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Liu Z, Wang W, Xia Y, Gao Y, Wang Z, Li M, Presicce GA, An L, Du F. Overcoming the H4K20me3 epigenetic barrier improves somatic cell nuclear transfer reprogramming efficiency in mice. Cell Prolif 2024; 57:e13519. [PMID: 37322828 PMCID: PMC10771106 DOI: 10.1111/cpr.13519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/25/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
Epigenetic reprogramming during fertilization and somatic cell nuclear transfer (NT) is required for cell plasticity and competent development. Here, we characterize the epigenetic modification pattern of H4K20me3, a repressive histone signature in heterochromatin, during fertilization and NT reprogramming. Importantly, the dynamic H4K20me3 signature identified during preimplantation development in fertilized embryos differed from NT and parthenogenetic activation (PA) embryos. In fertilized embryos, only maternal pronuclei carried the canonical H4K20me3 peripheral nucleolar ring-like signature. H4K20me3 disappeared at the 2-cell stage and reappeared in fertilized embryos at the 8-cell stage and in NT and PA embryos at the 4-cell stage. H4K20me3 intensity in 4-cell, 8-cell, and morula stages of fertilized embryos was significantly lower than in NT and PA embryos, suggesting aberrant regulation of H4K20me3 in PA and NT embryos. Indeed, RNA expression of the H4K20 methyltransferase Suv4-20h2 in 4-cell fertilized embryos was significantly lower than NT embryos. Knockdown of Suv4-20h2 in NT embryos rescued the H4K20me3 pattern similar to fertilized embryos. Compared to control NT embryos, knockdown of Suv4-20h2 in NT embryos improved blastocyst development ratios (11.1% vs. 30.5%) and full-term cloning efficiencies (0.8% vs. 5.9%). Upregulation of reprogramming factors, including Kdm4b, Kdm4d, Kdm6a, and Kdm6b, as well as ZGA-related factors, including Dux, Zscan4, and Hmgpi, was observed with Suv4-20h2 knockdown in NT embryos. Collectively, these are the first findings to demonstrate that H4K20me3 is an epigenetic barrier of NT reprogramming and begin to unravel the epigenetic mechanisms of H4K20 trimethylation in cell plasticity during natural reproduction and NT reprogramming in mice.
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Affiliation(s)
- Zhihui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Weiguo Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yuhan Xia
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Yuan Gao
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhisong Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | - Mingyang Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
| | | | - Liyou An
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and TechnologyXinjiang UniversityUrumqiChina
| | - Fuliang Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life SciencesNanjing Normal UniversityNanjingChina
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2
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Agredo A, Kasinski AL. Histone 4 lysine 20 tri-methylation: a key epigenetic regulator in chromatin structure and disease. Front Genet 2023; 14:1243395. [PMID: 37671044 PMCID: PMC10475950 DOI: 10.3389/fgene.2023.1243395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/07/2023] [Indexed: 09/07/2023] Open
Abstract
Chromatin is a vital and dynamic structure that is carefully regulated to maintain proper cell homeostasis. A great deal of this regulation is dependent on histone proteins which have the ability to be dynamically modified on their tails via various post-translational modifications (PTMs). While multiple histone PTMs are studied and often work in concert to facilitate gene expression, here we focus on the tri-methylation of histone H4 on lysine 20 (H4K20me3) and its function in chromatin structure, cell cycle, DNA repair, and development. The recent studies evaluated in this review have shed light on how H4K20me3 is established and regulated by various interacting partners and how H4K20me3 and the proteins that interact with this PTM are involved in various diseases. Through analyzing the current literature on H4K20me3 function and regulation, we aim to summarize this knowledge and highlights gaps that remain in the field.
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Affiliation(s)
- Alejandra Agredo
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Life Sciences Interdisciplinary Program (PULSe), Purdue University, West Lafayette, IN, United States
| | - Andrea L. Kasinski
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
- Purdue Institute for Cancer Research, Purdue University, West Lafayette, IN, United States
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3
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McCarthy RL, Zhang J, Zaret KS. Diverse heterochromatin states restricting cell identity and reprogramming. Trends Biochem Sci 2023; 48:513-526. [PMID: 36990958 PMCID: PMC10182259 DOI: 10.1016/j.tibs.2023.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/29/2023]
Abstract
Heterochromatin is defined as a chromosomal domain harboring repressive H3K9me2/3 or H3K27me3 histone modifications and relevant factors that physically compact the chromatin. Heterochromatin can restrict where transcription factors bind, providing a barrier to gene activation and changes in cell identity. While heterochromatin thus helps maintain cell differentiation, it presents a barrier to overcome during efforts to reprogram cells for biomedical purposes. Recent findings have revealed complexity in the composition and regulation of heterochromatin, and shown that transiently disrupting the machinery of heterochromatin can enhance reprogramming. Here, we discuss how heterochromatin is established and maintained during development, and how our growing understanding of the mechanisms regulating H3K9me3 heterochromatin can be leveraged to improve our ability to direct changes in cell identity.
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Affiliation(s)
- Ryan L McCarthy
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jingchao Zhang
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Penn Epigenetics Institute, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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4
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Rang FJ, Kind J, Guerreiro I. The role of heterochromatin in 3D genome organization during preimplantation development. Cell Rep 2023; 42:112248. [PMID: 37059092 DOI: 10.1016/j.celrep.2023.112248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/21/2022] [Accepted: 02/27/2023] [Indexed: 04/16/2023] Open
Abstract
During the early stages of mammalian development, the epigenetic state of the parental genome is completely reprogrammed to give rise to the totipotent embryo. An important aspect of this remodeling concerns the heterochromatin and the spatial organization of the genome. While heterochromatin and genome organization are intricately linked in pluripotent and somatic systems, little is known about their relationship in the totipotent embryo. In this review, we summarize the current knowledge on the reprogramming of both regulatory layers. In addition, we discuss available evidence on their relationship and put this in the context of findings in other systems.
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Affiliation(s)
- Franka J Rang
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands
| | - Jop Kind
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Houtlaan 4, 6525 XZ Nijmegen, the Netherlands.
| | - Isabel Guerreiro
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands; Oncode Institute, the Netherlands.
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5
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Guthmann M, Qian C, Gialdini I, Nakatani T, Ettinger A, Schauer T, Kukhtevich I, Schneider R, Lamb DC, Burton A, Torres-Padilla ME. A change in biophysical properties accompanies heterochromatin formation in mouse embryos. Genes Dev 2023; 37:336-350. [PMID: 37072228 PMCID: PMC10153458 DOI: 10.1101/gad.350353.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/31/2023] [Indexed: 04/20/2023]
Abstract
The majority of our genome is composed of repeated DNA sequences that assemble into heterochromatin, a highly compacted structure that constrains their mutational potential. How heterochromatin forms during development and how its structure is maintained are not fully understood. Here, we show that mouse heterochromatin phase-separates after fertilization, during the earliest stages of mammalian embryogenesis. Using high-resolution quantitative imaging and molecular biology approaches, we show that pericentromeric heterochromatin displays properties consistent with a liquid-like state at the two-cell stage, which change at the four-cell stage, when chromocenters mature and heterochromatin becomes silent. Disrupting the condensates results in altered transcript levels of pericentromeric heterochromatin, suggesting a functional role for phase separation in heterochromatin function. Thus, our work shows that mouse heterochromatin forms membrane-less compartments with biophysical properties that change during development and provides new insights into the self-organization of chromatin domains during mammalian embryogenesis.
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Affiliation(s)
- Manuel Guthmann
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Chen Qian
- Department of Chemistry, Center for NanoScience (CeNS), Ludwig Maximilians-Universität München, 81377 München, Germany
| | - Irene Gialdini
- Department of Chemistry, Center for NanoScience (CeNS), Ludwig Maximilians-Universität München, 81377 München, Germany
| | - Tsunetoshi Nakatani
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Andreas Ettinger
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Tamas Schauer
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Igor Kukhtevich
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, D-85764 Neuherberg, Germany
| | - Don C Lamb
- Department of Chemistry, Center for NanoScience (CeNS), Ludwig Maximilians-Universität München, 81377 München, Germany
| | - Adam Burton
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, D-81377 München, Germany;
- Faculty of Biology, Ludwig-Maximilians Universität, München, 82152 Planegg, Germany
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6
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Goissis MD, Cibelli JB. Early Cell Specification in Mammalian Fertilized and Somatic Cell Nuclear Transfer Embryos. Methods Mol Biol 2023; 2647:59-81. [PMID: 37041329 DOI: 10.1007/978-1-0716-3064-8_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Early cell specification in mammalian preimplantation embryos is an intricate cellular process that leads to coordinated spatial and temporal expression of specific genes. Proper segregation into the first two cell lineages, the inner cell mass (ICM) and the trophectoderm (TE), is imperative for developing the embryo proper and the placenta, respectively. Somatic cell nuclear transfer (SCNT) allows the formation of a blastocyst containing both ICM and TE from a differentiated cell nucleus, which means that this differentiated genome must be reprogrammed to a totipotent state. Although blastocysts can be generated efficiently through SCNT, the full-term development of SCNT embryos is impaired mostly due to placental defects. In this review, we examine the early cell fate decisions in fertilized embryos and compare them to observations in SCNT-derived embryos, in order to understand if these processes are affected by SCNT and could be responsible for the low success of reproductive cloning.
