1
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Fu B, Ma H, Liu D. Essential roles of the nucleolus during early embryonic development: a regulatory hub for chromatin organization. Open Biol 2024; 14:230358. [PMID: 38689555 PMCID: PMC11065130 DOI: 10.1098/rsob.230358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.
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Affiliation(s)
- Bo Fu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Hong Ma
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
| | - Di Liu
- Institute of Animal Husbandry, HeiLongJiang Academy of
Agricultural Sciences, Harbin150086, People's Republic of China
- Key Laboratory of Combining Farming and Animal Husbandry,
Ministry of Agriculture and Rural Affairs, Harbin150086, People's Republic of China
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2
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Han Q, Ma R, Liu N. Epigenetic reprogramming in the transition from pluripotency to totipotency. J Cell Physiol 2024; 239:e31222. [PMID: 38375873 DOI: 10.1002/jcp.31222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/08/2024] [Accepted: 02/05/2024] [Indexed: 02/21/2024]
Abstract
Mammalian development commences with the zygote, which can differentiate into both embryonic and extraembryonic tissues, a capability known as totipotency. Only the zygote and embryos around zygotic genome activation (ZGA) (two-cell embryo stage in mice and eight-cell embryo in humans) are totipotent cells. Epigenetic modifications undergo extremely extensive changes during the acquisition of totipotency and subsequent development of differentiation. However, the underlying molecular mechanisms remain elusive. Recently, the discovery of mouse two-cell embryo-like cells, human eight-cell embryo-like cells, extended pluripotent stem cells and totipotent-like stem cells with extra-embryonic developmental potential has greatly expanded our understanding of totipotency. Experiments with these in vitro models have led to insights into epigenetic changes in the reprogramming of pluri-to-totipotency, which have informed the exploration of preimplantation development. In this review, we highlight the recent findings in understanding the mechanisms of epigenetic remodeling during totipotency capture, including RNA splicing, DNA methylation, chromatin configuration, histone modifications, and nuclear organization.
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Affiliation(s)
- Qingsheng Han
- School of Medicine, Nankai University, Tianjin, China
| | - Ru Ma
- School of Medicine, Nankai University, Tianjin, China
| | - Na Liu
- School of Medicine, Nankai University, Tianjin, China
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3
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Ye Y, Homer HA. A surge in cytoplasmic viscosity triggers nuclear remodeling required for Dux silencing and pre-implantation embryo development. Cell Rep 2024; 43:113917. [PMID: 38446665 DOI: 10.1016/j.celrep.2024.113917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/17/2023] [Accepted: 02/16/2024] [Indexed: 03/08/2024] Open
Abstract
Embryonic genome activation (EGA) marks the transition from dependence on maternal transcripts to an embryonic transcriptional program. The precise temporal regulation of gene expression, specifically the silencing of the Dux/murine endogenous retrovirus type L (MERVL) program during late 2-cell interphase, is crucial for developmental progression in mouse embryos. How this finely tuned regulation is achieved within this specific window is poorly understood. Here, using particle-tracking microrheology throughout the mouse oocyte-to-embryo transition, we identify a surge in cytoplasmic viscosity specific to late 2-cell interphase brought about by high microtubule and endomembrane density. Importantly, preventing the rise in 2-cell viscosity severely impairs nuclear reorganization, resulting in a persistently open chromatin configuration and failure to silence Dux/MERVL. This, in turn, derails embryo development beyond the 2- and 4-cell stages. Our findings reveal a mechanical role of the cytoplasm in regulating Dux/MERVL repression via nuclear remodeling during a temporally confined period in late 2-cell interphase.
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Affiliation(s)
- Yunan Ye
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia
| | - Hayden Anthony Homer
- The Christopher Chen Oocyte Biology Research Laboratory, Centre for Clinical Research, The University of Queensland, Herston, QLD 4029, Australia.
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4
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Li J, Yuan P, Ma G, Liu Y, Zhang Q, Wang W, Guo Y. The composition dynamics of transposable elements in human blastocysts. J Hum Genet 2023; 68:681-688. [PMID: 37308564 DOI: 10.1038/s10038-023-01169-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/11/2023] [Accepted: 06/03/2023] [Indexed: 06/14/2023]
Abstract
Transposable elements (TEs) are mobile DNA sequences that can replicate themselves and play significant roles in embryo development and chromosomal structure remodeling. In this study, we investigated the variation of TEs in blastocysts with different parental genetic backgrounds. We analyzed the proportions of 1137 TEs subfamilies from six classes at the DNA level using Bowtie2 and PopoolationTE2 in 196 blastocysts with abnormal parental chromosomal diseases. Our findings revealed that the parental karyotype was the dominant factor influencing TEs frequencies. Out of the 1116 subfamilies, different frequencies were observed in blastocysts with varying parental karyotypes. The development stage of blastocysts was the second most crucial factor influencing TEs proportions. A total of 614 subfamilies exhibited different proportions at distinct blastocyst stages. Notably, subfamily members belonging to the Alu family showed a high proportion at stage 6, while those from the LINE class exhibited a high proportion at stage 3 and a low proportion at stage 6. Moreover, the proportions of some TEs subfamilies also varied depending on blastocyst karyotype, inner cell mass status, and outer trophectoderm status. We found that 48 subfamilies displayed different proportions between balanced and unbalanced blastocysts. Additionally, 19 subfamilies demonstrated varying proportions among different inner cell mass scores, and 43 subfamilies exhibited different proportions among outer trophectoderm scores. This study suggests that the composition of TEs subfamilies may be influenced by various factors and undergoes dynamic modulation during embryo development.
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Affiliation(s)
- Jian Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping Yuan
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- IVF Center, The First People's Hospital of Kashi Prefecture, Kashi, China
| | - Guangwei Ma
- Ministry of Education Key Laboratory for Ecology of Tropical Islands, Key Laboratory of Tropical Animal and Plant Ecology of Hainan Province, College of Life Sciences, Hainan Normal University, Haikou, China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Reproductive Medical Center, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qingxue Zhang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenjun Wang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China.
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5
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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] [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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6
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Djeghloul D, Dimond A, Cheriyamkunnel S, Kramer H, Patel B, Brown K, Montoya A, Whilding C, Wang YF, Futschik ME, Veland N, Montavon T, Jenuwein T, Merkenschlager M, Fisher AG. Loss of H3K9 trimethylation alters chromosome compaction and transcription factor retention during mitosis. Nat Struct Mol Biol 2023; 30:489-501. [PMID: 36941433 PMCID: PMC10113154 DOI: 10.1038/s41594-023-00943-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 02/13/2023] [Indexed: 03/23/2023]
Abstract
Recent studies have shown that repressive chromatin machinery, including DNA methyltransferases and polycomb repressor complexes, binds to chromosomes throughout mitosis and their depletion results in increased chromosome size. In the present study, we show that enzymes that catalyze H3K9 methylation, such as Suv39h1, Suv39h2, G9a and Glp, are also retained on mitotic chromosomes. Surprisingly, however, mutants lacking histone 3 lysine 9 trimethylation (H3K9me3) have unusually small and compact mitotic chromosomes associated with increased histone H3 phospho Ser10 (H3S10ph) and H3K27me3 levels. Chromosome size and centromere compaction in these mutants were rescued by providing exogenous first protein lysine methyltransferase Suv39h1 or inhibiting Ezh2 activity. Quantitative proteomic comparisons of native mitotic chromosomes isolated from wild-type versus Suv39h1/Suv39h2 double-null mouse embryonic stem cells revealed that H3K9me3 was essential for the efficient retention of bookmarking factors such as Esrrb. These results highlight an unexpected role for repressive heterochromatin domains in preserving transcription factor binding through mitosis and underscore the importance of H3K9me3 for sustaining chromosome architecture and epigenetic memory during cell division.
