genome activation (EGA). However, the majority of PRD-like genes are lost in rodents, thus prompting an investigation into PRD-like TFs in other mammals. Here, we showed that PRD-like TFs were transiently expressed during EGA in human, monkey, and porcine fertilized embryos, yet they exhibited inadequate expression in their cloned embryos. This study, using pig as the research model, identified LEUTX as a key PRD-like activator of porcine EGA through genomic profiling and found that LEUTX overexpression restored EGA failure and improved preimplantation development and cloning efficiency in porcine cloned embryos. Mechanistically, LEUTX opened EGA-related genomic regions and established histone acetylation via recruiting acetyltransferases p300 and KAT2A. These findings reveal the regulatory mechanism of LEUTX to govern EGA in pigs, which may provide valuable insights into the study of early embryo development for other non-rodent mammals.
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Affiliation(s)
- Kai Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Tingting Wang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Jingjing Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Jingcheng Zhang
- Key Laboratory of Animal Biotechnology of the Ministry of Agriculture, College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Xingchen Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqi Guan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Peng Su
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Linhui Wu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xin Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Ruifeng Hu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Qiaoran Sun
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Zhengang Fan
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Shichun Yang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xiaoyu Chu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Wenting Song
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Yan Shang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Songxian Zhou
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xingkun Hao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Xia Zhang
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China
| | - Qiang Sun
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Xin Liu
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China.
| | - Yi-Liang Miao
- Institute of Stem Cell and Regenerative Biology, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Agricultural Animal Genetics, Breeding, and Reproduction, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Frontiers Science Center for Animal Breeding and Sustainable Production, Huazhong Agricultural University, Ministry of Education, Wuhan 430070, China.
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5
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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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6
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Li Y, Mo Y, Chen C, He J, Guo Z. Research advances of polycomb group proteins in regulating mammalian development. Front Cell Dev Biol 2024; 12:1383200. [PMID: 38505258 PMCID: PMC10950033 DOI: 10.3389/fcell.2024.1383200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 02/26/2024] [Indexed: 03/21/2024] Open
Abstract
Polycomb group (PcG) proteins are a subset of epigenetic factors that are highly conserved throughout evolution. In mammals, PcG proteins can be classified into two muti-proteins complexes: Polycomb repressive complex 1 (PRC1) and PRC2. Increasing evidence has demonstrated that PcG complexes play critical roles in the regulation of gene expression, genomic imprinting, chromosome X-inactivation, and chromatin structure. Accordingly, the dysfunction of PcG proteins is tightly orchestrated with abnormal developmental processes. Here, we summarized and discussed the current knowledge of the biochemical and molecular functions of PcG complexes, especially the PRC1 and PRC2 in mammalian development including embryonic development and tissue development, which will shed further light on the deep understanding of the basic knowledge of PcGs and their functions for reproductive health and developmental disorders.
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Affiliation(s)
| | | | | | - Jin He
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Zhiheng Guo
- Department of Obstetrics and Gynecology, The First Hospital of Jilin University, Changchun, Jilin, China
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7
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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [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: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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8
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Malcore RM, Kalantry S. A Comparative Analysis of Mouse Imprinted and Random X-Chromosome Inactivation. EPIGENOMES 2024; 8:8. [PMID: 38390899 PMCID: PMC10885068 DOI: 10.3390/epigenomes8010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation mechanism. During X-inactivation, most genes on one of the two X chromosomes in females are transcriptionally silenced, thus equalizing X-linked gene expression between the sexes. Two forms of X-inactivation characterize eutherian mammals, imprinted and random. Imprinted X-inactivation is defined by the exclusive inactivation of the paternal X chromosome in all cells, whereas random X-inactivation results in the silencing of genes on either the paternal or maternal X chromosome in individual cells. Both forms of X-inactivation have been studied intensively in the mouse model system, which undergoes both imprinted and random X-inactivation early in embryonic development. Stable imprinted and random X-inactivation requires the induction of the Xist long non-coding RNA. Following its induction, Xist RNA recruits proteins and complexes that silence genes on the inactive-X. In this review, we present a current understanding of the mechanisms of Xist RNA induction, and, separately, the establishment and maintenance of gene silencing on the inactive-X by Xist RNA during imprinted and random X-inactivation.
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Affiliation(s)
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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9
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Chen S, Liu S, Shi S, Yin H, Tang Y, Zhang J, Li W, Liu G, Qu K, Ding X, Wang Y, Liu J, Zhang S, Fang L, Yu Y. Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats. Mol Biol Evol 2024; 41:msae003. [PMID: 38266195 PMCID: PMC10834038 DOI: 10.1093/molbev/msae003] [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: 07/24/2023] [Revised: 12/28/2023] [Accepted: 01/04/2024] [Indexed: 01/26/2024] Open
Abstract
The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.
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Affiliation(s)
- Siqian Chen
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shuli Liu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
| | - Shaolei Shi
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hongwei Yin
- Agriculture Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Yongjie Tang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jinning Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Wenlong Li
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- National Animal Husbandry Service, Beijing 100125, China
| | - Kaixing Qu
- Academy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jianfeng Liu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark
| | - Ying Yu
- National Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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10
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Hubert JN, Iannuccelli N, Cabau C, Jacomet E, Billon Y, Serre RF, Vandecasteele C, Donnadieu C, Demars J. Detection of DNA methylation signatures through the lens of genomic imprinting. Sci Rep 2024; 14:1694. [PMID: 38242932 PMCID: PMC10798973 DOI: 10.1038/s41598-024-52114-3] [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: 10/03/2023] [Accepted: 01/14/2024] [Indexed: 01/21/2024] Open
Abstract
Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. We show here that enzymatic methyl-seq consistently outperforms the bisulfite-based standard in capturing 165 candidate regions for genomic imprinting in the pig. This highlights the potential for a turnkey, fully customizable and reliable capture tool of genomic regions regulated by cytosine methylation in any population of interest. For the field of genomic imprinting, it opens up the possibility of detecting multilocus imprinting variations across the genome, with implications for basic research, agrigenomics and clinical practice.