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Affiliation(s)
- Marcelo D Goissis
- Department of Animal Reproduction, School of Veterinary Medicine and Animal Science, University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Jose B Cibelli
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
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Chomiak AA, Guo Y, Kopsidas CA, Mcdaniel DP, Lowe CC, Pan H, Zhou X, Zhou Q, Doughty ML, Feng Y. Nde1 is Required for Heterochromatin Compaction and Stability in Neocortical Neurons. iScience 2022. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction. Cortical neurogenesis is coupled with heterochromatin compaction marked by H4K20me3 Nde1 undergoes liquid-liquid phase separation and interacts with heterochromatin Nde1 mutations impair H4K20me3 during neural progenitor differentiation Neurons lacking Nde1 derepress heterochromatin and lose nuclear and genomic integrity
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8
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Gabellini D, Pedrotti S. The SUV4-20H Histone Methyltransferases in Health and Disease. Int J Mol Sci 2022; 23:ijms23094736. [PMID: 35563127 PMCID: PMC9102147 DOI: 10.3390/ijms23094736] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 02/05/2023] Open
Abstract
The post-translational modification of histone tails is a dynamic process that provides chromatin with high plasticity. Histone modifications occur through the recruitment of nonhistone proteins to chromatin and have the potential to influence fundamental biological processes. Many recent studies have been directed at understanding the role of methylated lysine 20 of histone H4 (H4K20) in physiological and pathological processes. In this review, we will focus on the function and regulation of the histone methyltransferases SUV4-20H1 and SUV4-20H2, which catalyze the di- and tri-methylation of H4K20 at H4K20me2 and H4K20me3, respectively. We will highlight recent studies that have elucidated the functions of these enzymes in various biological processes, including DNA repair, cell cycle regulation, and DNA replication. We will also provide an overview of the pathological conditions associated with H4K20me2/3 misregulation as a result of mutations or the aberrant expression of SUV4-20H1 or SUV4-20H2. Finally, we will critically analyze the data supporting these functions and outline questions for future research.
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9
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Yang Y, Shen S, Cai Y, Zeng K, Liu K, Li S, Zeng L, Chen L, Tang J, Hu Z, Xia Z, Zhang L. Dynamic Patterns of N6-Methyladenosine Profiles of Messenger RNA Correlated with the Cardiomyocyte Regenerability during the Early Heart Development in Mice. Oxid Med Cell Longev 2021; 2021:5537804. [PMID: 34413927 DOI: 10.1155/2021/5537804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/13/2021] [Indexed: 12/16/2022]
Abstract
N6-Methyladenosine (m6A) plays important roles in regulating mRNA processing. Despite rapid progress in this field, little is known about the role and mechanism of m6A modification in myocardial development and cardiomyocyte regeneration. Existing studies have shown that the heart tissues of newborn mice have the capability of proliferation and regeneration, but its mechanism, particularly its relation to m6A methylation, remains unknown. Methods. To systematically profile the mRNA m6A modification pattern in the heart tissues of mice at different developmental stages, we jointly performed methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA sequencing (RNA-seq) of heart tissues of mice, respectively, aged 1 day old, 7 days old, and 28 days old. Results. We identified the linkages and association between differentially expressed mRNA transcripts and hyper or hypomethylated m6A peaks in C57BL/6J mice at different heart developmental stages. Results showed that the amount of m6A peaks and the level of m6A modification were the lowest in the heart of mice at 1 day old. By contrast, heart tissues from 7-day-old mice tended to possess the most m6A peaks and the highest global m6A level. However, the m6A characteristics of myocardial tissue changed little after 7 days old as compared to that of 1 day old. Specifically, we found 1269 downmethylated genes of 1434 methylated genes in 7-day-old mouse heart tissues as compared to those in 1-day-old mice. Hypermethylation of some specific genes may correlate with the heart's strong proliferative and regenerative capability at the first day after birth. In terms of m6A density, the tendency shifted from coding sequences (CDS) to 3′-untranslated regions (3′UTR) and stop codon with the progression of heart development. In addition, some genes demonstrated remarkable changes both in methylation and expression, like kiss1, plekha6, and megf6, which may play important roles in proliferation. Furthermore, signaling pathways highly related to proliferation such as “Wnt signaling pathway,” “ECM-receptor interaction,” and “cardiac chamber formation” were significantly enriched in 1-day-old methylated genes. Conclusions. Our results reveal a pattern that different m6A modifications are distributed in C57BL/6J heart tissue at different developmental stages, which provides new insights into a novel function of m6A methylation of mRNA in myocardial development and regeneration.
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10
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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11
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Zhou S, Guo Y, Sun H, Liu L, Yao L, Liu C, He Y, Cao S, Zhou C, Li M, Cao Y, Wang C, Lu Q, Li W, Guo X, Huo R. Maternal RNF114-mediated target substrate degradation regulates zygotic genome activation in mouse embryos. Development 2021; 148:269079. [PMID: 34104941 DOI: 10.1242/dev.199426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Accepted: 05/27/2021] [Indexed: 12/16/2022]
Abstract
Zygotic genomic activation (ZGA) is a landmark event in the maternal-to-zygotic transition (MZT), and the regulation of ZGA by maternal factors remains to be elucidated. In this study, the depletion of maternal ring finger protein 114 (RNF114), a ubiquitin E3 ligase, led to developmental arrest of two-cell mouse embryos. Using immunofluorescence and transcriptome analysis, RNF114 was proven to play a crucial role in major ZGA. To study the underlying mechanism, we performed protein profiling in mature oocytes and found a potential substrate for RNF114, chromobox 5 (CBX5), ubiquitylation and degradation of which was regulated by RNF114. The overexpression of CBX5 prevented embryonic development and impeded major ZGA. Furthermore, TAB1 was abnormally accumulated in mutant two-cell embryos, which was consistent with the result of in vitro knockdown of Rnf114. Knockdown of Cbx5 or Tab1 in maternal RNF114-depleted embryos partially rescued developmental arrest and the defect of major ZGA. In summary, our study reveals that maternal RNF114 plays a precise role in degrading some important substrates during the MZT, the misregulation of which may impede the appropriate activation of major ZGA in mouse embryos.
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Affiliation(s)
- Shuai Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China.,Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Haifeng Sun
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Lu Liu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Liping Yao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Chao Liu
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanlin He
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Shanren Cao
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing 210004, China
| | - Cheng Zhou
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Mingrui Li
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Yumeng Cao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Congjing Wang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Qianneng Lu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Wei Li
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
| | - Ran Huo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing 211166, China
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12
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Xing S, Tian JZ, Yang SH, Huang XT, Ding YF, Lu QY, Yang JS, Yang WJ. Setd4 controlled quiescent c-Kit + cells contribute to cardiac neovascularization of capillaries beyond activation. Sci Rep 2021; 11:11603. [PMID: 34079011 PMCID: PMC8172824 DOI: 10.1038/s41598-021-91105-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/21/2021] [Indexed: 12/14/2022] Open
Abstract
Blood vessels in the adult mammal exist in a highly organized and stable state. In the ischemic heart, limited expansion capacity of the myocardial vascular bed cannot satisfy demands for oxygen supply and the myocardium eventually undergoes irreversible damage. The predominant contribution of endogenous c-Kit+ cells is understood to be in the development and homeostasis of cardiac endothelial cells, which suggests potential for their targeting in treatments for cardiac ischemic injury. Quiescent cells in other tissues are known to contribute to the long-term maintenance of a cell pool, preserve proliferation capacity and, upon activation, facilitate tissue homeostasis and regeneration in response to tissue injury. Here, we present evidence of a Setd4-expressing quiescent c-Kit+ cell population in the adult mouse heart originating from embryonic stages. Conditional knock-out of Setd4 in c-Kit-CreERT2;Setd4f/f;Rosa26TdTomato mice induced an increase in vascular endothelial cells of capillaries in both neonatal and adult mice. We show that Setd4 regulates quiescence of c-Kit+ cells by the PI3K-Akt-mTOR signaling pathway via H4K20me3 catalysis. In myocardial infarction injured mice, Setd4 knock-out resulted in attenuated cardiomyocyte apoptosis, decreased infarction size and improved cardiac function. Lineage tracing in Setd4-Cre;Rosa26mT/mG mice showed that Setd4+ cells contribute to each cardiac lineage. Overall, Setd4 epigenetically controls c-Kit+ cell quiescence in the adult heart by facilitating heterochromatin formation via H4K20me3. Beyond activation, endogenous quiescent c-Kit+ cells were able to improve cardiac function in myocardial infarction injured mice via the neovascularization of capillaries.
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Affiliation(s)
- Sheng Xing
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Ze Tian
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shu-Hua Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xue-Ting Huang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Yan-Fu Ding
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Qian-Yun Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jin-Shu Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei-Jun Yang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life, Sciences, Zhejiang University, Hangzhou, 310058, China.
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13
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Abstract
Liquid-liquid phase separation (LLPS) mediated formation of membraneless organelles has been proposed to coordinate biological processes in space and time. Previously, the formation of phase-separated droplets was described as a unique property of HP1α. Here, we demonstrate that the positive net charge of the intrinsically disordered hinge region (IDR-H) of HP1 proteins is critical for phase separation and that the exchange of four acidic amino acids is sufficient to confer LLPS properties to HP1β. Surprisingly, the addition of mono-nucleosomes promoted H3K9me3-dependent LLPS of HP1β which could be specifically disrupted with methylated but not acetylated H3K9 peptides. HP1β mutants defective in H3K9me3 binding were less efficient in phase separationin vitro and failed to accumulate at heterochromatin in vivo. We propose that multivalent interactions of HP1β with H3K9me3-modified nucleosomes via its chromodomain and dimerization via its chromoshadow domain enable phase separation and contribute to the formation of heterochromatin compartments in vivo.