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Affiliation(s)
- Dounia Djeghloul
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
| | - Andrew Dimond
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Sherry Cheriyamkunnel
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Holger Kramer
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Bhavik Patel
- Flow Cytometry Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Karen Brown
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Alex Montoya
- Biological Mass Spectrometry and Proteomics Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Chad Whilding
- Microscopy Facility, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Yi-Fang Wang
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Matthias E Futschik
- Bioinformatics, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Nicolas Veland
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Thomas Montavon
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Thomas Jenuwein
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Matthias Merkenschlager
- Lymphocyte Development Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK
| | - Amanda G Fisher
- Epigenetic Memory Group, MRC London Institute of Medical Sciences, Imperial College London, London, UK.
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7
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Zhu J, Chen K, Sun YH, Ye W, Liu J, Zhang D, Su N, Wu L, Kou X, Zhao Y, Wang H, Gao S, Kang L. LSM1-mediated Major Satellite RNA decay is required for nonequilibrium histone H3.3 incorporation into parental pronuclei. Nat Commun 2023; 14:957. [PMID: 36810573 PMCID: PMC9944933 DOI: 10.1038/s41467-023-36584-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 02/06/2023] [Indexed: 02/24/2023] Open
Abstract
Epigenetic reprogramming of the parental genome is essential for zygotic genome activation and subsequent embryo development in mammals. Asymmetric incorporation of histone H3 variants into the parental genome has been observed previously, but the underlying mechanism remains elusive. In this study, we discover that RNA-binding protein LSM1-mediated major satellite RNA decay plays a central role in the preferential incorporation of histone variant H3.3 into the male pronucleus. Knockdown of Lsm1 disrupts nonequilibrium pronucleus histone incorporation and asymmetric H3K9me3 modification. Subsequently, we find that LSM1 mainly targets major satellite repeat RNA (MajSat RNA) for decay and that accumulated MajSat RNA in Lsm1-depleted oocytes leads to abnormal incorporation of H3.1 into the male pronucleus. Knockdown of MajSat RNA reverses the anomalous histone incorporation and modifications in Lsm1-knockdown zygotes. Our study therefore reveals that accurate histone variant incorporation and incidental modifications in parental pronuclei are specified by LSM1-dependent pericentromeric RNA decay.
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Affiliation(s)
- Jiang Zhu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Kang Chen
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China.,Institute of Biophysics, Chinese Academy of Sciences, 100101, Beijing, China.,University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yu H Sun
- Departments of Biology, University of Rochester, 14642, Rochester, NY, USA
| | - Wen Ye
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Juntao Liu
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Dandan Zhang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Nan Su
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China
| | - Li Wu
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Xiaochen Kou
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Yanhong Zhao
- Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China
| | - Hong Wang
- Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
| | - Shaorong Gao
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China. .,Clinical and Translation Research Center of Shanghai First Maternity & Infant Hospital, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
| | - Lan Kang
- Institute for Regenerative Medicine, Shanghai East Hospital, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, 200120, Shanghai, China. .,Frontier Science Center for Stem Cell Research, Tongji University, 200092, Shanghai, China.
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8
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Bari MW, Morishita Y, Kishigami S. Heterogeneity of nucleolar morphology in four-cell mouse embryos after IVF: association with developmental potential. Anim Sci J 2023; 94:e13907. [PMID: 38102887 DOI: 10.1111/asj.13907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 11/22/2023] [Accepted: 11/27/2023] [Indexed: 12/17/2023]
Abstract
In mammals, around fertilization, the nucleolus of embryos transforms into the nucleolus precursor bodies (NPBs), which continue to mature until the blastocyst stage, leading to distinct morphological changes. In our study, we observed two types of nucleolar morphology in mouse in vitro fertilized embryos at the four-cell stage, which we refer to single nucleolus (SN) and multiple nucleoli (MN). To visualize nucleolar morphology, four-cell embryos were immunostained with anti-NOPP140 antibody. These embryos were categorized into five types based on the number of blastomeres carrying SN: SN4/MN0, SN3/MN1, SN2/MN2, SN1/MN3, and SN0/MN4, with percentages of 13, 27, 21, 23 and 9, respectively. Next, using a light microscope, we divided the four-cell in vitro fertilized embryos without fixation into two groups: those with at least two blastomeres displaying SN (SN embryos) and those without (MN embryos). Notably, significantly more SN embryos developed into blastocysts and offspring at 18.5 dpc compared with MN embryos. Furthermore, SN embryos displayed a higher NANOG-positive cell number at the blastocyst stage, significantly lower body and placental weights, resulting in a higher fetal/placental ratio. These findings suggest a close association between nucleolar state at the four-cell stage and subsequent developmental potential.
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Affiliation(s)
- Md Wasim Bari
- Department of Integrated Applied Life Science, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, Kofu, Japan
| | - Yoshiya Morishita
- Graduate School of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi Kofu, Japan
| | - Satoshi Kishigami
- Department of Integrated Applied Life Science, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi, Kofu, Japan
- Graduate School of Life and Environmental Sciences, Integrated Graduate School of Medicine, Engineering, and Agricultural Sciences, University of Yamanashi Kofu, Japan
- Center for advanced Assisted Reproductive Technologies, University of Yamanashi, Kofu, Japan
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9
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SPRITE: a genome-wide method for mapping higher-order 3D interactions in the nucleus using combinatorial split-and-pool barcoding. Nat Protoc 2022; 17:36-75. [PMID: 35013617 DOI: 10.1038/s41596-021-00633-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 09/13/2021] [Indexed: 12/23/2022]
Abstract
A fundamental question in gene regulation is how cell-type-specific gene expression is influenced by the packaging of DNA within the nucleus of each cell. We recently developed Split-Pool Recognition of Interactions by Tag Extension (SPRITE), which enables mapping of higher-order interactions within the nucleus. SPRITE works by cross-linking interacting DNA, RNA and protein molecules and then mapping DNA-DNA spatial arrangements through an iterative split-and-pool barcoding method. All DNA molecules within a cross-linked complex are barcoded by repeatedly splitting complexes across a 96-well plate, ligating molecules with a unique tag sequence, and pooling all complexes into a single well before repeating the tagging. Because all molecules in a cross-linked complex are covalently attached, they will sort together throughout each round of split-and-pool and will obtain the same series of SPRITE tags, which we refer to as a barcode. The DNA fragments and their associated barcodes are sequenced, and all reads sharing identical barcodes are matched to reconstruct interactions. SPRITE accurately maps pairwise DNA interactions within the nucleus and measures higher-order spatial contacts occurring among up to thousands of simultaneously interacting molecules. Here, we provide a detailed protocol for the experimental steps of SPRITE, including a video ( https://youtu.be/6SdWkBxQGlg ). Furthermore, we provide an automated computational pipeline available on GitHub that allows experimenters to seamlessly generate SPRITE interaction matrices starting with raw fastq files. The protocol takes ~5 d from cell cross-linking to high-throughput sequencing for the experimental steps and 1 d for data processing.