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Affiliation(s)
- Jean-Noël Hubert
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Cédric Cabau
- Sigenae, GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Eva Jacomet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
- ENVT, 31326, Castanet-Tolosan, France
| | | | - Rémy-Félix Serre
- INRAE, GeT-PlaGe, Genotoul, 31326, Castanet-Tolosan, France
- Qualyse, Le Treuil, INRAE, 19000, Tulle, France
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
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11
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Zeng Y, Hoshino Y, Susami K, Honda S, Minami N, Ikeda S. Evaluating histone modification analysis of individual preimplantation embryos. BMC Genomics 2024; 25:75. [PMID: 38238676 PMCID: PMC10795292 DOI: 10.1186/s12864-024-09984-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 01/06/2024] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND We previously reported a modification of the CUT&Tag method (NTU-CAT) that allows genome-wide histone modification analysis in individual preimplantation embryos. In the present study, NTU-CAT was further simplified by taking advantage of the Well-of-the-Well (WOW) system, which enables the processing of multiple embryos in a shorter time with less reagent and cell loss during the procedure (WOW-CUT&Tag, WOW-CAT). RESULTS WOW-CAT allowed histone modification profiling from not only a single blastocyst but also from a portion of it. WOW-CAT generated similar H3K4me3 profiles as NTU-CAT, but they were closer to the profiles produced by chromatin immunoprecipitation-sequencing, such as a valley-like trend and relatively lower false positive rates, indicating that WOW-CAT may attenuate the bias of Tn5 transposase to cut open chromatin regions. Simultaneous WOW-CAT of two halves of single blastocysts was conducted to analyze two different histone modifications (H3K4me3 and H3K27ac) within the same embryo. Furthermore, trophectoderm cells were biopsied and subjected to WOW-CAT in anticipation of preimplantation diagnosis of histone modifications. WOW-CAT allowed the monitoring of epigenetic modifications in the main body of the embryo. For example, analysis of H3K4me3 modifications of XIST and DDX3Y in trophectoderm biopsies could be used to sex embryos in combination with quantitative PCR, but without the need for deep sequencing. CONCLUSIONS These results suggest the applicability of WOW-CAT for flexible epigenetic analysis of individual embryos in preimplantation epigenetic diagnosis.
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Affiliation(s)
- Yiren Zeng
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yoichiro Hoshino
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Kazuki Susami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shinnosuke Honda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Naojiro Minami
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Shuntaro Ikeda
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
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12
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Wilkinson AL, Zorzan I, Rugg-Gunn PJ. Epigenetic regulation of early human embryo development. Cell Stem Cell 2023; 30:1569-1584. [PMID: 37858333 DOI: 10.1016/j.stem.2023.09.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023]
Abstract
Studies of mammalian development have advanced our understanding of the genetic, epigenetic, and cellular processes that orchestrate embryogenesis and have uncovered new insights into the unique aspects of human embryogenesis. Recent studies have now produced the first epigenetic maps of early human embryogenesis, stimulating new ideas about epigenetic reprogramming, cell fate control, and the potential mechanisms underpinning developmental plasticity in human embryos. In this review, we discuss these new insights into the epigenetic regulation of early human development and the importance of these processes for safeguarding development. We also highlight unanswered questions and key challenges that remain to be addressed.
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Affiliation(s)
| | - Irene Zorzan
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | - Peter J Rugg-Gunn
- Epigenetics Programme, Babraham Institute, Cambridge, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge, UK; Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK.
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13
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Jiang Z. Molecular and cellular programs underlying the development of bovine pre-implantation embryos. Reprod Fertil Dev 2023; 36:34-42. [PMID: 38064195 PMCID: PMC10962643 DOI: 10.1071/rd23146] [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] [Indexed: 12/18/2023] Open
Abstract
Early embryonic mortality is a major cause of infertility in cattle, yet the underlying molecular causes remain a mystery. Over the past half century, assisted reproductive technologies such as in vitro fertilisation and somatic cell nuclear transfer have been used to improve cattle reproductive efficiency; however, reduced embryo developmental potential is seen compared to their in vivo counterparts. Recent years have seen exciting progress across bovine embryo research, including genomic profiling of embryogenesis, new methods for improving embryo competence, and experimenting on building bovine embryos from stem cell cultures. These advances are beginning to define bovine embryo molecular and cellular programs and could potentially lead to improved embryo health. Here, I highlight the current status of molecular determinants and cellular programs of bovine embryo development and new opportunities to improve the bovine embryo health.