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Affiliation(s)
- Weihua Qin
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Stengl
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Enes Ugur
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute for Biochemistry, Martinsried, Germany
| | - Susanne Leidescher
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Joel Ryan
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Heinrich Leonhardt
- Center for Molecular Biosystems (BioSysM), Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
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14
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Shukla R, Mjoseng HK, Thomson JP, Kling S, Sproul D, Dunican DS, Ramsahoye B, Wongtawan T, Treindl F, Templin MF, Adams IR, Pennings S, Meehan RR. Activation of transcription factor circuity in 2i-induced ground state pluripotency is independent of repressive global epigenetic landscapes. Nucleic Acids Res 2020; 48:7748-7766. [PMID: 32585002 PMCID: PMC7641322 DOI: 10.1093/nar/gkaa529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 06/02/2020] [Accepted: 06/15/2020] [Indexed: 01/07/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) cultured with MEK/ERK and GSK3β (2i) inhibitors transition to ground state pluripotency. Gene expression changes, redistribution of histone H3K27me3 profiles and global DNA hypomethylation are hallmarks of 2i exposure, but it is unclear whether epigenetic alterations are required to achieve and maintain ground state or occur as an outcome of 2i signal induced changes. Here we show that ESCs with three epitypes, WT, constitutively methylated, or hypomethylated, all undergo comparable morphological, protein expression and transcriptome changes independently of global alterations of DNA methylation levels or changes in H3K27me3 profiles. Dazl and Fkbp6 expression are induced by 2i in all three epitypes, despite exhibiting hypermethylated promoters in constitutively methylated ESCs. We identify a number of activated gene promoters that undergo 2i dependent loss of H3K27me3 in all three epitypes, however genetic and pharmaceutical inhibition experiments show that H3K27me3 is not required for their silencing in non-2i conditions. By separating and defining their contributions, our data suggest that repressive epigenetic systems play minor roles in mESC self-renewal and naïve ground state establishment by core sets of dominant pluripotency associated transcription factor networks, which operate independently from these epigenetic processes.
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Affiliation(s)
- Ruchi Shukla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
- Newcastle University Centre for Cancer, Biosciences Institute, Newcastle University, Newcastle-upon-Tyne NE2 4HH, UK
| | - Heidi K Mjoseng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Simon Kling
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Donncha S Dunican
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Bernard Ramsahoye
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Tuempong Wongtawan
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Fridolin Treindl
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
- Pharmaceutical Biotechnology, Tübingen University, Tübingen, Germany
| | - Markus F Templin
- NMI Natural and Medical Sciences Institute, Tübingen University, Reutlingen, Germany
- Pharmaceutical Biotechnology, Tübingen University, Tübingen, Germany
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, WGH, University of Edinburgh, Edinburgh EH4 2XU, UK
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15
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Abstract
The hallmarks of constitutive heterochromatin, HP1 and H3K9me2/3, assemble heterochromatin-like domains/complexes outside canonical constitutively heterochromatic territories where they regulate chromatin template-dependent processes. Domains are more than 100 kb in size; complexes less than 100 kb. They are present in the genomes of organisms ranging from fission yeast to human, with an expansion in size and number in mammals. Some of the likely functions of domains/complexes include silencing of the donor mating type region in fission yeast, preservation of DNA methylation at imprinted germline differentially methylated regions (gDMRs) and regulation of the phylotypic progression during vertebrate development. Far cis- and trans-contacts between micro-phase separated domains/complexes in mammalian nuclei contribute to the emergence of epigenetic compartmental domains (ECDs) detected in Hi-C maps. A thermodynamic description of micro-phase separation of heterochromatin-like domains/complexes may require a gestalt shift away from the monomer as the "unit of incompatibility" that determines the sign and magnitude of the Flory-Huggins parameter, χ. Instead, a more dynamic structure, the oligo-nucleosomal "clutch", consisting of between 2 and 10 nucleosomes is both the long sought-after secondary structure of chromatin and its unit of incompatibility. Based on this assumption we present a simple theoretical framework that enables an estimation of χ for domains/complexes flanked by euchromatin and thereby an indication of their tendency to phase separate. The degree of phase separation is specified by χN, where N is the number of "clutches" in a domain/complex. Our approach could provide an additional tool for understanding the biophysics of the 3D genome.
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Affiliation(s)
- Prim B. Singh
- Nazarbayev University School of Medicine, Nur-Sultan City 010000, Kazakhstan
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
| | - Stepan N. Belyakin
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
| | - Petr P. Laktionov
- Epigenetics Laboratory, Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Genomics laboratory, Institute of molecular and cellular biology SD RAS, Lavrentyev ave, 8/2, 630090 Novosibirsk, Russia; (S.N.B.); (P.P.L.)
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16
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Milazzotto MP, de Lima CB, da Fonseca AM, dos Santos EC, Ispada J. Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming. Anim Reprod 2020; 17:e20200015. [PMID: 33029209 PMCID: PMC7534565 DOI: 10.1590/1984-3143-ar2020-0015] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/23/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.
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Affiliation(s)
- Marcella Pecora Milazzotto
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Camila Bruna de Lima
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
- Département des Sciences Animales, Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Quebec, Canada
| | - Aldcejam Martins da Fonseca
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Erika Cristina dos Santos
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
| | - Jessica Ispada
- Laboratório de Epigenética e Metabolismo Embrionário, Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brasil
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17
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Zhang K, Wu DY, Zheng H, Wang Y, Sun QR, Liu X, Wang LY, Xiong WJ, Wang Q, Rhodes JDP, Xu K, Li L, Lin Z, Yu G, Xia W, Huang B, Du Z, Yao Y, Nasmyth KA, Klose RJ, Miao YL, Xie W. Analysis of Genome Architecture during SCNT Reveals a Role of Cohesin in Impeding Minor ZGA. Mol Cell 2020; 79:234-250.e9. [PMID: 32579944 DOI: 10.1016/j.molcel.2020.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 05/27/2020] [Accepted: 05/28/2020] [Indexed: 12/13/2022]
Abstract
Somatic cell nuclear transfer (SCNT) can reprogram a somatic nucleus to a totipotent state. However, the re-organization of 3D chromatin structure in this process remains poorly understood. Using low-input Hi-C, we revealed that, during SCNT, the transferred nucleus first enters a mitotic-like state (premature chromatin condensation). Unlike fertilized embryos, SCNT embryos show stronger topologically associating domains (TADs) at the 1-cell stage. TADs become weaker at the 2-cell stage, followed by gradual consolidation. Compartments A/B are markedly weak in 1-cell SCNT embryos and become increasingly strengthened afterward. By the 8-cell stage, somatic chromatin architecture is largely reset to embryonic patterns. Unexpectedly, we found cohesin represses minor zygotic genome activation (ZGA) genes (2-cell-specific genes) in pluripotent and differentiated cells, and pre-depleting cohesin in donor cells facilitates minor ZGA and SCNT. These data reveal multi-step reprogramming of 3D chromatin architecture during SCNT and support dual roles of cohesin in TAD formation and minor ZGA repression.
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Affiliation(s)
- Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Dan-Ya 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
| | - Hui Zheng
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Yao Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Qiao-Ran 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
| | - 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
| | - Li-Yan 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
| | - Wen-Jing Xiong
- 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
| | - Qiujun Wang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | | | - Kai Xu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Lijia Li
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Zili Lin
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Guang Yu
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Weikun Xia
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Bo Huang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Yao Yao
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China
| | - Kim A Nasmyth
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - 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.
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, School of Life Sciences, THU-PKU Center for Life Science, Tsinghua University, Beijing 100084, China.
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18
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Burton A, Brochard V, Galan C, Ruiz-Morales ER, Rovira Q, Rodriguez-Terrones D, Kruse K, Le Gras S, Udayakumar VS, Chin HG, Eid A, Liu X, Wang C, Gao S, Pradhan S, Vaquerizas JM, Beaujean N, Jenuwein T, Torres-Padilla ME. Heterochromatin establishment during early mammalian development is regulated by pericentromeric RNA and characterized by non-repressive H3K9me3. Nat Cell Biol 2020; 22:767-78. [PMID: 32601371 DOI: 10.1038/s41556-020-0536-6] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2017] [Accepted: 05/24/2020] [Indexed: 01/24/2023]
Abstract
Upon fertilization in mammals the gametes are reprogrammed to create a totipotent zygote, a process that involves de novo establishment of chromatin domains. A major feature occurring during preimplantation development is the dramatic remodeling of constitutive heterochromatin, although the functional relevance of this is unknown. Here we show that heterochromatin establishment relies on the stepwise expression and regulated activity of Suv39h enzymes. Enforcing precocious acquisition of constitutive heterochromatin results in compromised development and epigenetic reprogramming, demonstrating that heterochromatin remodeling is essential for natural reprogramming at fertilization. We find that de novo H3K9 trimethylation in the paternal pronucleus after fertilization is catalyzed by Suv39h2 and that pericentromeric RNAs inhibit Suv39h2 activity and reduce H3K9me3. De novo H3K9me3 is initially non-repressive for gene expression but instead can bookmark promoters for compaction. Overall, we uncover the functional importance for the restricted transmission of constitutive heterochromatin during reprogramming and a non-repressive role for H3K9me3.