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10
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Borsuk E, Michalkiewicz J, Kubiak JZ, Kloc M. Histone Modifications in Mouse Pronuclei and Consequences for Embryo Development. Results Probl Cell Differ 2022; 70:397-415. [PMID: 36348116 DOI: 10.1007/978-3-031-06573-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Epigenetic marks, such as DNA methylation and posttranslational modifications of core histones, are the key regulators of gene expression. In the mouse, many of these marks are erased during gamete formation and must be introduced de novo after fertilization. Some of them appear synchronously, but the others are deposited asynchronously and/or remain differently distributed on maternal and paternal chromatin. Although the mechanisms regulating these processes are not entirely understandable, it is commonly accepted that epigenetic reprogramming occurring during the first cell cycle of a mouse embryo is crucial for its further development. This chapter focuses on selected epigenetic modifications, such as DNA methylation, the introduction of histone variants, histones acetylation, phosphorylation, and methylation. Properly depositing these marks on maternal and paternal chromatin is crucial for normal embryonic development.
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Affiliation(s)
- Ewa Borsuk
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Julia Michalkiewicz
- Department of Embryology, Institute of Developmental Biology and Biomedical Sciences, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jacek Z Kubiak
- Dynamics and Mechanics of Epithelia Group, Institute of Genetics and Development of Rennes, UMR 6290, CNRS, Faculty of Medicine, University of Rennes, Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Department of Oncology, Military Institute of Medicine, Warsaw, Poland
| | - Malgorzata Kloc
- The Houston Methodist Research Institute, Houston, TX, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX, USA
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11
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FULKA H, LOI P, PALAZZESE L, BENC M, FULKA, Jr. J. Nucleus reprogramming/remodeling through selective enucleation (SE) of immature oocytes and zygotes: a nucleolus point of view. J Reprod Dev 2022; 68:165-172. [PMID: 35431279 PMCID: PMC9184824 DOI: 10.1262/jrd.2022-004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is now approximately 25 years since the sheep Dolly, the first cloned mammal where the somatic cell nucleus from an adult donor was used for transfer, was born. So far, somatic cell
nucleus transfer, where G1-phase nuclei are transferred into cytoplasts obtained by enucleation of mature metaphase II (MII) oocytes followed by the activation of the reconstructed cells, is
the most efficient approach to reprogram/remodel the differentiated nucleus. In general, in an enucleated oocyte (cytoplast), the nuclear envelope (NE, membrane) of an injected somatic cell
nucleus breaks down and chromosomes condense. This condensation phase is followed, after subsequent activation, by chromatin decondensation and formation of a pseudo-pronucleus (i) whose
morphology should resemble the natural postfertilization pronuclei (PNs). Thus, the volume of the transferred nuclei increases considerably by incorporating the content released from the
germinal vesicles (GVs). In parallel, the transferred nucleus genes must be reset and function similarly as the relevant genes in normal embryo reprogramming. This, among others, covers the
relevant epigenetic modifications and the appropriate organization of chromatin in pseudo-pronuclei. While reprogramming in SCNT is often discussed, the remodeling of transferred nuclei is
much less studied, particularly in the context of the developmental potential of SCNT embryos. It is now evident that correct reprogramming mirrors appropriate remodeling. At the same time,
it is widely accepted that the process of rebuilding the nucleus following SCNT is instrumental to the overall success of this procedure. Thus, in our contribution, we will mostly focus on
the remodeling of transferred nuclei. In particular, we discuss the oocyte organelles that are essential for the development of SCNT embryos.
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Affiliation(s)
- Helena FULKA
- Institute of Experimental Medicine, Prague, Czech Republic
| | - Pasqualino LOI
- Faculty of Veterinary Medicine, University of Teramo, Teramo, Italy
| | - Luca PALAZZESE
- Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland
| | - Michal BENC
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Slovak Republic
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12
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Yuan L, Sun B, Xu L, Chen L, Ou W. The Updating of Biological Functions of Methyltransferase SETDB1 and Its Relevance in Lung Cancer and Mesothelioma. Int J Mol Sci 2021; 22:ijms22147416. [PMID: 34299035 PMCID: PMC8306223 DOI: 10.3390/ijms22147416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/11/2022] Open
Abstract
SET domain bifurcated 1 (SETDB1) is a histone H3 lysine 9 (H3K9) methyltransferase that exerts important effects on epigenetic gene regulation. SETDB1 complexes (SETDB1-KRAB-KAP1, SETDB1-DNMT3A, SETDB1-PML, SETDB1-ATF7IP-MBD1) play crucial roles in the processes of histone methylation, transcriptional suppression and chromatin remodelling. Therefore, aberrant trimethylation at H3K9 due to amplification, mutation or deletion of SETDB1 may lead to transcriptional repression of various tumour-suppressing genes and other related genes in cancer cells. Lung cancer is the most common type of cancer worldwide in which SETDB1 amplification and H3K9 hypermethylation have been indicated as potential tumourigenesis markers. In contrast, frequent inactivation mutations of SETDB1 have been revealed in mesothelioma, an asbestos-associated, locally aggressive, highly lethal, and notoriously chemotherapy-resistant cancer. Above all, the different statuses of SETDB1 indicate that it may have different biological functions and be a potential diagnostic biomarker and therapeutic target in lung cancer and mesothelioma.
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Affiliation(s)
| | | | | | | | - Wenbin Ou
- Correspondence: ; Tel./Fax: +86-571-86843303
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13
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Hale BJ, Li Y, Adur MK, Keating AF, Baumgard LH, Ross JW. Characterization of the effects of heat stress on autophagy induction in the pig oocyte. Reprod Biol Endocrinol 2021; 19:107. [PMID: 34243771 PMCID: PMC8268447 DOI: 10.1186/s12958-021-00791-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/23/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Heat stress (HS) occurs when body heat accumulation exceeds heat dissipation and is associated with swine seasonal infertility. HS contributes to compromised oocyte integrity and reduced embryo development. Autophagy is a potential mechanism for the oocyte to mitigate the detrimental effects of HS by recycling damaged cellular components. METHODS To characterize the effect of HS on autophagy in oocyte maturation, we utilized an in vitro maturation (IVM) system where oocytes underwent thermal neutral (TN) conditions throughout the entire maturation period (TN/TN), HS conditions during the first half of IVM (HS/TN), or HS conditions during the second half of IVM (TN/HS). RESULTS To determine the effect of HS on autophagy induction within the oocyte, we compared the relative abundance and localization of autophagy-related proteins. Heat stress treatment affected the abundance of two well described markers of autophagy induction: autophagy related gene 12 (ATG12) in complex with ATG5 and the cleaved form of microtubule-associated protein 1 light chain 3 beta (LC3B-II). The HS/TN IVM treatment increased the abundance of the ATG12-ATG5 complex and exacerbated the loss of LC3B-II in oocytes. The B-cell lymphoma 2 like 1 protein (BCL2L1) can inhibit autophagy or apoptosis through its interaction with either beclin1 (BECN1) or BCL2 associated X, apoptosis regulator (BAX), respectively. We detected colocalization of BCL2L1 with BAX but not BCL2L1 with BECN1, suggesting that apoptosis is inhibited under the HS/TN treatment but not autophagy. Interestingly, low doses of the autophagy inducer, rapamycin, increased oocyte maturation. CONCLUSIONS Our results here suggest that HS increases autophagy induction in the oocyte during IVM, and that artificial induction of autophagy increases the maturation rate of oocytes during IVM. These data support autophagy as a potential mechanism activated in the oocyte during HS to recycle damaged cellular components and maintain developmental competence.
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Affiliation(s)
- Benjamin J Hale
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA
| | - Yunsheng Li
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA
| | - Malavika K Adur
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA
| | - Aileen F Keating
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA
| | - Lance H Baumgard
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA
| | - Jason W Ross
- Department of Animal Science, Iowa State University, 2356 Kildee Hall, Ames, IA, 50011, USA.