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Affiliation(s)
- Zongliang Jiang
- Department of Animal Sciences, Genetics Institute, University of Florida, Gainesville, FL 32610, USA
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14
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Behluli L, Fontanilla AM, Andessner-Angleitner L, Tolar N, Molina JM, Gahurova L. Expression analysis suggests that DNMT3L is required for oocyte de novo DNA methylation only in Muridae and Cricetidae rodents. Epigenetics Chromatin 2023; 16:43. [PMID: 37924163 PMCID: PMC10625200 DOI: 10.1186/s13072-023-00518-2] [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: 08/23/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023] Open
Abstract
BACKGROUND During early mammalian development, DNA methylation undergoes two waves of reprogramming, enabling transitions between somatic cells, oocyte and embryo. The first wave of de novo DNA methylation establishment occurs in oocytes. Its molecular mechanisms have been studied in mouse, a classical mammalian model. Current model describes DNA methyltransferase 3A (DNMT3A) and its cofactor DNMT3L as two essential factors for oocyte DNA methylation-the ablation of either leads to nearly complete abrogation of DNA methylation. However, DNMT3L is not expressed in human oocytes, suggesting that the mechanism uncovered in mouse is not universal across mammals. RESULTS We analysed available RNA-seq data sets from oocytes of multiple mammals, including our novel data sets of several rodent species, and revealed that Dnmt3l is expressed only in the oocytes of mouse, rat and golden hamster, and at a low level in guinea pigs. We identified a specific promoter sequence recognised by an oocyte transcription factor complex associated with strong Dnmt3l activity and demonstrated that it emerged in the rodent clade Eumuroida, comprising the families Muridae (mice, rats, gerbils) and Cricetidae (hamsters). In addition, an evolutionarily novel promoter emerged in the guinea pig, driving weak Dnmt3l expression, likely without functional relevance. Therefore, Dnmt3l is expressed and consequently plays a role in oocyte de novo DNA methylation only in a small number of rodent species, instead of being an essential pan-mammalian factor. In contrast to somatic cells, where catalytically inactive DNMT3B interacts with DNMT3A, forming a heterotetramer, we did not find evidence for the expression of such inactive Dnmt3b isoforms in the oocytes of the tested species. CONCLUSIONS The analysis of RNA-seq data and genomic sequences revealed that DNMT3L is likely to play a role in oocytes de novo DNA methylation only in mice, rats, gerbils and hamsters. The mechanism governing de novo DNA methylation in the oocytes of most mammalian species, including humans, occurs through a yet unknown mechanism that differs from the current model discovered in mouse.
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Affiliation(s)
- Lirik Behluli
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Alyssa M Fontanilla
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Laura Andessner-Angleitner
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Nikolas Tolar
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Julia M Molina
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
- Department of Biological Sciences, Faculty of Sciences and Languages, São Paulo State University "Júlio de Mesquita Filho" - UNESP, Assis, São Paulo, Brazil
| | - Lenka Gahurova
- Department of Molecular Biology and Genetics, Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic.
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15
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Ahn J, Hwang IS, Park MR, Hwang S, Lee K. Imprinting at the KBTBD6 locus involves species-specific maternal methylation and monoallelic expression in livestock animals. J Anim Sci Biotechnol 2023; 14:131. [PMID: 37817239 PMCID: PMC10565993 DOI: 10.1186/s40104-023-00931-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/21/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The primary differentially methylated regions (DMRs) which are maternally hypermethylated serve as imprinting control regions (ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting. RESULTS Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter CpG island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter CpG islands were methylated in oocytes and/or allelically methylated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these CpG islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting. CONCLUSIONS In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting.
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Affiliation(s)
- Jinsoo Ahn
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
| | - In-Sul Hwang
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
- Columbia Center for Translational Immunology, Columbia University Irving Medical Center, Columbia University, New York, NY 10032 USA
| | - Mi-Ryung Park
- Animal Biotechnology Division, Rural Development Administration, National Institute of Animal Science, Jeonbuk, 55365 Republic of Korea
| | - Seongsoo Hwang
- Animal Welfare Research Team, National Institute of Animal Science, RDA, 1500, Kongjwipatjwi-ro, Jeollabuk-do, 55365 Republic of Korea
| | - Kichoon Lee
- Department of Animal Sciences, The Ohio State University, Columbus, OH 43210 USA
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16
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Wu X, Wu X, Xie W. Activation, decommissioning, and dememorization: enhancers in a life cycle. Trends Biochem Sci 2023; 48:673-688. [PMID: 37221124 DOI: 10.1016/j.tibs.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Spatiotemporal regulation of cell type-specific gene expression is essential to convert a zygote into a complex organism that contains hundreds of distinct cell types. A class of cis-regulatory elements called enhancers, which have the potential to enhance target gene transcription, are crucial for precise gene expression programs during development. Following decades of research, many enhancers have been discovered and how enhancers become activated has been extensively studied. However, the mechanisms underlying enhancer silencing are less well understood. We review current understanding of enhancer decommissioning and dememorization, both of which enable enhancer silencing. We highlight recent progress from genome-wide perspectives that have revealed the life cycle of enhancers and how its dynamic regulation underlies cell fate transition, development, cell regeneration, and epigenetic reprogramming.
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Affiliation(s)
- Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China; Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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17
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Chen Y, Wang L, Guo F, Dai X, Zhang X. Epigenetic reprogramming during the maternal-to-zygotic transition. MedComm (Beijing) 2023; 4:e331. [PMID: 37547174 PMCID: PMC10397483 DOI: 10.1002/mco2.331] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 08/08/2023] Open
Abstract
After fertilization, sperm and oocyte fused and gave rise to a zygote which is the beginning of a new life. Then the embryonic development is monitored and regulated precisely from the transition of oocyte to the embryo at the early stage of embryogenesis, and this process is termed maternal-to-zygotic transition (MZT). MZT involves two major events that are maternal components degradation and zygotic genome activation. The epigenetic reprogramming plays crucial roles in regulating the process of MZT and supervising the normal development of early development of embryos. In recent years, benefited from the rapid development of low-input epigenome profiling technologies, new epigenetic modifications are found to be reprogrammed dramatically and may play different roles during MZT whose dysregulation will cause an abnormal development of embryos even abortion at various stages. In this review, we summarized and discussed the important novel findings on epigenetic reprogramming and the underlying molecular mechanisms regulating MZT in mammalian embryos. Our work provided comprehensive and detailed references for the in deep understanding of epigenetic regulatory network in this key biological process and also shed light on the critical roles for epigenetic reprogramming on embryonic failure during artificial reproductive technology and nature fertilization.