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19
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Shikata D, Yamamoto T, Honda S, Ikeda S, Minami N. H4K20 monomethylation inhibition causes loss of genomic integrity in mouse preimplantation embryos. J Reprod Dev 2020; 66:411-419. [PMID: 32378528 PMCID: PMC7593633 DOI: 10.1262/jrd.2020-036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Maintaining genomic integrity in mammalian early embryos, which are deficient in DNA damage repair, is critical for normal preimplantation and subsequent
development. Abnormalities in DNA damage repair in preimplantation embryos can cause not only developmental arrest, but also diseases such as congenital
disorders and cancers. Histone H4 lysine 20 monomethylation (H4K20me1) is involved in DNA damage repair and regulation of gene expression. However, little is
known about the role of H4K20me1 during mouse preimplantation development. In this study, we revealed that H4K20me1 mediated by SETD8 is involved in maintaining
genomic integrity. H4K20me1 was present throughout preimplantation development. In addition, reduction in the level of H4K20me1 by inhibition of SETD8 activity
or a dominant-negative mutant of histone H4 resulted in developmental arrest at the S/G2 phase and excessive accumulation of DNA double-strand breaks. Together,
our results suggest that H4K20me1, a type of epigenetic modification, is associated with the maintenance of genomic integrity and is essential for
preimplantation development. A better understanding of the mechanisms involved in maintaining genome integrity during preimplantation development could
contribute to advances in reproductive medicine and technology.
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Affiliation(s)
- Daiki Shikata
- Laboratory of Reproductive Biology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Takuto Yamamoto
- 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
| | - Shuntaro Ikeda
- 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
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20
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Chioccarelli T, Pierantoni R, Manfrevola F, Porreca V, Fasano S, Chianese R, Cobellis G. Histone Post-Translational Modifications and CircRNAs in Mouse and Human Spermatozoa: Potential Epigenetic Marks to Assess Human Sperm Quality. J Clin Med 2020; 9:jcm9030640. [PMID: 32121034 PMCID: PMC7141194 DOI: 10.3390/jcm9030640] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/20/2020] [Accepted: 02/20/2020] [Indexed: 12/14/2022] Open
Abstract
Spermatozoa (SPZ) are motile cells, characterized by a cargo of epigenetic information including histone post-translational modifications (histone PTMs) and non-coding RNAs. Specific histone PTMs are present in developing germ cells, with a key role in spermatogenic events such as self-renewal and commitment of spermatogonia (SPG), meiotic recombination, nuclear condensation in spermatids (SPT). Nuclear condensation is related to chromatin remodeling events and requires a massive histone-to-protamine exchange. After this event a small percentage of chromatin is condensed by histones and SPZ contain nucleoprotamines and a small fraction of nucleohistone chromatin carrying a landascape of histone PTMs. Circular RNAs (circRNAs), a new class of non-coding RNAs, characterized by a nonlinear back-spliced junction, able to play as microRNA (miRNA) sponges, protein scaffolds and translation templates, have been recently characterized in both human and mouse SPZ. Since their abundance in eukaryote tissues, it is challenging to deepen their biological function, especially in the field of reproduction. Here we review the critical role of histone PTMs in male germ cells and the profile of circRNAs in mouse and human SPZ. Furthermore, we discuss their suggested role as novel epigenetic biomarkers to assess sperm quality and improve artificial insemination procedure.
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21
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Marcho C, Oluwayiose OA, Pilsner JR. The preconception environment and sperm epigenetics. Andrology 2020; 8:924-942. [PMID: 31901222 DOI: 10.1111/andr.12753] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/12/2019] [Accepted: 12/31/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Infertility is a common reproductive disorder, with male factor infertility accounting for approximately half of all cases. Taking a paternal perceptive, recent research has shown that sperm epigenetics, such as changes in DNA methylation, histone modification, chromatin structure, and noncoding RNA expression, can impact reproductive and offspring health. Importantly, environmental conditions during the preconception period has been demonstrated to shape sperm epigenetics. OBJECTIVES To provide an overview on epigenetic modifications that regulate normal gene expression and epigenetic remodeling that occurs during spermatogenesis, and to discuss the epigenetic alterations that may occur to the paternal germline as a consequence of preconception environmental conditions and exposures. MATERIALS AND METHODS We examined published literature available on databases (PubMed, Google Scholar, ScienceDirect) focusing on adult male preconception environmental exposures and sperm epigenetics in epidemiologic studies and animal models. RESULTS The preconception period is a sensitive developmental window in which a variety of exposures such as toxicants, nutrition, drugs, stress, and exercise, affects sperm epigenetics. DISCUSSION AND CONCLUSION Understanding the environmental legacy of the sperm epigenome during spermatogenesis will enhance our understanding of reproductive health and improve reproductive success and offspring well-being.
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Affiliation(s)
- Chelsea Marcho
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
| | - Oladele A Oluwayiose
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
| | - J Richard Pilsner
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, Amherst, Massachusetts
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22
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Li YC, Wang GW, Xu SR, Zhang XN, Yang QE. The expression of histone methyltransferases and distribution of selected histone methylations in testes of yak and cattle-yak hybrid. Theriogenology 2020; 144:164-173. [PMID: 31972460 DOI: 10.1016/j.theriogenology.2020.01.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 01/01/2020] [Accepted: 01/01/2020] [Indexed: 01/23/2023]
Abstract
Interspecies hybridization exists widely in nature and plays an important role in animal evolution and adaptation. It is commonly recognized that male offspring of interspecies hybrid are often sterile, which presents a crucial way of reproductive isolation. Currently, the mechanisms underlying interspecies hybrid male sterility are not well understood. Cattle-yak, progeny of yak (Bos grunniens) and cattle (Bos taurus) cross, is a unique animal model for investigating hybrid male sterility. Because histone modifications are vital for spermatogenesis, herein, we examined expressions of histone methyltransferases (HMTs) and distributions of histone methylations in the yak and cattle-yak testis. Histological examination of seminiferous tubules revealed that gonocytes and spermatocytes were established normally, however, spermatogenesis was arrested at the meiosis phase began at 10 months after birth in the hybrids. SUV420H1 was the only HMT examined showing a significant enrichment in cattle-yak testes at 3 months. Relative expressions of MLL5, SETDB1 and SUV420H1 were increased while SETDB2 and EZH2 were decreased in cattle-yak testes at 10 months. Relative concentrations of MLL5 and SUV420H1 were again increased while EHMT2 and PRDM9 expressions were decreased at 24 months. Immunofluorescent detection of selected histone methylations in cross-sections of testicular tissues or meiotic chromosomes demonstrated that depletion of H3K4me3 and significant enrichment of H3K27me3 and H4K20me3 were observed in Sertoli cells of cattle-yak. Levels and localizations of H3K4me3, H3K9me1, H3K9me3 and H4K20me3 were strikingly different in meiotic chromosomes of cattle-yak spermatocytes. These results highlighted the potential roles of histone methylations in spermatogenic failure and hybrid male sterility.
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Affiliation(s)
- Yong-Chang Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guo-Wen Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shang-Rong Xu
- Qinghai Academy of Animal Sciences and Veterinary Medicine, Xining, Qinghai, 810008, China
| | - Xiao-Na Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi-En Yang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810000, China; Qinghai Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai, 810001, China; CAS Center for Excellence in Tibetan Plateau Earth Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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Guthmann M, Burton A, Torres‐Padilla M. Expression and phase separation potential of heterochromatin proteins during early mouse development. EMBO Rep 2019; 20:e47952. [PMID: 31701657 PMCID: PMC6893284 DOI: 10.15252/embr.201947952] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/03/2019] [Accepted: 10/16/2019] [Indexed: 12/29/2022] Open
Abstract
In most eukaryotes, constitutive heterochromatin is associated with H3K9me3 and HP1α. The latter has been shown to play a role in heterochromatin formation through liquid-liquid phase separation. However, many other proteins are known to regulate and/or interact with constitutive heterochromatic regions in several species. We postulate that some of these heterochromatic proteins may play a role in the regulation of heterochromatin formation by liquid-liquid phase separation. Indeed, an analysis of the constitutive heterochromatin proteome shows that proteins associated with constitutive heterochromatin are significantly more disordered than a random set or a full nucleome set of proteins. Interestingly, their expression begins low and increases during preimplantation development. These observations suggest that the preimplantation embryo is a useful model to address the potential role for phase separation in heterochromatin formation, anticipating exciting research in the years to come.
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Affiliation(s)
- Manuel Guthmann
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Adam Burton
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
| | - Maria‐Elena Torres‐Padilla
- Institute of Epigenetics and Stem Cells (IES)Helmholtz Zentrum MünchenMünchenGermany
- Faculty of BiologyLudwig‐Maximilians UniversitätMünchenGermany
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24
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McLaughlin K, Flyamer IM, Thomson JP, Mjoseng HK, Shukla R, Williamson I, Grimes GR, Illingworth RS, Adams IR, Pennings S, Meehan RR, Bickmore WA. DNA Methylation Directs Polycomb-Dependent 3D Genome Re-organization in Naive Pluripotency. Cell Rep 2019; 29:1974-1985.e6. [PMID: 31722211 PMCID: PMC6856714 DOI: 10.1016/j.celrep.2019.10.031] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 09/09/2019] [Accepted: 10/09/2019] [Indexed: 11/14/2022] Open
Abstract
The DNA hypomethylation that occurs when embryonic stem cells (ESCs) are directed to the ground state of naive pluripotency by culturing in two small molecule inhibitors (2i) results in redistribution of polycomb (H3K27me3) away from its target loci. Here, we demonstrate that 3D genome organization is also altered in 2i, with chromatin decompaction at polycomb target loci and a loss of long-range polycomb interactions. By preventing DNA hypomethylation during the transition to the ground state, we are able to restore to ESC in 2i the H3K27me3 distribution, as well as polycomb-mediated 3D genome organization that is characteristic of primed ESCs grown in serum. However, these cells retain the functional characteristics of 2i ground-state ESCs. Our findings demonstrate the central role of DNA methylation in shaping major aspects of 3D genome organization but caution against assuming causal roles for the epigenome and 3D genome in gene regulation and function in ESCs.