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14
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Kawamura M, Funaya S, Sugie K, Suzuki MG, Aoki F. Asymmetrical deposition and modification of histone H3 variants are essential for zygote development. Life Sci Alliance 2021; 4:4/8/e202101102. [PMID: 34168076 PMCID: PMC8321678 DOI: 10.26508/lsa.202101102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 01/02/2023] Open
Abstract
A low level of H3.1/2 deposition in the perinucleolar regions of male pronuclei in zygotes prevents accumulation of H3.1/2K27me3 modification which has detrimental effect on DNA replication. The pericentromeric heterochromatin of one-cell embryos forms a unique, ring-like structure around the nucleolar precursor body, which is absent in somatic cells. Here, we found that the histone H3 variants H3.1 and/or H3.2 (H3.1/H3.2) were localized asymmetrically between the male and female perinucleolar regions of the one-cell embryos; moreover, asymmetrical histone localization influenced DNA replication timing. The nuclear deposition of H3.1/3.2 in one-cell embryos was low relative to other preimplantation stages because of reduced H3.1/3.2 mRNA expression and incorporation efficiency. The forced incorporation of H3.1/3.2 into the pronuclei of one-cell embryos triggered a delay in DNA replication, leading to developmental failure. Methylation of lysine residue 27 (H3K27me3) of the deposited H3.1/3.2 in the paternal perinucleolar region caused this delay in DNA replication. These results suggest that reduced H3.1/3.2 in the paternal perinucleolar region is essential for controlled DNA replication and preimplantation development. The nuclear deposition of H3.1/3.2 is presumably maintained at a low level to avoid the detrimental effect of K27me3 methylation on DNA replication in the paternal perinucleolar region.
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Affiliation(s)
- Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Kenta Sugie
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
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15
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Benc M, Strejcek F, Morovic M, Bartkova A, Murin M, Gad A, Bonnet-Garnier A, Percinic FP, Laurincik J. Improving the Quality of Oocytes with the Help of Nucleolotransfer Therapy. Pharmaceuticals (Basel) 2021; 14:ph14040328. [PMID: 33918523 PMCID: PMC8066131 DOI: 10.3390/ph14040328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022] Open
Abstract
The nucleolus is an important nucleus sub-organelle found in almost all eukaryotic cells. On the one hand, it is known as a differentiated active site of ribosome biogenesis in somatic cells, but on the other hand, in fully grown oocytes, zygotes, and early embryos (up to the major embryonic genome activation), it is in the form of a particular homogenous and compact structure called a fibrillar sphere. Nowadays, thanks to recent studies, we know many important functions of this, no doubt, interesting membraneless nucleus sub-organelle involved in oocyte maturation, embryonic genome activation, rRNA synthesis, etc. However, many questions are still unexplained and remain a mystery. Our aim is to create a comprehensive overview of the recent knowledge on the fibrillar sphere and envision how this knowledge could be utilized in further research in the field of biotechnology and nucleolotransfer therapy.
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Affiliation(s)
- Michal Benc
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
| | - Frantisek Strejcek
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Correspondence: ; Tel.: +421-037-6408-584
| | - Martin Morovic
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
| | - Alexandra Bartkova
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Matej Murin
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Ahmed Gad
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
| | - Amelie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350 Jouy-en-Josas, France;
- Ecole Nationale Vétérinaire d’Alfort, BREED, 94700 Maisons-Alfort, France
| | - Florina Popovska Percinic
- Faculty of Veterinary Medicine, St. Cyril and Methodius University in Skopje, 1000 Skopje, North Macedonia;
| | - Jozef Laurincik
- Faculty of Natural Sciences, Constantine the Philosopher University in Nitra, Nabrezie mladeze 91, 94974 Nitra, Slovakia; (M.B.); (M.M.); (A.B.); (J.L.)
- Institute of Animal Physiology and Genetics, The Czech Academy of Sciences, 27721 Libechov, Czech Republic; (M.M.); (A.G.)
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16
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Abstract
Somatic cell nuclear transfer (SCNT) is a powerful technique, although challenging, to study reprograming into the totipotent state of differentiated nuclei in mammals. This procedure was initially applied in farm animals, then rodents, and more recently in primates. Nuclear transfer of embryonic stem cells is known to be more efficient, but many types of somatic cells have now been successfully reprogramed with this procedure. Moreover, SCNT reprograming is more effective on a per cell basis than induced Pluripotent Stem Cells (iPSC) and provides interesting clues regarding the underlying processes. In this chapter, we describe the protocol of nuclear transfer in mouse that combines cell cycle synchronization of the donor cells, enucleation of metaphase II oocyte and Piezo-driven injection of a donor cell nucleus followed by activation of the reconstructed embryos and nonsurgical transfer into pseudo-pregnant mice. Moreover, this protocol includes two facultative steps to erase the epigenetic "memory" of the donor cells and improve chromatin remodeling by histones modifications targeting.
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Affiliation(s)
- Vincent Brochard
- Université Paris-Saclay, INRAE, ENVA, BREED U1198, Jouy-en-Josas, France
| | - Nathalie Beaujean
- Université Paris-Saclay, INRAE, ENVA, BREED U1198, Jouy-en-Josas, France. .,Univ Lyon, Université Lyon 1, Inserm, INRAE, Stem Cell and Brain Research Institute U1208, USC 1361, Bron, France.
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17
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The nucleolus-like and precursor bodies of mammalian oocytes and embryos and their possible role in post-fertilization centromere remodelling. Biochem Soc Trans 2021; 48:581-593. [PMID: 32318710 DOI: 10.1042/bst20190847] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 12/14/2022]
Abstract
In nearly all somatic cells, the ribosome biosynthesis is a key activity. The same is true also for mammalian oocytes and early embryos. This activity is intimately linked to the most prominent nuclear organelles - the nucleoli. Interestingly, during a short period around fertilization, the nucleoli in oocytes and embryos transform into ribosome-biosynthesis-inactive structures termed nucleolus-like or nucleolus precursor bodies (NPBs). For decades, researchers considered these structures to be passive repositories of nucleolar proteins used by the developing embryo to rebuild fully functional, ribosome-synthesis competent nucleoli when required. Recent evidence, however, indicates that while these structures are unquestionably essential for development, the material is largely dispensable for the formation of active embryonic nucleoli. In this mini-review, we will describe some unique features of oocytes and embryos with respect to ribosome biogenesis and the changes in the structure of oocyte and embryonic nucleoli that reflect this. We will also describe some of the different approaches that can be used to study nucleoli and NPBs in embryos and discuss the different results that might be expected. Finally, we ask whether the main function of nucleolar precursor bodies might lie in the genome organization and remodelling and what the involved components might be.
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18
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Ancelin K, Miyanari Y, Leroy O, Torres-Padilla ME, Heard E. Mapping of Chromosome Territories by 3D-Chromosome Painting During Early Mouse Development. Methods Mol Biol 2021; 2214:175-187. [PMID: 32944910 DOI: 10.1007/978-1-0716-0958-3_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Following fertilization in mammals, the chromatin landscape inherited from the two parental genomes and the nuclear organization are extensively reprogrammed. A tight regulation of nuclear organization is important for developmental success. One main nuclear feature is the organization of the chromosomes in discrete and individual nuclear spaces known as chromosome territories (CTs). In culture cells, their arrangements can be constrained depending on their genomic content (e.g., gene density or repeats) or by specific nuclear constrains such as the periphery or the nucleolus. However, during the early steps of mouse embryonic development, much less is known, specifically regarding how and when the two parental genomes intermingle. Here, we describe a three-dimensional fluorescence in situ hybridization (3D-FISH) for chromosome painting (3D-ChromoPaint) optimized to gain understanding in nuclear organization of specific CTs following fertilization. Our approach preserves the nuclear structure, and the acquired images allow full spatial analysis of interphase chromosome positioning and morphology across the cell cycle and during early development. This method will be useful in understanding the dynamics of chromosome repositioning during development as well as the alteration of chromosome territories upon changes in transcriptional status during key developmental steps. This protocol can be adapted to any other species or organoids in culture.