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Affiliation(s)
- Yurong Chen
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Luyao Wang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Fucheng Guo
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiangpeng Dai
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
| | - Xiaoling Zhang
- Key Laboratory of Organ Regeneration and Transplantation of Ministry of Education First Hospital of Jilin University Changchun China
- National-Local Joint Engineering Laboratory of Animal Models for Human Disease First Hospital of Jilin University Changchun China
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18
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Yuan X, Chen N, Feng Y, Li N, Pan X, Tian Y, Wang J, Jiang Y, He D, Li J, Gao F. Single-cell multi-omics profiling reveals key regulatory mechanisms that poise germinal vesicle oocytes for maturation in pigs. Cell Mol Life Sci 2023; 80:222. [PMID: 37480402 PMCID: PMC11072314 DOI: 10.1007/s00018-023-04873-x] [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: 01/28/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/24/2023]
Abstract
The molecular mechanisms controlling the transition from meiotic arrest to meiotic resumption in mammalian oocytes have not been fully elucidated. Single-cell omics technology provides a new opportunity to decipher the early molecular events of oocyte growth in mammals. Here we focused on analyzing oocytes that were collected from antral follicles in different diameters of porcine pubertal ovaries, and used single-cell M&T-seq technology to analyze the nuclear DNA methylome and cytoplasmic transcriptome in parallel for 62 oocytes. 10× Genomics single-cell transcriptomic analyses were also performed to explore the bi-directional cell-cell communications within antral follicles. A new pipeline, methyConcerto, was developed to specifically and comprehensively characterize the methylation profile and allele-specific methylation events for a single-cell methylome. We characterized the gene expressions and DNA methylations of individual oocyte in porcine antral follicle, and both active and inactive gene's bodies displayed high methylation levels, thereby enabled defining two distinct types of oocytes. Although the methylation levels of Type II were higher than that of Type I, Type II contained nearly two times more of cytoplasmic transcripts than Type I. Moreover, the imprinting methylation patterns of Type II were more dramatically divergent than Type I, and the gene expressions and DNA methylations of Type II were more similar with that of MII oocytes. The crosstalk between granulosa cells and Type II oocytes was active, and these observations revealed that Type II was more poised for maturation. We further confirmed Insulin Receptor Substrate-1 in insulin signaling pathway is a key regulator on maturation by in vitro maturation experiments. Our study provides new insights into the regulatory mechanisms between meiotic arrest and meiotic resumption in mammalian oocytes. We also provide a new analytical package for future single-cell methylomics study.
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Affiliation(s)
- Xiaolong Yuan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Na Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yance Feng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Nian Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Xiangchun Pan
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Yuhan Tian
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | | | - Yao Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dou He
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiaqi Li
- Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, State Key Laboratory of Livestock and Poultry Breeding, Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Fei Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark.
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19
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Karam G, Molaro A. Casting histone variants during mammalian reproduction. Chromosoma 2023:10.1007/s00412-023-00803-9. [PMID: 37347315 PMCID: PMC10356639 DOI: 10.1007/s00412-023-00803-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/23/2023]
Abstract
During mammalian reproduction, germ cell chromatin packaging is key to prepare parental genomes for fertilization and to initiate embryonic development. While chromatin modifications such as DNA methylation and histone post-translational modifications are well known to carry regulatory information, histone variants have received less attention in this context. Histone variants alter the stability, structure and function of nucleosomes and, as such, contribute to chromatin organization in germ cells. Here, we review histone variants expression dynamics during the production of male and female germ cells, and what is currently known about their parent-of-origin effects during reproduction. Finally, we discuss the apparent conundrum behind these important functions and their recent evolutionary diversification.
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Affiliation(s)
- Germaine Karam
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Antoine Molaro
- Genetics, Reproduction and Development Institute (iGReD), CNRS UMR 6293, INSERM U1103, Université Clermont Auvergne, Clermont-Ferrand, France.
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20
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Gòdia M, Lian Y, Naval-Sanchez M, Ponte I, Rodríguez-Gil JE, Sanchez A, Clop A. Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development. PeerJ 2023; 11:e15520. [PMID: 37361042 PMCID: PMC10290446 DOI: 10.7717/peerj.15520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm's chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genomic locations of retained nucleosomes in sperm could help understanding the molecular basis of both sperm development and function as well as embryo development. This information could then be useful to identify molecular markers for sperm quality and fertility traits. Here, micrococcal nuclease digestion coupled with high throughput sequencing was performed on pig sperm to map the genomic location of mono- and sub-nucleosomal chromatin fractions in relation to a set of diverse functional elements of the genome, some of which were related to semen quality and early embryogenesis. In particular, the investigated elements were promoters, the different sections of the gene body, coding and non-coding RNAs present in the pig sperm, potential transcription factor binding sites, genomic regions associated to semen quality traits and repeat elements. The analysis yielded 25,293 and 4,239 peaks in the mono- and sub-nucleosomal fractions, covering 0.3% and 0.02% of the porcine genome, respectively. A cross-species comparison revealed positional conservation of the nucleosome retention in sperm between the pig data and a human dataset that found nucleosome enrichment in genomic regions of importance in development. Both gene ontology analysis of the genes mapping nearby the mono-nucleosomal peaks and the identification of putative transcription factor binding motifs within the mono- and the sub- nucleosomal peaks showed enrichment for processes related to sperm function and embryo development. There was significant motif enrichment for Znf263, which in humans was suggested to be a key regulator of genes with paternal preferential expression during early embryogenesis. Moreover, enriched positional intersection was found in the genome between the mono-nucleosomal peaks and both the RNAs present in pig sperm and the RNAs related to sperm quality. There was no co-location between GWAS hits for semen quality in swine and the nucleosomal sites. Finally, the data evidenced depletion of mono-nucleosomes in long interspersed nuclear elements and enrichment of sub-nucleosomes in short interspersed repeat elements.These results suggest that retained nucleosomes in sperm could both mark regulatory elements or genes expressed during spermatogenesis linked to semen quality and fertility and act as transcriptional guides during early embryogenesis. The results of this study support the undertaking of ambitious research using a larger number of samples to robustly assess the positional relationship between histone retention in sperm and the reproductive ability of boars.