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Affiliation(s)
- Katy McLaughlin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Ilya M Flyamer
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - John P Thomson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Heidi K Mjoseng
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Ruchi Shukla
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK; Northern Institute for Cancer Research, Framlington Place, Medical Faculty, Newcastle upon Tyne NE2 4HH, UK
| | - Iain Williamson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Graeme R Grimes
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Robert S Illingworth
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Ian R Adams
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, 47 Little France Crescent, Edinburgh EH16 4TJ, UK
| | - Richard R Meehan
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK.
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK.
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. Epigenetics and Regeneration 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Pennings S, Liu KJ, Qian H. The Stem Cell Niche: Interactions between Stem Cells and Their Environment. Stem Cells Int. 2018;2018:4879379. [PMID: 30405721 PMCID: PMC6204189 DOI: 10.1155/2018/4879379] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 08/26/2018] [Indexed: 12/14/2022] Open
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Abstract
Epigenetic mechanisms allow the establishment and maintenance of multiple cellular phenotypes from a single genomic code. At the initiation of development, the oocyte and spermatozoa provide their fully differentiated chromatin that soon after fertilization undergo extensive remodeling, resulting in a totipotent state that can then drive cellular differentiation towards all cell types. These remodeling involves different epigenetic modifications, including DNA methylation, post-translational modifications of histones, non-coding RNAs, and large-scale chromatin conformation changes. Moreover, epigenetic remodeling is responsible for reprogramming somatic cells to totipotency upon somatic cell nuclear transfer/cloning, which is often incomplete and inefficient. Given that environmental factors, such as assisted reproductive techniques (ARTs), can affect epigenetic remodeling, there is interest in understanding the mechanisms driving these changes. We describe and discuss our current understanding of mechanisms responsible for the epigenetic remodeling that ensues during preimplantation development of mammals, presenting findings from studies of mouse embryos and when available comparing them to what is known for human and cattle embryos.
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Affiliation(s)
- Pablo J Ross
- Department of Animal Science, University of California Davis, Davis, CA, United States
| | - Rafael V Sampaio
- Department of Animal Science, University of California Davis, Davis, CA, United States.,Department of Animal Science, University of California Davis, Davis, CA, United States
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28
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Bosch-Presegué L, Raurell-Vila H, Thackray JK, González J, Casal C, Kane-Goldsmith N, Vizoso M, Brown JP, Gómez A, Ausió J, Zimmermann T, Esteller M, Schotta G, Singh PB, Serrano L, Vaquero A. Mammalian HP1 Isoforms Have Specific Roles in Heterochromatin Structure and Organization. Cell Rep 2017; 21:2048-57. [PMID: 29166597 DOI: 10.1016/j.celrep.2017.10.092] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 09/15/2017] [Accepted: 10/24/2017] [Indexed: 11/24/2022] Open
Abstract
HP1 is a structural component of heterochromatin. Mammalian HP1 isoforms HP1α, HP1β, and HP1γ play different roles in genome stability, but their precise role in heterochromatin structure is unclear. Analysis of Hp1α-/-, Hp1β-/-, and Hp1γ-/- MEFs show that HP1 proteins have both redundant and unique functions within pericentric heterochromatin (PCH) and also act globally throughout the genome. HP1α confines H4K20me3 and H3K27me3 to regions within PCH, while its absence results in a global hyper-compaction of chromatin associated with a specific pattern of mitotic defects. In contrast, HP1β is functionally associated with Suv4-20h2 and H4K20me3, and its loss induces global chromatin decompaction and an abnormal enrichment of CTCF in PCH and other genomic regions. Our work provides insight into the roles of HP1 proteins in heterochromatin structure and genome stability.
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29
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Beaujean N, Salvaing J, Hadi NAA, Pennings S. Antibody-Based Detection of Global Nuclear DNA Methylation in Cells, Tissue Sections, and Mammalian Embryos. Methods Mol Biol 2018; 1708:59-80. [PMID: 29224139 DOI: 10.1007/978-1-4939-7481-8_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Immunostaining is widely used in cell biology for the in situ detection of proteins in fixed cells. The method is based on the specificity of antibodies for recognizing and binding to a selected target, combined with immunolabeling techniques for microscopic imaging. Antibodies with high specificities for modified nucleotides have also been widely developed, and among those, antibodies that recognize modified cytosine: 5-methylcytosine (5mC), and more recently, its derivates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). To allow for their detection, primary antibody signals can be amplified using secondary antibodies coupled to fluorophores for immunofluorescence, or other molecules for immunocytochemistry.Immunostaining can be used to gain information on the spatial distribution and levels of DNA methylation states within the nucleus. Although the resolution remains quite low in genomic terms, advanced microscopy techniques and image analysis can obtain detailed spatial information content from immunostained sites. The technique complements genomic approaches that permit the assessment of DNA methylation on specific sequences, but that cannot provide global nuclear spatial context. Immunostaining is an accessible method of great benefit in several cases: when working with limited material (such as embryos or primary cells), to quickly assess at the level of individual cells the effect of siRNA, drugs, or biological processes that promote or inhibit DNA methylation or demethylation, or to study the 3D nuclear organization of regions with high DNA methylation, such as constitutive heterochromatin.Here, we review and outline protocols for the fluorescent and enzymatic immunodetection of DNA methylation in the nuclei of cells, tissue sections, and mammalian embryos.
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Affiliation(s)
- Nathalie Beaujean
- INRA, UMR1198 Biologie du Développement et Reproduction, 78350, Jouy-en-Josas, France. .,Univ Lyon, Université Claude Bernard Lyon 1, Inserm, INRA, Stem Cell and Brain Research Institute U1208, USC1361, 69500, Bron, France.
| | - Juliette Salvaing
- INRA, UMR1198 Biologie du Développement et Reproduction, 78350, Jouy-en-Josas, France.,Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG-LPCV, 38000, Grenoble, France
| | - Nur Annies Abd Hadi
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK
| | - Sari Pennings
- Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh EH16 4TJ, UK.
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30
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Aguilar-Sanchez C, Michael M, Pennings S. Cardiac Stem Cells in the Postnatal Heart: Lessons from Development. Stem Cells Int 2018; 2018:1247857. [PMID: 30034478 DOI: 10.1155/2018/1247857] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 05/23/2018] [Indexed: 12/26/2022] Open
Abstract
Heart development in mammals is followed by a postnatal decline in cell proliferation and cell renewal from stem cell populations. A better understanding of the developmental changes in cardiac microenvironments occurring during heart maturation will be informative regarding the loss of adult regenerative potential. We reevaluate the adult heart's mitotic potential and the reported adult cardiac stem cell populations, as these are two topics of ongoing debate. The heart's early capacity for cell proliferation driven by progenitors and reciprocal signalling is demonstrated throughout development. The mature heart architecture and environment may be more restrictive on niches that can host progenitor cells. The engraftment issues observed in cardiac stem cell therapy trials using exogenous stem cells may indicate a lack of supporting stem cell niches, while tissue injury adds to a hostile microenvironment for transplanted cells. Engraftment may be improved by preconditioning the cultured stem cells and modulating the microenvironment to host these cells. These prospective areas of further research would benefit from a better understanding of cardiac progenitor interactions with their microenvironment throughout development and may lead to enhanced cardiac niche support for stem cell therapy engraftment.
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31
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Yang L, Chen L, Cai C, Li H. Differential gene regulatory plasticity between upper and lower layer cortical excitatory neurons. Mol Cell Neurosci 2018; 90:22-32. [PMID: 29802938 DOI: 10.1016/j.mcn.2018.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 05/20/2018] [Accepted: 05/22/2018] [Indexed: 11/16/2022] Open
Abstract
Neocortical projection neurons consist of intracortical connected upper layer (UL, layer II-IV) neurons and subcortical connected lower layer (LL, layer V-VI) neurons. Afferent activity from the thalamus regulates layer-specific gene expression during postnatal development, which is critical for the formation of proper neocortical cytoarchitecture. Here, we show that activity-dependent gene regulation is confined to UL cortical neurons, but not LL neurons, and that this distinction is likely due to epigenetic modifications of chromatin. We found that the immediate early genes (IEGs), EGR1 and c-FOS, are downregulated in all cortical laminar layers in the absence of afferent activity in vivo. Transcriptional assays demonstrated that EGR1 and c-FOS are able to bind to the promoters of UL- and LL-specific genes to induce transcription. Furthermore, we discovered that LL neurons express higher levels of heterochromatin markers, such as H3K9m3 and H4K20m3, compared to UL neurons. Our results suggest that differential epigenetic modifications of chromatin is an intrinsic mechanism that underlies the different sensitivities of cortical neurons to activity-dependent gene regulation.
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Affiliation(s)
- Lingling Yang
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Anhui 230022, China
| | - Liuzeng Chen
- School of Pharmacy, Anhui Medical University, Anhui, China
| | - Chunlin Cai
- Department of Pathophysiology, School of Basic Medical Sciences, Anhui Medical University, Anhui, China; Anhui Duoneng Biotechnology Corporation, Hefei, Anhui, China
| | - Hong Li
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Anhui 230022, China.