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Affiliation(s)
- Katia Ancelin
- Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris, France.
| | - Yusuke Miyanari
- Division of Nuclear Dynamics, Exploratory Research Center on Life and Living Systems: ExCELLS National Institute for Basic Biology, Okazaki, Japan
| | - Olivier Leroy
- Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris, France
| | | | - Edith Heard
- Institut Curie, CNRS UMR3215/ INSERM U934, Paris Sciences & Lettres Research University (PSL), Paris, France.,EMBL, Heidelberg, Germany
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19
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Bizhanova A, Kaufman PD. Close to the edge: Heterochromatin at the nucleolar and nuclear peripheries. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2021; 1864:194666. [PMID: 33307247 PMCID: PMC7855492 DOI: 10.1016/j.bbagrm.2020.194666] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 11/11/2020] [Accepted: 11/29/2020] [Indexed: 02/06/2023]
Abstract
Chromatin is a dynamic structure composed of DNA, RNA, and proteins, regulating storage and expression of the genetic material in the nucleus. Heterochromatin plays a crucial role in driving the three-dimensional arrangement of the interphase genome, and in preserving genome stability by maintaining a subset of the genome in a silent state. Spatial genome organization contributes to normal patterns of gene function and expression, and is therefore of broad interest. Mammalian heterochromatin, the focus of this review, mainly localizes at the nuclear periphery, forming Lamina-associated domains (LADs), and at the nucleolar periphery, forming Nucleolus-associated domains (NADs). Together, these regions comprise approximately one-half of mammalian genomes, and most but not all loci within these domains are stochastically placed at either of these two locations after exit from mitosis at each cell cycle. Excitement about the role of these heterochromatic domains in early development has recently been heightened by the discovery that LADs appear at some loci in the preimplantation mouse embryo prior to other chromosomal features like compartmental identity and topologically-associated domains (TADs). While LADs have been extensively studied and mapped during cellular differentiation and early embryonic development, NADs have been less thoroughly studied. Here, we summarize pioneering studies of NADs and LADs, more recent advances in our understanding of cis/trans-acting factors that mediate these localizations, and discuss the functional significance of these associations.
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Affiliation(s)
- Aizhan Bizhanova
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Paul D Kaufman
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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20
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Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation. Nat Commun 2020; 11:4654. [PMID: 32943640 PMCID: PMC7498599 DOI: 10.1038/s41467-020-18508-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 08/24/2020] [Indexed: 11/08/2022] Open
Abstract
The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to totipotent blastomeres, but the identity of transcription factors (TF) and genomic elements regulating embryonic genome activation (EGA) are poorly defined. The timing of EGA is species-specific, e.g., the timing of murine and human EGA differ significantly. To deepen our understanding of mammalian EGA, here we profile changes in open chromatin during bovine preimplantation development. Before EGA, open chromatin is enriched for maternal TF binding, similar to that observed in humans and mice. During EGA, homeobox factor binding becomes more prevalent and requires embryonic transcription. A cross-species comparison of open chromatin during preimplantation development reveals strong similarity in the regulatory circuitry underlying bovine and human EGA compared to mouse. Moreover, TFs associated with murine EGA are not enriched in cattle or humans, indicating that cattle may be a more informative model for human preimplantation development than mice. Preimplantation embryos undergo extensive transcriptomic and epigenomic remodeling. Here the authors assay open chromatin in bovine oocytes, embryos, and embryonic stem cells, and compare the transcriptomes and epigenomes of cattle, human and mouse embryos, revealing species-specific regulation of genome activation.
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21
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Bogolyubova I, Bogolyubov D. Heterochromatin Morphodynamics in Late Oogenesis and Early Embryogenesis of Mammals. Cells 2020; 9:cells9061497. [PMID: 32575486 PMCID: PMC7348780 DOI: 10.3390/cells9061497] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/15/2022] Open
Abstract
During the period of oocyte growth, chromatin undergoes global rearrangements at both morphological and molecular levels. An intriguing feature of oogenesis in some mammalian species is the formation of a heterochromatin ring-shaped structure, called the karyosphere or surrounded "nucleolus", which is associated with the periphery of the nucleolus-like bodies (NLBs). Morphologically similar heterochromatin structures also form around the nucleolus-precursor bodies (NPBs) in zygotes and persist for several first cleavage divisions in blastomeres. Despite recent progress in our understanding the regulation of gene silencing/expression during early mammalian development, as well as the molecular mechanisms that underlie chromatin condensation and heterochromatin structure, the biological significance of the karyosphere and its counterparts in early embryos is still elusive. We pay attention to both the changes of heterochromatin morphology and to the molecular mechanisms that can affect the configuration and functional activity of chromatin. We briefly discuss how DNA methylation, post-translational histone modifications, alternative histone variants, and some chromatin-associated non-histone proteins may be involved in the formation of peculiar heterochromatin structures intimately associated with NLBs and NPBs, the unique nuclear bodies of oocytes and early embryos.
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22
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White MD, Plachta N. Specification of the First Mammalian Cell Lineages In Vivo and In Vitro. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a035634. [PMID: 31615786 DOI: 10.1101/cshperspect.a035634] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Our understanding of how the first mammalian cell lineages arise has been shaped largely by studies of the preimplantation mouse embryo. Painstaking work over many decades has begun to reveal how a single totipotent cell is transformed into a multilayered structure representing the foundations of the body plan. Here, we review how the first lineage decision is initiated by epigenetic regulation but consolidated by the integration of morphological features and transcription factor activity. The establishment of pluripotent and multipotent stem cell lines has enabled deeper analysis of molecular and epigenetic regulation of cell fate decisions. The capability to assemble these stem cells into artificial embryos is an exciting new avenue of research that offers a long-awaited window into cell fate specification in the human embryo. Together, these approaches are poised to profoundly increase our understanding of how the first lineage decisions are made during mammalian embryonic development.
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Affiliation(s)
- Melanie D White
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673
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23
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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] [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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Fulka H, Ogura A, Loi P, Fulka Jr J. Dissecting the role of the germinal vesicle nuclear envelope and soluble content in the process of somatic cell remodelling and reprogramming. J Reprod Dev 2019; 65:433-441. [PMID: 31423000 PMCID: PMC6815741 DOI: 10.1262/jrd.2019-017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Differentiated nuclei can be reprogrammed/remodelled to totipotency after their transfer to enucleated metaphase II (MII) oocytes. The process of reprogramming/remodelling is, however, only
partially characterized. It has been shown that the oocyte nucleus (germinal vesicle – GV) components are essential for a successful remodelling of the transferred nucleus by providing the
materials for pseudo-nucleus formation. However, the nucleus is a complex structure and exactly what nuclear components are required for a successful nucleus remodelling and reprogramming is
unknown. Till date, the only nuclear sub-structure experimentally demonstrated to be essential is the oocyte nucleolus (nucleolus-like body, NLB). In this study, we investigated what other
GV components might be necessary for the formation of normal-sized pseudo-pronuclei (PNs). Our results showed that the removal of the GV nuclear envelope with attached chromatin and
chromatin-bound factors does not substantially influence the size of the remodelled nuclei in reconstructed cells and that their nuclear envelopes seem to have normal parameters. Rather than
the insoluble nuclear lamina, the GV content, which is dissolved in the cytoplasm with the onset of oocyte maturation, influences the characteristics and size of transferred nuclei.