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Affiliation(s)
- Marta Gòdia
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal Breeding and Genomics, Wageningen University and Research, Wageninger, Netherlands
| | - Yu Lian
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
| | | | - Inma Ponte
- Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Joan Enric Rodríguez-Gil
- Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Armand Sanchez
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal and food sciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Alex Clop
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, Spain
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21
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Grow EJ, Liu Y, Fan Z, Perisse IV, Patrick T, Regouski M, Shadle S, Polejaeva I, White KL, Cairns BR. Chromatin Reprogramming of In Vitro Fertilized and Somatic Cell Nuclear Transfer Bovine Embryos During Embryonic Genome Activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536281. [PMID: 37090641 PMCID: PMC10120652 DOI: 10.1101/2023.04.10.536281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Reprogramming of the gamete into a developmentally competent embryo identity is a fundamental aspect of preimplantation development. One of the most important processes of this reprogramming is the transcriptional awakening during embryonic genome activation (EGA), which robustly occurs in fertilized embryos but is defective in most somatic cell nuclear transfer (SCNT) embryos. However, little is known about the genome-wide underlying chromatin landscape during EGA in SCNT embryos and how it differs from a fertilized embryo. By profiling open chromatin genome-wide in both types of bovine embryos, we find that SCNT embryos fail to reprogram a subset of the EGA gene targets that are normally activated in fertilized embryos. Importantly, a small number of transcription factor (TF) motifs explain most chromatin regions that fail to open in SCNT embryos suggesting that over-expression of a limited number of TFs may provide more robust reprogramming. One such TF, the zygotically-expressed bovine gene DUXC which is a homologue of EGA factors DUX/DUX4 in mouse/human, is alone capable of activating ∼84% of all EGA transcripts that fail to activate normally in SCNT embryos. Additionally, single-cell chromatin profiling revealed low intra-embryo heterogeneity but high inter-embryo heterogeneity in SCNT embryos and an uncoupling of cell division and open chromatin reprogramming during EGA. Surprisingly, our data also indicate that transcriptional defects may arise downstream of promoter chromatin opening in SCNT embryos, suggesting additional mechanistic insights into how and why transcription at EGA is dysregulated. We anticipate that our work will lead to altered SCNT protocols to increase the developmental competency of bovine SCNT embryos.
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22
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Fukushima HS, Takeda H, Nakamura R. Incomplete erasure of histone marks during epigenetic reprogramming in medaka early development. Genome Res 2023; 33:572-586. [PMID: 37117034 PMCID: PMC10234297 DOI: 10.1101/gr.277577.122] [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: 12/07/2022] [Accepted: 03/29/2023] [Indexed: 04/30/2023]
Abstract
Epigenetic modifications undergo drastic erasure and reestablishment after fertilization. This reprogramming is required for proper embryonic development and cell differentiation. In mammals, some histone modifications are not completely reprogrammed and play critical roles in later development. In contrast, in nonmammalian vertebrates, most histone modifications are thought to be more intensively erased and reestablished by the stage of zygotic genome activation (ZGA). However, histone modifications that escape reprogramming in nonmammalian vertebrates and their potential functional roles remain unknown. Here, we quantitatively and comprehensively analyzed histone modification dynamics during epigenetic reprogramming in Japanese killifish, medaka (Oryzias latipes) embryos. Our data revealed that H3K27ac, H3K27me3, and H3K9me3 escape complete reprogramming, whereas H3K4 methylation is completely erased during cleavage stage. Furthermore, we experimentally showed the functional roles of such retained modifications at early stages: (i) H3K27ac premarks promoters during the cleavage stage, and inhibition of histone acetyltransferases disrupts proper patterning of H3K4 and H3K27 methylation at CpG-dense promoters, but does not affect chromatin accessibility after ZGA; (ii) H3K9me3 is globally erased but specifically retained at telomeric regions, which is required for maintenance of genomic stability during the cleavage stage. These results expand the understanding of diversity and conservation of reprogramming in vertebrates, and unveil previously uncharacterized functions of histone modifications retained during epigenetic reprogramming.