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32
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Eckersley-Maslin MA, Alda-Catalinas C, Reik W. Dynamics of the epigenetic landscape during the maternal-to-zygotic transition. Nat Rev Mol Cell Biol 2018; 19:436-450. [DOI: 10.1038/s41580-018-0008-z] [Citation(s) in RCA: 198] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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33
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Bonnet-Garnier A, Kiêu K, Aguirre-Lavin T, Tar K, Flores P, Liu Z, Peynot N, Chebrout M, Dinnyés A, Duranthon V, Beaujean N. Three-dimensional analysis of nuclear heterochromatin distribution during early development in the rabbit. Chromosoma 2018; 127:387-403. [PMID: 29666907 PMCID: PMC6096579 DOI: 10.1007/s00412-018-0671-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/06/2018] [Accepted: 04/03/2018] [Indexed: 01/29/2023]
Abstract
Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis). We observed that the pericentromeric regions (identified with specific probes for Rsat I and Rsat II genomic sequences) changed their shapes (from pearl necklaces to clusters), their nuclear localizations (from central to peripheral), as from the 4-cell stage. This reorganization goes along with histone modification changes and reduced amount of interactions with nucleolar precursor body surface. Altogether, our results suggest that the 4-cell stage may be a crucial window for events necessary before major EGA, which occurs during the 8-cell stage in the rabbit.
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Affiliation(s)
| | - Kiên Kiêu
- UR341 MaIAGE, INRA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | | | - Krisztina Tar
- Present Address: Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- BioTalentum Ltd., Aulich Lajos str. 26, Gödöllő, 2100 Hungary
| | - Pierre Flores
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Zichuan Liu
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
- Present Address: Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- State Key Laboratory of Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Nathalie Peynot
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - Martine Chebrout
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
| | - András Dinnyés
- BioTalentum Ltd., Aulich Lajos str. 26, Gödöllő, 2100 Hungary
| | | | - Nathalie Beaujean
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy-en-Josas, France
- Present Address: Univ Lyon, Université Claude Bernard Lyon 1, Inserm, INRA, Stem Cell and Brain Research Institute U1208, USC1361, 69500 Bron, France
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Schuler N, Timm S, Rübe CE. Hair Follicle Stem Cell Faith Is Dependent on Chromatin Remodeling Capacity Following Low-Dose Radiation. Stem Cells 2018; 36:574-588. [PMID: 29282803 DOI: 10.1002/stem.2768] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/21/2017] [Accepted: 12/03/2017] [Indexed: 12/17/2022]
Abstract
The main function of the skin, to protect against the environment, is supported by the activity of different stem cell populations. The main focus of this study was elucidating the coping mechanisms of stem cells against the stimulation of constant exposure to genotoxic stresses, both endogenous and exogenous, to ensure long-term function. Investigation of various mouse strains, differing in their DNA repair capacity, enables us to clarify fractionated low-dose irradiation (LDR)-induced consequences for different stem cell populations of the murine hair follicle (HF) in their physiological stem cell niche. Using microscopic techniques combined with flow cytometry, we could show that LDR induces accumulation of persisting; pKu70-independent 53BP1-foci ("chromatin-alterations") in heterochromatic regions of the HF stem cells (HFSCs). These remaining chromatin-alterations result in varying stem cell consequences. CD34-positive HFSCs react by ataxia telangiectasia mutated-dependent, premature senescence, which correlates with global chromatin compaction, whereby apoptosis is prevented by the activity of DNA-dependent protein kinase catalytic subunit. However, distinctively highly damaged HFSCs seem to be sorted out of the niche by differentiation, transferring their chromatin-alterations to more proliferative G protein-coupled receptor 5-positive stem cells. Consequentially, the loss of basal HFSCs is compensated by increased proliferation within the stem cell pool. Despite the initial success of these mechanisms in stem cell population maintenance, the combined effect of the chromatin-alterations and the modification in stem cell pool composition may lead to downstream long-term functional loss of tissue or organs. Stem Cells 2018;36:574-588.
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Affiliation(s)
- Nadine Schuler
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Sara Timm
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
| | - Claudia E Rübe
- Department of Radiation Oncology, Saarland University, Homburg/Saar, Germany
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35
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Abstract
When reflecting about cell fate commitment we think of differentiation. Be it during embryonic development or in an adult stem cell niche, where cells of a higher potency specialize and cell fate decisions are taken. Under normal circumstances this process is definitive and irreversible. Cell fate commitment is achieved by the establishment of cell-type-specific transcriptional programmes, which in turn are guided, reinforced, and ultimately locked-in by epigenetic mechanisms. Yet, this plunging drift in cellular potency linked to epigenetically restricted access to genomic information is problematic for reproduction. Particularly in mammals where germ cells are not set aside early on like in other species. Instead they are rederived from the embryonic ectoderm, a differentiating embryonic tissue with somatic epigenetic features. The epigenomes of germ cell precursors are efficiently reprogrammed against the differentiation trend, only to specialize once more into highly differentiated, sex-specific gametes: oocyte and sperm. Their differentiation state is reflected in their specialized epigenomes, and erasure of these features is required to enable the acquisition of the totipotent cell fate to kick start embryonic development of the next generation. Recent technological advances have enabled unprecedented insights into the epigenetic dynamics, first of DNA methylation and then of histone modifications, greatly expanding the historically technically limited understanding of this processes. In this chapter we will focus on the details of embryonic epigenetic reprogramming, a cell fate determination process against the tide to a higher potency.
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Affiliation(s)
- Michelle K Y Seah
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel M Messerschmidt
- Developmental Epigenetics and Disease Group, Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
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36
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Watchrarat K, Korchunjit W, Buranasinsup S, Taylor J, Ritruechai P, Wongtawan T. MEM α Promotes Cell Proliferation and Expression of Bone Marrow Derived Equine Mesenchymal Stem Cell Gene Markers but Depresses Differentiation Gene Markers. J Equine Vet Sci 2017; 50:8-14. [DOI: 10.1016/j.jevs.2016.10.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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37
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de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de Las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P. Repo-Man/PP1 regulates heterochromatin formation in interphase. Nat Commun 2017; 8:14048. [PMID: 28091603 PMCID: PMC5241828 DOI: 10.1038/ncomms14048] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment. Using a novel proteogenomic approach, we show that Repo-Man is enriched at subtelomeric regions together with H2AZ and H3.3 and that depletion of Repo-Man alters the peripheral localization of a subset of these regions and alleviates repression of some polycomb telomeric genes. This study shows a role for a mitotic phosphatase in the regulation of the epigenetic landscape and gene expression in interphase. Repo-Man is a chromosome-binding subunit of protein phosphatase 1 to regulate mitosis. Here, de Castro and colleagues show that Repo-Man also regulates heterochromatin during interphase, and regulates gene repression and chromatin organization.
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Affiliation(s)
- Inês J de Castro
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - James Budzak
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Maria L Di Giacinto
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Lorena Ligammari
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
| | - Daniela Moralli
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Silvia Salatino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Eric C Schirmer
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
| | - Katharine S Ullman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Catherine Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK.,Technische Universitat Berlin, 13355 Berlin, Germany
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Martin W Goldberg
- School of Biological and Medical Science, Durham University, Durham DH1 3LE, UK
| | - Veronica Vinciotti
- College of Engineering, Design and Technology, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
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Eid A, Rodriguez-Terrones D, Burton A, Torres-Padilla ME. SUV4-20 activity in the preimplantation mouse embryo controls timely replication. Genes Dev 2016; 30:2513-26. [PMID: 27920088 DOI: 10.1101/gad.288969.116] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/07/2016] [Indexed: 11/25/2022]
Abstract
Eid et al. show that ectopic expression of Suv4-20h2 leads to sustained levels of H4K20me3, developmental arrest, and defects in S-phase progression. The developmental phenotype can be partially overcome through inhibition of the ATR pathway, suggesting that the main function for the remodeling of H4K20me3 after fertilization is to allow the timely and coordinated progression of replication. Extensive chromatin remodeling after fertilization is thought to take place to allow a new developmental program to start. This includes dynamic changes in histone methylation and, in particular, the remodeling of constitutive heterochromatic marks such as histone H4 Lys20 trimethylation (H4K20me3). While the essential function of H4K20me1 in preimplantation mouse embryos is well established, the role of the additional H4K20 methylation states through the action of the SUV4-20 methyltransferases has not been addressed. Here we show that Suv4-20h1/h2 are mostly absent in mouse embryos before implantation, underscoring a rapid decrease of H4K20me3 from the two-cell stage onward. We addressed the functional significance of this remodeling by introducing Suv4-20h1 and Suv4-20h2 in early embryos. Ectopic expression of Suv4-20h2 leads to sustained levels of H4K20me3, developmental arrest, and defects in S-phase progression. The developmental phenotype can be partially overcome through inhibition of the ATR pathway, suggesting that the main function for the remodeling of H4K20me3 after fertilization is to allow the timely and coordinated progression of replication. This is in contrast to the replication program in somatic cells, where H4K20me3 has been shown to promote replication origin licensing, and anticipates a different regulation of replication during this early developmental time window.