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Affiliation(s)
- Helena Fulka
- Institute of Molecular Genetics of the ASCR, 142 20 Prague, Czech Republic.,Institute of Experimental Medicine, 142 20 Prague, Czech Republic
| | - Atsuo Ogura
- RIKEN BioResource Center, Ibaraki 305-0074, Japan
| | - Pasqualino Loi
- Faculty of Veterinary Medicine, University of Teramo, Teramo 64100, Italy
| | - Josef Fulka Jr
- Institute of Animal Science, 140 00 Prague, Czech Republic
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25
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The Impact of Centromeres on Spatial Genome Architecture. Trends Genet 2019; 35:565-578. [PMID: 31200946 DOI: 10.1016/j.tig.2019.05.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 05/06/2019] [Accepted: 05/09/2019] [Indexed: 01/01/2023]
Abstract
The development of new technologies and experimental techniques is enabling researchers to see what was once unable to be seen. For example, the centromere was first seen as the mediator between spindle fiber and chromosome during mitosis and meiosis. Although this continues to be its most prominent role, we now know that the centromere functions beyond cellular division with important roles in genome organization and chromatin regulation. Here we aim to share the structures and functions of centromeres in various organisms beginning with the diversity of their DNA sequence anatomies. We zoom out to describe their position in the nucleus and ultimately detail the different ways they contribute to genome organization and regulation at the spatial level.
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26
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Yandım C, Karakülah G. Expression dynamics of repetitive DNA in early human embryonic development. BMC Genomics 2019; 20:439. [PMID: 31151386 PMCID: PMC6545021 DOI: 10.1186/s12864-019-5803-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 05/15/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The last decade witnessed a number of genome-wide studies on human pre-implantation, which mostly focused on genes and provided only limited information on repeats, excluding the satellites. Considering the fact that repeats constitute a large portion of our genome with reported links to human physiology and disease, a thorough understanding of their spatiotemporal regulation during human embryogenesis will give invaluable clues on chromatin dynamics across time and space. Therefore, we performed a detailed expression analysis of all repetitive DNA elements including the satellites across stages of human pre-implantation and embryonic stem cells. RESULTS We uncovered stage-specific expressions of more than a thousand repeat elements whose expressions fluctuated with a mild global decrease at the blastocyst stage. Most satellites were highly expressed at the 4-cell level and expressions of ACRO1 and D20S16 specifically peaked at this point. Whereas all members of the SVA elements were highly upregulated at 8-cell and morula stages, other transposons and small RNA repeats exhibited a high level of variation among their specific subtypes. Our repeat enrichment analysis in gene promoters coupled with expression correlations highlighted potential links between repeat expressions and nearby genes, emphasising mostly 8-cell and morula specific genes together with SVA_D, LTR5_Hs and LTR70 transposons. The DNA methylation analysis further complemented the understanding on the mechanistic aspects of the repeatome's regulation per se and revealed critical stages where DNA methylation levels are negatively correlating with repeat expression. CONCLUSIONS Taken together, our study shows that specific expression patterns are not exclusive to genes and long non-coding RNAs but the repeatome also exhibits an intriguingly dynamic pattern at the global scale. Repeats identified in this study; particularly satellites, which were historically associated with heterochromatin, and those with potential links to nearby gene expression provide valuable insights into the understanding of key events in genomic regulation and warrant further research in epigenetics, genomics and developmental biology.
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Affiliation(s)
- Cihangir Yandım
- İzmir Biomedicine and Genome Center (IBG), 35340, İnciraltı, İzmir, Turkey.,Department of Genetics and Bioengineering, İzmir University of Economics, Faculty of Engineering, 35330, Balçova, İzmir, Turkey.,Department of Medicine, Division of Brain Sciences, Hammersmith Hospital, Imperial College London, Faculty of Medicine, W12 0NN, London, UK
| | - Gökhan Karakülah
- İzmir Biomedicine and Genome Center (IBG), 35340, İnciraltı, İzmir, Turkey. .,İzmir International Biomedicine and Genome Institute (iBG-İzmir), Dokuz Eylül University, 35340, İnciraltı, İzmir, Turkey.
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Genome activation and architecture in the early mammalian embryo. Curr Opin Genet Dev 2019; 55:52-58. [DOI: 10.1016/j.gde.2019.04.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/11/2019] [Accepted: 04/15/2019] [Indexed: 01/09/2023]
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28
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Bogolyubova IO, Sailau ZK, Bogolyubov DS. Peculiarities of the molecular composition of heterochromatin associated with pronucleoli in mouse embryos. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The nucleus of pre-implantation mammalian embryos is characterized by peculiar structural organization. At the initial stages of cleavage, the nucleus of the embryo contains the so-called nucleolus precursor bodies (NPBs) or pronucleoli rather than functionally active nucleoli. The NPBs are fibrillar electron-dense structures inactive in RNA synthesis. The vast majority of NPBs are surrounded by a ring-shaped zone of transcriptionally inactive heterochromatin. Intriguingly, these zones contain not only tri-methylated histone Н3K9me3 as an epigenetic mark of repressed chromatin but also acetylated histone H4K5ac, a well-known marker of active chromatin. Immunocytochemical data suggest that the molecular composition of this ‘ring heterochromatin’ in mouse embryos changes during the realization of embryonic genome activation events, as well as during artificial suppression of transcription. In zygotes, some factors of mRNA biogenesis including splicing factor SC35 (SRSF2) and basal transcription factor TFIID are detectable in the ring chromatin. At later stages of development, other nuclear proteins such as Y14, a core component of the exon-exon junction complex (EJC), as well as the proteins involved in chromatin remodeling (ATRX, Daxx) are also detectable in this area. A typical component of the ‘ring heterochromatin’ is actin. Anti-actin immunocytochemical labeling is most expressed at the two-cell cleavage stage after activation of the embryonic genome. Indicatively, the molecular composition of the ‘ring heterochromatin’ associated with different NPBs may differ significantly even in the same nucleus. This seems to reflect the functional heterogeneity of morphologically similar NPBs according to their competence to the process of nucleologenesis. Here, we discuss briefly some peculiarities of the molecular composition and possible functions of the NPB-associated heterochromatin in mouse early embryos.