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Affiliation(s)
- Hiroto S Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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23
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Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H. Conservation and divergence of canonical and non-canonical imprinting in murids. Genome Biol 2023; 24:48. [PMID: 36918927 PMCID: PMC10012579 DOI: 10.1186/s13059-023-02869-1] [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: 04/21/2022] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Genomic imprinting affects gene expression in a parent-of-origin manner and has a profound impact on complex traits including growth and behavior. While the rat is widely used to model human pathophysiology, few imprinted genes have been identified in this murid. To systematically identify imprinted genes and genomic imprints in the rat, we use low input methods for genome-wide analyses of gene expression and DNA methylation to profile embryonic and extraembryonic tissues at allele-specific resolution. RESULTS We identify 14 and 26 imprinted genes in these tissues, respectively, with 10 of these genes imprinted in both tissues. Comparative analyses with mouse reveal that orthologous imprinted gene expression and associated canonical DNA methylation imprints are conserved in the embryo proper of the Muridae family. However, only 3 paternally expressed imprinted genes are conserved in the extraembryonic tissue of murids, all of which are associated with non-canonical H3K27me3 imprints. The discovery of 8 novel non-canonical imprinted genes unique to the rat is consistent with more rapid evolution of extraembryonic imprinting. Meta-analysis of novel imprinted genes reveals multiple mechanisms by which species-specific imprinted expression may be established, including H3K27me3 deposition in the oocyte, the appearance of ZFP57 binding motifs, and the insertion of endogenous retroviral promoters. CONCLUSIONS In summary, we provide an expanded list of imprinted loci in the rat, reveal the extent of conservation of imprinted gene expression, and identify potential mechanisms responsible for the evolution of species-specific imprinting.
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Affiliation(s)
| | - Toshihiro Kobayashi
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Azusa Inoue
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Soichiro Kumamoto
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | | | - Asuka Miura
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Mami Oikawa
- Division of Mammalian Embryology, Center for Stem Cell Biology and Regenerative Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Fumihito Miura
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Shuji Takada
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Masumi Hirabayashi
- Center for Genetic Analysis of Behavior, National Institute for Physiological Sciences, Okazaki, Japan
| | - Keegan Korthauer
- Department of Statistics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Kazuki Kurimoto
- Department of Embryology, Nara Medical University, Nara, Japan
| | | | - Matthew Lorincz
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
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24
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Zhou C, Halstead MM, Bonnet‐Garnier A, Schultz RM, Ross PJ. Histone remodeling reflects conserved mechanisms of bovine and human preimplantation development. EMBO Rep 2023; 24:e55726. [PMID: 36779365 PMCID: PMC9986824 DOI: 10.15252/embr.202255726] [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: 07/05/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 02/14/2023] Open
Abstract
How histone modifications regulate changes in gene expression during preimplantation development in any species remains poorly understood. Using CUT&Tag to overcome limiting amounts of biological material, we profiled two activating (H3K4me3 and H3K27ac) and two repressive (H3K9me3 and H3K27me3) marks in bovine oocytes, 2-, 4-, and 8-cell embryos, morula, blastocysts, inner cell mass, and trophectoderm. In oocytes, broad bivalent domains mark developmental genes, and prior to embryonic genome activation (EGA), H3K9me3 and H3K27me3 co-occupy gene bodies, suggesting a global mechanism for transcription repression. During EGA, chromatin accessibility is established before canonical H3K4me3 and H3K27ac signatures. Embryonic transcription is required for this remodeling, indicating that maternally provided products alone are insufficient for reprogramming. Last, H3K27me3 plays a major role in restriction of cellular potency, as blastocyst lineages are defined by differential polycomb repression and transcription factor activity. Notably, inferred regulators of EGA and blastocyst formation strongly resemble those described in humans, as opposed to mice. These similarities suggest that cattle are a better model than rodents to investigate the molecular basis of human preimplantation development.
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Affiliation(s)
- Chuan Zhou
- Department of Animal Science University of CaliforniaDavisCAUSA
| | - Michelle M Halstead
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Amélie Bonnet‐Garnier
- Université Paris‐Saclay, UVSQ, INRAE, BREEDJouy‐en‐JosasFrance
- Ecole Nationale Vétérinaire d'Alfort, BREEDMaisons‐AlfortFrance
| | - Richard M Schultz
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary MedicineUniversity of CaliforniaDavisCAUSA
- Department of BiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pablo J Ross
- Department of Animal Science University of CaliforniaDavisCAUSA
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25
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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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26
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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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27
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Macrae TA, Fothergill-Robinson J, Ramalho-Santos M. Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 60] [Impact Index Per Article: 60.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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Affiliation(s)
- Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA.
| | - Julie Fothergill-Robinson
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Miguel Ramalho-Santos
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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28
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Choe YH, Sorensen J, Garry DJ, Garry MG. Blastocyst complementation and interspecies chimeras in gene edited pigs. Front Cell Dev Biol 2022; 10:1065536. [PMID: 36568986 PMCID: PMC9773398 DOI: 10.3389/fcell.2022.1065536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022] Open
Abstract
The only curative therapy for many endstage diseases is allograft organ transplantation. Due to the limited supply of donor organs, relatively few patients are recipients of a transplanted organ. Therefore, new strategies are warranted to address this unmet need. Using gene editing technologies, somatic cell nuclear transfer and human induced pluripotent stem cell technologies, interspecies chimeric organs have been pursued with promising results. In this review, we highlight the overall technical strategy, the successful early results and the hurdles that need to be addressed in order for these approaches to produce a successful organ that could be transplanted in patients with endstage diseases.