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Saleh S, Lu HK, Evans V, Harisson D, Zhou J, Jaworowski A, Sallmann G, Cheong KY, Mota TM, Tennakoon S, Angelovich TA, Anderson J, Harman A, Cunningham A, Gray L, Churchill M, Mak J, Drummer H, Vatakis DN, Lewin SR, Cameron PU. HIV integration and the establishment of latency in CCL19-treated resting CD4(+) T cells require activation of NF-κB. Retrovirology 2016; 13:49. [PMID: 27459960 DOI: 10.1186/s12977-016-0284-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 07/15/2016] [Indexed: 12/17/2022] Open
Abstract
Background Eradication of HIV cannot be achieved with combination antiretroviral therapy (cART) because of the persistence of long-lived latently infected resting memory CD4+ T cells. We previously reported that HIV latency could be established in resting CD4+ T cells in the presence of the chemokine CCL19. To define how CCL19 facilitated the establishment of latent HIV infection, the role of chemokine receptor signalling was explored. Results In resting CD4+ T cells, CCL19 induced phosphorylation of RAC-alpha serine/threonine-protein kinase (Akt), nuclear factor kappa B (NF-κB), extracellular-signal-regulated kinase (ERK) and p38. Inhibition of the phosphoinositol-3-kinase (PI3K) and Ras/Raf/Mitogen-activated protein kinase/ERK kinase (MEK)/ERK signalling pathways inhibited HIV integration, without significant reduction in HIV nuclear entry (measured by Alu-LTR and 2-LTR circle qPCR respectively). Inhibiting activation of MEK1/ERK1/2, c-Jun N-terminal kinase (JNK), activating protein-1 (AP-1) and NF-κB, but not p38, also inhibited HIV integration. We also show that HIV integrases interact with Pin1 in CCL19-treated CD4+ T cells and inhibition of JNK markedly reduced this interaction, suggesting that CCL19 treatment provided sufficient signals to protect HIV integrase from degradation via the proteasome pathway. Infection of CCL19-treated resting CD4+ T cells with mutant strains of HIV, lacking NF-κB binding sites in the HIV long terminal repeat (LTR) compared to infection with wild type virus, led to a significant reduction in integration by up to 40-fold (range 1–115.4, p = 0.03). This was in contrast to only a modest reduction of 5-fold (range 1.7–11, p > 0.05) in fully activated CD4+ T cells infected with the same mutants. Finally, we demonstrated significant differences in integration sites following HIV infection of unactivated, CCL19-treated, and fully activated CD4+ T cells. Conclusions HIV integration in CCL19-treated resting CD4+ T cells depends on NF-κB signalling and increases the stability of HIV integrase, which allow subsequent integration and establishment of latency. These findings have implications for strategies needed to prevent the establishment, and potentially reverse, latent infection. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0284-7) contains supplementary material, which is available to authorized users.
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Bunkar N, Pathak N, Lohiya NK, Mishra PK. Epigenetics: A key paradigm in reproductive health. Clin Exp Reprod Med 2016; 43:59-81. [PMID: 27358824 PMCID: PMC4925870 DOI: 10.5653/cerm.2016.43.2.59] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 02/06/2016] [Accepted: 03/16/2016] [Indexed: 12/17/2022] Open
Abstract
It is well established that there is a heritable element of susceptibility to chronic human ailments, yet there is compelling evidence that some components of such heritability are transmitted through non-genetic factors. Due to the complexity of reproductive processes, identifying the inheritance patterns of these factors is not easy. But little doubt exists that besides the genomic backbone, a range of epigenetic cues affect our genetic programme. The inter-generational transmission of epigenetic marks is believed to operate via four principal means that dramatically differ in their information content: DNA methylation, histone modifications, microRNAs and nucleosome positioning. These epigenetic signatures influence the cellular machinery through positive and negative feedback mechanisms either alone or interactively. Understanding how these mechanisms work to activate or deactivate parts of our genetic programme not only on a day-to-day basis but also over generations is an important area of reproductive health research.
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Affiliation(s)
- Neha Bunkar
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India
| | - Neelam Pathak
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Nirmal Kumar Lohiya
- Reproductive Physiology Laboratory, Centre for Advanced Studies, University of Rajasthan, Jaipur, India
| | - Pradyumna Kumar Mishra
- Translational Research Laboratory, School of Biological Sciences, Dr. Hari Singh Central University, Sagar, India.; Department of Molecular Biology, National Institute for Research in Environmental Health (ICMR), Bhopal, India
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Abstract
Although the genes sequentially transcribed in the mammalian embryo prior to implantation have been identified, understanding of the molecular processes ensuring this transcription is still in development. The genomes of the sperm and egg are hypermethylated, hence transcriptionally silent. Their union, in the prepared environment of the egg, initiates their epigenetic genomic reprogramming into a totipotent zygote, in which the genome gradually becomes transcriptionally activated. During gametogenesis, sex-specific processes result in sperm and eggs with disparate epigenomes, both of which require drastic reprogramming to establish the totipotent genome of the zygote and the pluripotent inner cell mass of the blastocyst. Herein, we describe the factors, DNA and histone modifications, activation and repression of retrotransposons, and cytoplasmic localizations, known to influence the activation of the mammalian genome at the initiation of new life.
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Affiliation(s)
- C Y Lim
- Institute of Medical Biology, A*STAR, Singapore, Singapore
| | - B B Knowles
- Emerita, The Jackson Laboratory, Bar Harbor, ME, United States; Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok, Thailand
| | - D Solter
- Siriraj Center of Excellence for Stem Cell Research, Mahidol University, Bangkok, Thailand; Emeritus, Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - D M Messerschmidt
- Institute of Molecular and Cell Biology, A*STAR, Singapore, Singapore.
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Alvarenga EM, Rodrigues VL, Moraes AS, Naves LS, Mondin M, Felisbino MB, Mello MLS. Histone epigenetic marks in heterochromatin and euchromatin of the Chagas' disease vector, Triatoma infestans. Acta Histochem 2016; 118:401-12. [PMID: 27079857 DOI: 10.1016/j.acthis.2016.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/31/2016] [Accepted: 04/05/2016] [Indexed: 01/23/2023]
Abstract
Triatoma infestans, a vector of Chagas' disease, shows several particular cell biology characteristics, including the presence of conspicuous heterochromatic bodies (chromocenters) where DNA methylation has not been previously detected. Whether histone modifications contribute to the condensed state of these bodies has not yet been studied. Here, we investigated epigenetic modifications of histones H3 and H4 and presence of the non-histone heterochromatin protein (HP1-α) in the chromocenters and euchromatin of T. infestans cell nuclei, using immunocytochemistry. The effect of different concentrations of the histone deacetylase inhibitors valproic acid (VPA) and sodium butyrate (NaBt) on chromocenter condensation was visually examined; in VPA-treated specimens, this effect was also analyzed by image analysis. Trimethylated H3K9 signals, which were revealed in chromocenter and non-chromocenter areas, were strongest in chromocenters, whereas selected acetylated histone marks and mono- and dimethylated H3K9 and H4K20 signals were detected only in euchromatin. Weak trimethylated H4K20 signals and variable distribution of HP1-α were detected in chromocenters of part of the cellular population analyzed. Although specific VPA and NaBt treatment conditions affected the heterochromatin condensation pattern, they did not induce a decrease in survival and molting rates of the T. infestans nymphs. The VPA-induced chromatin remodeling was not accompanied by induction of H3K9 acetylation in chromocenters. Present findings regarding histone modifications and effects following VPA or NaBt treatments did not yet solve the question of which factors are responsible for maintenance of the condensed state of chromocenters in T. infestans. A possibility requiring further investigation remains on histone methylation marks and/or non-histone proteins.
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Panamarova M, Cox A, Wicher KB, Butler R, Bulgakova N, Jeon S, Rosen B, Seong RH, Skarnes W, Crabtree G, Zernicka-Goetz M. The BAF chromatin remodelling complex is an epigenetic regulator of lineage specification in the early mouse embryo. Development 2016; 143:1271-83. [PMID: 26952987 PMCID: PMC4852518 DOI: 10.1242/dev.131961] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 02/22/2016] [Indexed: 12/16/2022]
Abstract
Dynamic control of gene expression is essential for the development of a totipotent zygote into an embryo with defined cell lineages. The accessibility of genes responsible for cell specification to transcriptional machinery is dependent on chromatin remodelling complexes such as the SWI\SNF (BAF) complex. However, the role of the BAF complex in early mouse development has remained unclear. Here, we demonstrate that BAF155, a major BAF complex subunit, regulates the assembly of the BAF complex in vivo and regulates lineage specification of the mouse blastocyst. We find that associations of BAF155 with other BAF complex subunits become enriched in extra-embryonic lineages just prior to implantation. This enrichment is attributed to decreased mobility of BAF155 in extra-embryonic compared with embryonic lineages. Downregulation of BAF155 leads to increased expression of the pluripotency marker Nanog and its ectopic expression in extra-embryonic lineages, whereas upregulation of BAF155 leads to the upregulation of differentiation markers. Finally, we show that the arginine methyltransferase CARM1 methylates BAF155, which differentially influences assembly of the BAF complex between the lineages and the expression of pluripotency markers. Together, our results indicate a novel role of BAF-dependent chromatin remodelling in mouse development via regulation of lineage specification. Summary: Associations of BAF155 with other BAF complex subunits are enriched in extra-embryonic lineages prior to implantation, while changes in BAF155 levels modulate the expression of early developmental markers.
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Affiliation(s)
- Maryna Panamarova
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Andy Cox
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Krzysztof B Wicher
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
| | - Richard Butler
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Natalia Bulgakova
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK Bateson Centre and Department of Biomedical Science, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Shin Jeon
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-747, South Korea
| | - Barry Rosen
- Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Rho H Seong
- Department of Biological Sciences, Institute of Molecular Biology and Genetics, Seoul National University, Seoul 151-747, South Korea
| | | | - Gerald Crabtree
- Department of Developmental Biology, Stanford University Medical School, Stanford, CA 94305, USA
| | - Magdalena Zernicka-Goetz
- Wellcome Trust Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, UK
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Roshan A, Murai K, Fowler J, Simons BD, Nikolaidou-Neokosmidou V, Jones PH. Human keratinocytes have two interconvertible modes of proliferation. Nat Cell Biol 2016; 18:145-56. [PMID: 26641719 PMCID: PMC4872834 DOI: 10.1038/ncb3282] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 11/05/2015] [Indexed: 02/08/2023]
Abstract
Single stem cells, including those in human epidermis, have a remarkable ability to reconstitute tissues in vitro, but the cellular mechanisms that enable this are ill-defined. Here we used live imaging to track the outcome of thousands of divisions in clonal cultures of primary human epidermal keratinocytes. Two modes of proliferation were seen. In 'balanced' mode, similar proportions of proliferating and differentiating cells were generated, achieving the 'population asymmetry' that sustains epidermal homeostasis in vivo. In 'expanding' mode, an excess of cycling cells was produced, generating large expanding colonies. Cells in expanding mode switched their behaviour to balanced mode once local confluence was attained. However, when a confluent area was wounded in a scratch assay, cells near the scratch switched back to expanding mode until the defect was closed. We conclude that the ability of a single epidermal stem cell to reconstitute an epithelium is explained by two interconvertible modes of proliferation regulated by confluence.