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Ho NTK, Nguyen TVT, Nguyen TV, Bui HT. Epigenetic impairments in development of parthenogenetic preimplantation mouse embryos. J Reprod Dev 2018; 65:83-90. [PMID: 30606958 PMCID: PMC6379762 DOI: 10.1262/jrd.2018-028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Parthenogenesis is an activation process of oocytes that occur without the participation of sperm. Evidence suggests that normal development of embryos requires proper expression of several
imprinted genes inherited from both the paternal and maternal genomes. Compared to gene expression, histone modifications and chromatin remodeling are not well-documented. In this research,
by using immunofluorescence staining for several developmental-associated histone modifications, we investigated whether epigenetic impairments in parthenogenetic embryos act as constraints
for proper development. At early stages, fertilized embryos exhibited high methylation of histone H3 at lysine 9 (Me-H3-K9) and Heterochromatin Protein 1 (HP1) present in the maternal
chromatin, while paternal chromatin showed weaker HP1 signals. We found that at the two-cell stage in fertilized embryos, HP1, initially detected around the nucleolus, colocalized with
chromocenters at one pole of the blastomere, while parthenotes showed a diffused distribution pattern of HP1 throughout the entire nucleoplasm. At the four-cell stage, methylation of histone
H3 at arginine 26 (Me-H3-R26) increased at nascent RNA repression sites in fertilized embryos, while parthenotes recorded weaker signals throughout the nucleoplasm, suggesting differences in
pluripotency of the ICM cells between the two types of embryos. Moreover, at the blastocyst stage, we observed that the acetylation level of histone H4 at lysine 12 (Ac-H4-K12) was
significantly decreased in parthenogenetic ICM compared to that in its fertilized counterpart. To summarize, differences in epigenetic modifications correlating with paternal chromatin’s
capacity to regulate nascent RNA repression may contribute to aberrant development and lineage allocation in mouse parthenogenetic embryos.
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Affiliation(s)
- Ngan Thi Kim Ho
- Cellular Reprogramming Laboratory, School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Thuy Van Thi Nguyen
- Cellular Reprogramming Laboratory, School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Thuan Van Nguyen
- Cellular Reprogramming Laboratory, School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
| | - Hong-Thuy Bui
- Cellular Reprogramming Laboratory, School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City 700000, Vietnam
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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] [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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31
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Ioannou D, Tempest HG. Does genome organization matter in spermatozoa? A refined hypothesis to awaken the silent vessel. Syst Biol Reprod Med 2018; 64:518-534. [DOI: 10.1080/19396368.2017.1421278] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- IVF Florida Reproductive Associates, Margate, FL, USA
| | - Helen G. Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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Abstract
It is well known that nucleoli of fully grown mammalian oocytes are indispensable for embryonic development. Therefore, the embryos originated from previously enucleolated (ENL) oocytes undergo only one or two cleavages and then their development ceases. In our study the interspecies (mouse/pig) nucleolus transferred embryos (NuTE) were produced and their embryonic development was analyzed by autoradiography, transmission electron microscopy (TEM) and immunofluorescence (C23 and upstream binding factor (UBF)). Our results show that the re-injection of isolated oocyte nucleoli, either from the pig (P + P) or mouse (P + M), into previously enucleolated and subsequently matured porcine oocytes rescues their development after parthenogenetic activation and some of these develop up to the blastocyst stage (P + P, 11.8%; P + M, 13.5%). In nucleolus re-injected 8-cell and blastocyst stage embryos the number of nucleoli labeled with C23 in P + P and P + M groups was lower than in control (non-manipulated) group. UBF was localized in small foci within the nucleoli of blastocysts in control and P + P embryos, however, in P + M embryos the labeling was evenly distributed in the nucleoplasm. The TEM and autoradiographic evaluations showed the formation of functional nucleoli and de novo rRNA synthesis at the 8-cell stage in both, control and P + P group. In the P + M group the formation of comparable nucleoli was delayed. In conclusion, our results indicate that the mouse nucleolus can rescue embryonic development of enucleolated porcine oocytes, but the localization of selected nucleolar proteins, the timing of transcription activation and the formation of the functional nucleoli in NuTE compared with control group show evident aberrations.
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33
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Chi D, Zeng Y, Xu M, Si L, Qu X, Liu H, Li J. LC3-Dependent Autophagy in Pig 2-Cell Cloned Embryos Could Influence the Degradation of Maternal mRNA and the Regulation of Epigenetic Modification. Cell Reprogram 2017; 19:354-362. [PMID: 29058487 DOI: 10.1089/cell.2017.0016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In this study, the distribution as well as the effect of autophagy on reprogramming in pig cloned embryos were observed immediately after somatic cell nuclear transfer. Results showed that the LC3 was at the highest level in cloned embryos at 2-cell stage, and it decreased with the development from 2-cell stage to blastocyst. Different to cloned embryos, the intensity of LC3 in parthenogenetic activation (PA) embryos was at the highest level at 4-cell stage. A markedly higher level of Bmp15, H1foo, and Dppa3 was shown in cloned embryos at 2-cell stage (p < 0.05 or p < 0.01), but a significantly lower level of LC3, Sox2, and eIF1A was observed at 4-cell stage (p < 0.05), compared with PA embryos. When the efficient interfering by the LC3 siRNA was performed on the cloned embryos (p < 0.01), not only the mRNA level of maternal Cyclin B, Bmp15, Gdf9, c-mos, H1foo, and Dppa3 was increased significantly (p < 0.05), but also the expression of Dnmt1 and Dnmt3b was obviously upregulated (p < 0.05). Although the expression of Sox2 and Oct4 is not changed, the expression of Stat3 decreased significantly (p < 0.05). Furthermore with the treatment of 200 nM rapamycin, the expression of eIF1A and Stat3 was significantly increased at 4-cell stage. In conclusion, the LC3-dependent autophagy mainly occurred in cloned embryos at 2-cell stage, but at 4-cell stage in PA embryos. In addition, the modulation of autophagy could affect genome activation by influencing the degradation of maternal mRNA and regulating the expression of DNA methyltransferase.
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Affiliation(s)
- Daming Chi
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Yaqiong Zeng
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Mingzhu Xu
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Linan Si
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Xiao Qu
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Honglin Liu
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
| | - Juan Li
- College of Animal Science and Technology, Nanjing Agricultural University , Nanjing Weigang No. 1, Jiangsu Province, P.R. China
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34
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Ioannou D, Millan NM, Jordan E, Tempest HG. A new model of sperm nuclear architecture following assessment of the organization of centromeres and telomeres in three-dimensions. Sci Rep 2017; 7:41585. [PMID: 28139771 PMCID: PMC5282497 DOI: 10.1038/srep41585] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 12/21/2016] [Indexed: 01/01/2023] Open
Abstract
The organization of chromosomes in sperm nuclei has been proposed to possess a unique “hairpin-loop” arrangement, which is hypothesized to aid in the ordered exodus of the paternal genome following fertilization. This study simultaneously assessed the 3D and 2D radial and longitudinal organization of telomeres, centromeres, and investigated whether chromosomes formed the same centromere clusters in sperm cells. Reproducible radial and longitudinal non-random organization was observed for all investigated loci using both 3D and 2D approaches in multiple subjects. We report novel findings, with telomeres and centromeres being localized throughout the nucleus but demonstrating roughly a 1:1 distribution in the nuclear periphery and the intermediate regions with <15% occupying the nuclear interior. Telomeres and centromeres were observed to aggregate in sperm nuclei, forming an average of 20 and 7 clusters, respectively. Reproducible
longitudinal organization demonstrated preferential localization of telomeres and centromeres in the mid region of the sperm cell. Preliminary evidence is also provided to support the hypothesis that specific chromosomes preferentially form the same centromere clusters. The more segmental distribution of telomeres and centromeres as described in this study could more readily accommodate and facilitate the sequential exodus of paternal chromosomes following fertilization.