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Affiliation(s)
- Yong-ho Choe
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jacob Sorensen
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Daniel J. Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
| | - Mary G. Garry
- Lillehei Heart Institute, University of Minnesota, Minneapolis, MN, United States
- Cardiovascular Division, Department of Medicine, University of Minnesota, Minneapolis, MN, United States
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, United States
- Paul and Sheila Wellstone Muscular Dystrophy Center, University of Minnesota, Minneapolis, MN, United States
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29
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Zhou Z, Tan C, Chau M, Jiang X, Ke Z, Chen X, Cao Y, Kwok YK, Bellgard M, Leung T, Choy K, Dong Z. TEDD: a database of temporal gene expression patterns during multiple developmental periods in human and model organisms. Nucleic Acids Res 2022; 51:D1168-D1178. [PMID: 36350663 PMCID: PMC9825605 DOI: 10.1093/nar/gkac978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/06/2022] [Accepted: 10/15/2022] [Indexed: 11/10/2022] Open
Abstract
Characterization of the specific expression and chromatin profiles of genes enables understanding how they contribute to tissue/organ development and the mechanisms leading to diseases. Whilst the number of single-cell sequencing studies is increasing dramatically; however, data mining and reanalysis remains challenging. Herein, we systematically curated the up-to-date and most comprehensive datasets of sequencing data originating from 2760 bulk samples and over 5.1 million single-cells from multiple developmental periods from humans and multiple model organisms. With unified and systematic analysis, we profiled the gene expression and chromatin accessibility among 481 cell-types, 79 tissue-types and 92 timepoints, and pinpointed cells with the co-expression of target genes. We also enabled the detection of gene(s) with a temporal and cell-type specific expression profile that is similar to or distinct from that of a target gene. Additionally, we illustrated the potential upstream and downstream gene-gene regulation interactions, particularly under the same biological process(es) or KEGG pathway(s). Thus, TEDD (Temporal Expression during Development Database), a value-added database with a user-friendly interface, not only enables researchers to identify cell-type/tissue-type specific and temporal gene expression and chromatin profiles but also facilitates the association of genes with undefined biological functions in development and diseases. The database URL is https://TEDD.obg.cuhk.edu.hk/.
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Affiliation(s)
| | | | - Matthew Hoi Kin Chau
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China
| | - Xiaosen Jiang
- BGI-Shenzhen, Shenzhen 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ziyuan Ke
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiaoyan Chen
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Maternal-Fetal Medicine Institute, Shenzhen Baoan Women's and Children's Hospital, Shenzhen University, Shenzhen, China
| | - Ye Cao
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Yvonne K Kwok
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Matthew Bellgard
- eResearch Office, Queensland University of Technology, Brisbane, QLD, Australia
| | - Tak Yeung Leung
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China,Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen 518057, China,Hong Kong Hub of Paediatric Excellence, The Chinese University of Hong Kong, Hong Kong, China,The Chinese University of Hong Kong-Baylor College of Medicine Joint Center for Medical Genetics, Hong Kong, China,The Fertility Preservation Research Center, Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Kwong Wai Choy
- Correspondence may also be addressed to Kwong Wai Choy. Tel: +852 3505 3099; Fax: +852 2636 0008;
| | - Zirui Dong
- To whom correspondence should be addressed. Tel: +852 3505 3099; Fax: +852 2636 0008;
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30
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Mu J, Zhou Z, Sang Q, Wang L. The physiological and pathological mechanisms of early embryonic development. FUNDAMENTAL RESEARCH 2022; 2:859-872. [PMID: 38933386 PMCID: PMC11197659 DOI: 10.1016/j.fmre.2022.08.011] [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: 06/02/2022] [Revised: 08/05/2022] [Accepted: 08/19/2022] [Indexed: 10/15/2022] Open
Abstract
Early embryonic development is a complex process. The zygote undergoes several rounds of division to form a blastocyst, and during this process, the zygote undergoes the maternal-to-zygotic transition to gain control of embryonic development and makes two cell fate decisions to differentiate into an embryonic and two extra-embryonic lineages. With the use of new molecular biotechnologies and animal models, we can now further study the molecular mechanisms of early embryonic development and the pathological causes of early embryonic arrest. Here, we first summarize the known molecular regulatory mechanisms of early embryonic development in mice. Then we discuss the pathological factors leading to the early embryonic arrest. We hope that this review will give researchers a relatively complete view of the physiology and pathology of early embryonic development.
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Affiliation(s)
- Jian Mu
- The State Key Laboratory of Genetic Engineering, Institute of Pediatrics, Children's Hospital of Fudan University, The Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Zhou Zhou
- The State Key Laboratory of Genetic Engineering, Institute of Pediatrics, Children's Hospital of Fudan University, The Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
- NHC Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai 200032, China
| | - Qing Sang
- The State Key Laboratory of Genetic Engineering, Institute of Pediatrics, Children's Hospital of Fudan University, The Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Wang
- The State Key Laboratory of Genetic Engineering, Institute of Pediatrics, Children's Hospital of Fudan University, The Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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31
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Zhu L, Zhou T, Iyyappan R, Ming H, Dvoran M, Wang Y, Chen Q, Roberts RM, Susor A, Jiang Z. High-resolution ribosome profiling reveals translational selectivity for transcripts in bovine preimplantation embryo development. Development 2022; 149:280468. [PMID: 36227586 PMCID: PMC9687001 DOI: 10.1242/dev.200819] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
High-resolution ribosome fractionation and low-input ribosome profiling of bovine oocytes and preimplantation embryos has enabled us to define the translational landscapes of early embryo development at an unprecedented level. We analyzed the transcriptome and the polysome- and non-polysome-bound RNA profiles of bovine oocytes (germinal vesicle and metaphase II stages) and early embryos at the two-cell, eight-cell, morula and blastocyst stages, and revealed four modes of translational selectivity: (1) selective translation of non-abundant mRNAs; (2) active, but modest translation of a selection of highly expressed mRNAs; (3) translationally suppressed abundant to moderately abundant mRNAs; and (4) mRNAs associated specifically with monosomes. A strong translational selection of low-abundance transcripts involved in metabolic pathways and lysosomes was found throughout bovine embryonic development. Notably, genes involved in mitochondrial function were prioritized for translation. We found that translation largely reflected transcription in oocytes and two-cell embryos, but observed a marked shift in the translational control in eight-cell embryos that was associated with the main phase of embryonic genome activation. Subsequently, transcription and translation become more synchronized in morulae and blastocysts. Taken together, these data reveal a unique spatiotemporal translational regulation that accompanies bovine preimplantation development.