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Affiliation(s)
- Amit Roshan
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, United Kingdom CB2 0XZ
- Present address: Norfolk & Norwich University Hospital, Colney Lane, Norwich, United Kingdom NR4 7UY
| | - Kasumi Murai
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom CB10 1SA
| | - Joanna Fowler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom CB10 1SA
| | - Benjamin D Simons
- Cavendish Laboratory, TCM, University of Cambridge, JJ Thomson Avenue, Cambridge, United Kingdom CB3 0HE
- Wellcome Trust/Cancer Research UK Gurdon Institute, The Henry Wellcome Building of Cancer and Developmental Biology, University of Cambridge, Tennis Court Road Cambridge, United Kingdom CB2 1QN
| | - Varvara Nikolaidou-Neokosmidou
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, United Kingdom CB2 0XZ
| | - Philip H Jones
- MRC Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre, Box 197, Cambridge Biomedical Campus, Cambridge, United Kingdom CB2 0XZ
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom CB10 1SA
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Çelik S, Li Y, O’Neill C. The effect of DNA damage on the pattern of immune-detectable DNA methylation in mouse embryonic fibroblasts. Exp Cell Res 2015; 339:20-34. [DOI: 10.1016/j.yexcr.2015.08.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 07/31/2015] [Accepted: 08/27/2015] [Indexed: 12/21/2022]
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van de Werken C, Avo Santos M, Laven J, Eleveld C, Fauser B, Lens S, Baart E. Chromosome segregation regulation in human zygotes: altered mitotic histone phosphorylation dynamics underlying centromeric targeting of the chromosomal passenger complex. Hum Reprod 2015. [DOI: 10.1093/humrep/dev186] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Masserdotti G, Gillotin S, Sutor B, Drechsel D, Irmler M, Jørgensen HF, Sass S, Theis FJ, Beckers J, Berninger B, Guillemot F, Götz M. Transcriptional Mechanisms of Proneural Factors and REST in Regulating Neuronal Reprogramming of Astrocytes. Cell Stem Cell 2015; 17:74-88. [PMID: 26119235 PMCID: PMC4509553 DOI: 10.1016/j.stem.2015.05.014] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 03/27/2015] [Accepted: 05/27/2015] [Indexed: 12/15/2022]
Abstract
Direct lineage reprogramming induces dramatic shifts in cellular identity, employing poorly understood mechanisms. Recently, we demonstrated that expression of Neurog2 or Ascl1 in postnatal mouse astrocytes generates glutamatergic or GABAergic neurons. Here, we take advantage of this model to study dynamics of neuronal cell fate acquisition at the transcriptional level. We found that Neurog2 and Ascl1 rapidly elicited distinct neurogenic programs with only a small subset of shared target genes. Within this subset, only NeuroD4 could by itself induce neuronal reprogramming in both mouse and human astrocytes, while co-expression with Insm1 was required for glutamatergic maturation. Cultured astrocytes gradually became refractory to reprogramming, in part by the repressor REST preventing Neurog2 from binding to the NeuroD4 promoter. Notably, in astrocytes refractory to Neurog2 activation, the underlying neurogenic program remained amenable to reprogramming by exogenous NeuroD4. Our findings support a model of temporal hierarchy for cell fate change during neuronal reprogramming. Neurog2 and Ascl1 regulate largely non-overlapping neurogenic targets A subset of genes is required and sufficient to convert astrocytes and fibroblasts Neurog2 and REST compete for binding to the NeuroD4 promoter REST deletion enhances Neurog2-mediated reprogramming in vitro
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Affiliation(s)
- Giacomo Masserdotti
- Physiological Genomics, Biomedical Center, University of Munich, 80336 Munich, Germany; Institute for Stem Cell Research, Helmholtz Centre Munich, 85764 Neuherberg, Germany
| | - Sébastien Gillotin
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, UK; Hutchison/MRC Research Center, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Bernd Sutor
- Physiological Genomics, Biomedical Center, University of Munich, 80336 Munich, Germany
| | - Daniela Drechsel
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, UK
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Centre Munich, 85764 Neuherberg, Germany
| | - Helle F Jørgensen
- Department of Medicine, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Steffen Sass
- Institute of Computational Biology, Helmholtz Centre Munich, 85764 Neuherberg, Germany
| | - Fabian J Theis
- Institute of Computational Biology, Helmholtz Centre Munich, 85764 Neuherberg, Germany; Department of Mathematics, Technical University Munich, 85748 Garching, Germany
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Centre Munich, 85764 Neuherberg, Germany; Center of Life and Food Sciences Weihenstephan, Technical University, 85354 Freising, Germany
| | - Benedikt Berninger
- Institute of Physiological Chemistry, University Medical Center of the Johannes Gutenberg University, D-55128 Mainz, Germany; Focus Program Translational Neuroscience, Johannes Gutenberg University, D-55128 Mainz, Germany
| | - François Guillemot
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London, NW7 1AA, UK.
| | - Magdalena Götz
- Physiological Genomics, Biomedical Center, University of Munich, 80336 Munich, Germany; Institute for Stem Cell Research, Helmholtz Centre Munich, 85764 Neuherberg, Germany; Munich Cluster for Systems Neurology "SyNergy," Ludwig Maximilian University of Munich, 80539 Munich, Germany.
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Abstract
During X-chromosome inactivation (XCI), nearly an entire X chromosome is permanently silenced and converted into a Barr body, providing dosage compensation for eutherians between the sexes. XCI is facilitated by the upregulation of the long non-coding RNA gene, XIST, which coats its chromosome of origin, recruits heterochromatin factors, and silences gene expression. During XCI, at least two distinct types of heterochromatin are established, and in this review we discuss the enrichment of facultative heterochromatin marks such as H3K27me3, H2AK119ub, and macroH2A as well as pericentric heterochromatin marks such as HP1, H3K9me3, and H4K20me3. The extremely stable maintenance of silencing is a product of reinforcing interactions within and between these domains. This paper "Xplores" the current knowledge of the pathways involved in XCI, how the pathways interact, and the gaps in our understanding that need to be filled.
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Affiliation(s)
- Thomas Dixon-McDougall
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Carolyn Brown
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
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Sherstyuk VV, Shevchenko AI, Zakian SM. Mapping of Replication Origins in the X Inactivation Center of Vole Microtus levis Reveals Extended Replication Initiation Zone. PLoS One 2015; 10:e0128497. [PMID: 26038842 PMCID: PMC4454516 DOI: 10.1371/journal.pone.0128497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/27/2015] [Indexed: 11/29/2022] Open
Abstract
DNA replication initiates at specific positions termed replication origins. Genome-wide studies of human replication origins have shown that origins are organized into replication initiation zones. However, only few replication initiation zones have been described so far. Moreover, few origins were mapped in other mammalian species besides human and mouse. Here we analyzed pattern of short nascent strands in the X inactivation center (XIC) of vole Microtus levis in fibroblasts, trophoblast stem cells, and extraembryonic endoderm stem cells and confirmed origins locations by ChIP approach. We found that replication could be initiated in a significant part of XIC. We also analyzed state of XIC chromatin in these cell types. We compared origin localization in the mouse and vole XIC. Interestingly, origins associated with gene promoters are conserved in these species. The data obtained allow us to suggest that the X inactivation center of M. levis is one extended replication initiation zone.
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Affiliation(s)
- Vladimir V. Sherstyuk
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- State Research Institute of Circulation Pathology, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Alexander I. Shevchenko
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- State Research Institute of Circulation Pathology, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Suren M. Zakian
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- State Research Institute of Circulation Pathology, Novosibirsk, Russia
- Institute of Chemical Biology and Fundamental Medicine, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
- * E-mail:
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50
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Abstract
Successful mammalian development requires descendants of single-cell zygotes to differentiate into diverse cell types even though they contain the same genetic material. Preimplantation dynamics are first driven by the necessity of reprogramming haploid parental epigenomes to reach a totipotent state. This process requires extensive erasure of epigenetic marks shortly after fertilization. During the few short days after formation of the zygote, epigenetic programs are established and are essential for the first lineage decisions and differentiation. Here we review the current understanding of DNA methylation and histone modification dynamics responsible for these early changes during mammalian preimplantation development. In particular, we highlight insights that have been gained through next-generation sequencing technologies comparing human embryos to other models as well as the recent discoveries of active DNA demethylation mechanisms at play during preimplantation.
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Affiliation(s)
- Chelsea Marcho
- Department of Veterinary and Animal ScienceUniversity of Massachusetts Amherst, 661 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Wei Cui
- Department of Veterinary and Animal ScienceUniversity of Massachusetts Amherst, 661 North Pleasant Street, Amherst, Massachusetts 01003, USA
| | - Jesse Mager
- Department of Veterinary and Animal ScienceUniversity of Massachusetts Amherst, 661 North Pleasant Street, Amherst, Massachusetts 01003, USA
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