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Affiliation(s)
- Linkai Zhu
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557-0352, USA
| | - Rajan Iyyappan
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Hao Ming
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Michal Dvoran
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Yinjuan Wang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, CA 92521, USA
| | - R Michael Roberts
- Department of Animal Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA
| | - Andrej Susor
- Laboratory of Biochemistry and Molecular Biology of Germ Cells, Institute of Animal Physiology and Genetics, CAS, 277 21 Liběchov, Czech Republic
| | - Zongliang Jiang
- School of Animal Sciences, AgCenter, Louisiana State University, Baton Rouge, LA 70803, USA
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32
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Super-enhancers conserved within placental mammals maintain stem cell pluripotency. Proc Natl Acad Sci U S A 2022; 119:e2204716119. [PMID: 36161929 DOI: 10.1073/pnas.2204716119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Despite pluripotent stem cells sharing key transcription factors, their maintenance involves distinct genetic inputs. Emerging evidence suggests that super-enhancers (SEs) can function as master regulatory hubs to control cell identity and pluripotency in humans and mice. However, whether pluripotency-associated SEs share an evolutionary origin in mammals remains elusive. Here, we performed comprehensive comparative epigenomic and transcription factor binding analyses among pigs, humans, and mice to identify pluripotency-associated SEs. Like typical enhancers, SEs displayed rapid evolution in mammals. We showed that BRD4 is an essential and conserved activator for mammalian pluripotency-associated SEs. Comparative motif enrichment analysis revealed 30 shared transcription factor binding motifs among the three species. The majority of transcriptional factors that bind to identified motifs are known regulators associated with pluripotency. Further, we discovered three pluripotency-associated SEs (SE-SOX2, SE-PIM1, and SE-FGFR1) that displayed remarkable conservation in placental mammals and were sufficient to drive reporter gene expression in a pluripotency-dependent manner. Disruption of these conserved SEs through the CRISPR-Cas9 approach severely impaired stem cell pluripotency. Our study provides insights into the understanding of conserved regulatory mechanisms underlying the maintenance of pluripotency as well as species-specific modulation of the pluripotency-associated regulatory networks in mammals.
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33
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Liu X, Zhang J, Zhou J, Bu G, Zhu W, He H, Sun Q, Yu Z, Xiong W, Wang L, Wu D, Dou C, Yu L, Zhou K, Wang S, Fan Z, Wang T, Hu R, Hu T, Zhang X, Miao Y. Hierarchical Accumulation of Histone Variant H2A.Z Regulates Transcriptional States and Histone Modifications in Early Mammalian Embryos. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200057. [PMID: 35717671 PMCID: PMC9376818 DOI: 10.1002/advs.202200057] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/25/2022] [Indexed: 05/09/2023]
Abstract
Early embryos undergo extensive epigenetic reprogramming to achieve gamete-to-embryo transition, which involves the loading and removal of histone variant H2A.Z on chromatin. However, how does H2A.Z regulate gene expression and histone modifications during preimplantation development remains unrevealed. Here, by using ultra-low-input native chromatin immunoprecipitation and sequencing, the genome-wide distribution of H2A.Z is delineated in mouse oocytes and early embryos. These landscapes indicate that paternal H2A.Z is removed upon fertilization, followed by unbiased accumulation on parental genomes during zygotic genome activation (ZGA). Remarkably, H2A.Z exhibits hierarchical accumulation as different peak types at promoters: promoters with double H2A.Z peaks are colocalized with H3K4me3 and indicate transcriptional activation; promoters with a single H2A.Z peak are more likely to occupy bivalent marks (H3K4me3+H3K27me3) and indicate development gene suppression; promoters with no H2A.Z accumulation exhibit persisting gene silencing in early embryos. Moreover, H2A.Z depletion changes the enrichment of histone modifications and RNA polymerase II binding at promoters, resulting in abnormal gene expression and developmental arrest during lineage commitment. Furthermore, similar transcription and accumulation patterns between mouse and porcine embryos indicate that a dual role of H2A.Z in regulating the epigenome required for proper gene expression is conserved during mammalian preimplantation development.
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34
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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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Hubert JN, Demars J. Genomic Imprinting in the New Omics Era: A Model for Systems-Level Approaches. Front Genet 2022; 13:838534. [PMID: 35368671 PMCID: PMC8965095 DOI: 10.3389/fgene.2022.838534] [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: 12/17/2021] [Accepted: 02/28/2022] [Indexed: 11/13/2022] Open
Abstract
Genomic imprinting represents a noteworthy inheritance mechanism leading to allele-specific regulations dependent of the parental origin. Imprinted loci are especially involved in essential mammalian functions related to growth, development and behavior. In this mini-review, we first offer a summary of current representations associated with genomic imprinting through key results of the three last decades. We then outline new perspectives allowed by the spread of new omics technologies tackling various interacting levels of imprinting regulations, including genomics, transcriptomics and epigenomics. We finally discuss the expected contribution of new omics data to unresolved big questions in the field.
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