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Affiliation(s)
- Dimitrios Ioannou
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Nicole M Millan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Elizabeth Jordan
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Helen G Tempest
- Department of Human and Molecular Genetics, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA.,Biomolecular Sciences Institute, Florida International University, Miami, FL, USA
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35
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Heterochromatin and the molecular mechanisms of ‘parent-of-origin’ effects in animals. J Biosci 2016; 41:759-786. [DOI: 10.1007/s12038-016-9650-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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36
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Borsos M, Torres-Padilla ME. Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes Dev 2016; 30:611-21. [PMID: 26980186 PMCID: PMC4803048 DOI: 10.1101/gad.273805.115] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In mammals, epigenetic reprogramming, the acquisition and loss of totipotency, and the first cell fate decision all occur within a 3-d window after fertilization from the one-cell zygote to the formation of the blastocyst. These processes are poorly understood in molecular detail, yet this is an essential prerequisite to uncover principles of stem cells, chromatin biology, and thus regenerative medicine. A unique feature of preimplantation development is the drastic genome-wide changes occurring to nuclear architecture. From studying somatic and in vitro cultured embryonic stem cells (ESCs) it is becoming increasingly established that the three-dimensional (3D) positions of genomic loci relative to each other and to specific compartments of the nucleus can act on the regulation of gene expression, potentially driving cell fate. However, the functionality, mechanisms, and molecular characteristics of the changes in nuclear organization during preimplantation development are only now beginning to be unraveled. Here, we discuss the peculiarities of nuclear compartments and chromatin organization during mammalian preimplantation development in the context of the transition from totipotency to pluripotency.
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Affiliation(s)
- Máté Borsos
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale F-67404 Illkirch, France; Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München D-81377 München, Germany
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, U964, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale F-67404 Illkirch, France; Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München D-81377 München, Germany
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37
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Sepulveda-Rincon LP, Solanas EDL, Serrano-Revuelta E, Ruddick L, Maalouf WE, Beaujean N. Early epigenetic reprogramming in fertilized, cloned, and parthenogenetic embryos. Theriogenology 2016; 86:91-8. [DOI: 10.1016/j.theriogenology.2016.04.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/25/2016] [Accepted: 03/14/2016] [Indexed: 12/17/2022]
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38
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Lim CY, Knowles BB, Solter D, Messerschmidt DM. Epigenetic Control of Early Mouse Development. Curr Top Dev Biol 2016; 120:311-60. [PMID: 27475856 DOI: 10.1016/bs.ctdb.2016.05.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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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39
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Newhart A, Powers SL, Shastrula PK, Sierra I, Joo LM, Hayden JE, Cohen AR, Janicki SM. RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition. Mol Biol Cell 2016; 27:1154-69. [PMID: 26842893 PMCID: PMC4814222 DOI: 10.1091/mbc.e15-02-0099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 01/28/2016] [Indexed: 11/15/2022] Open
Abstract
RNase P protein subunits Rpp29, POP1, and Rpp21 interact with histone H3.3 upstream of nucleosome deposition, suggesting that a variant of this enzyme regulates H3.3 function. Rpp29 knockdown increases H3.3 chromatin incorporation, suggesting that it represses H3.3 nucleosome deposition, which has important implications for epigenetic regulation. In mammals, histone H3.3 is a critical regulator of transcription state change and heritability at both euchromatin and heterochromatin. The H3.3-specific chaperone, DAXX, together with the chromatin-remodeling factor, ATRX, regulates H3.3 deposition and transcriptional silencing at repetitive DNA, including pericentromeres and telomeres. However, the events that precede H3.3 nucleosome incorporation have not been fully elucidated. We previously showed that the DAXX-ATRX-H3.3 pathway regulates a multi-copy array of an inducible transgene that can be visualized in single living cells. When this pathway is impaired, the array can be robustly activated. H3.3 is strongly recruited to the site during activation where it accumulates in a complex with transcribed sense and antisense RNA, which is distinct from the DNA/chromatin. This suggests that transcriptional events regulate H3.3 recruited to its incorporation sites. Here we report that the nucleolar RNA proteins Rpp29, fibrillarin, and RPL23a are also components of this H3.3/RNA complex. Rpp29 is a protein subunit of RNase P. Of the other subunits, POP1 and Rpp21 are similarly recruited suggesting that a variant of RNase P regulates H3.3 chromatin assembly. Rpp29 knockdown increases H3.3 chromatin incorporation, which suggests that Rpp29 represses H3.3 nucleosome deposition, a finding with implications for epigenetic regulation.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Sara Lawrence Powers
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Prashanth Krishna Shastrula
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104 Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | - Isabel Sierra
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Lucy M Joo
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - James E Hayden
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Andrew R Cohen
- Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA 19104
| | - Susan M Janicki
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
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40
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Politz JCR, Scalzo D, Groudine M. The redundancy of the mammalian heterochromatic compartment. Curr Opin Genet Dev 2015; 37:1-8. [PMID: 26706451 DOI: 10.1016/j.gde.2015.10.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 01/05/2023]
Abstract
Two chromatin compartments are present in most mammalian cells; the first contains primarily euchromatic, early replicating chromatin and the second, primarily late-replicating heterochromatin, which is the subject of this review. Heterochromatin is concentrated in three intranuclear regions: the nuclear periphery, the perinucleolar space and in pericentromeric bodies. We review recent evidence demonstrating that the heterochromatic compartment is critically involved in global nuclear organization and the maintenance of genome stability, and discuss models regarding how this compartment is formed and maintained. We also evaluate our understanding of how heterochromatic sequences (herein named heterochromatic associated regions (HADs)) might be tethered within these regions and review experiments that reveal the stochastic nature of individual HAD positioning within the compartment. These investigations suggest a substantial level of functional redundancy within the heterochromatic compartment.
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Affiliation(s)
| | - David Scalzo
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Mark Groudine
- Fred Hutchinson Cancer Research Center, Seattle, WA, United States.
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41
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Hogg K, Western PS. Refurbishing the germline epigenome: Out with the old, in with the new. Semin Cell Dev Biol 2015; 45:104-13. [PMID: 26597001 DOI: 10.1016/j.semcdb.2015.09.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 09/21/2015] [Indexed: 12/25/2022]
Abstract
Mammalian germline reprogramming involves the erasure and re-establishment of epigenetic information critical for germ cell function and inheritance in offspring. The bi-faceted nature of such reprogramming ensures germline repression of somatic programmes and the establishment of a carefully constructed epigenome essential for fertilisation and embryonic development in the next generation. While the majority of the germline epigenome is erased in preparation for embryonic development, certain genomic sequences remain resistant to this and may represent routes for transmission of epigenetic changes through the germline. Epigenetic reprogramming is regulated by highly conserved epigenetic modifiers, which function to establish, maintain and remove DNA methylation and chromatin modifications. In this review, we discuss recent findings from a considerable body of work illustrating the critical requirement of epigenetic modifiers that influence the epigenetic signature present in mature gametes, and have the potential to affect developmental outcomes in the offspring. We also briefly discuss the similarities of these mechanisms in the human germline and consider the potential for inheritance of epigenetically induced germline genetic errors that could impact on offspring phenotypes.
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Affiliation(s)
- Kirsten Hogg
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC 3168, Australia; Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia
| | - Patrick S Western
- Centre for Genetic Diseases, Hudson Institute of Medical Research, 27-31 Wright Street, Melbourne, VIC 3168, Australia; Department of Molecular and Translational Science, Monash University, Melbourne, VIC 3168, Australia.
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Abstract
In mammals, pluripotent stem cells can give rise to every cell type of embryonic lineage, and hold great potential in regenerative medicine and disease modeling. Guided by the mechanism underlying pluripotency, pluripotent stem cells have been successfully induced through manipulating the transcriptional and epigenetic networks of various differentiated cell types. However, the factors that confer totipotency, the ability to give rise to cells in both embryonic and extra-embryonic lineages, still remain poorly understood. It is currently unknown whether totipotency can be induced and maintained in vitro. In this review, we summarize the current progress in the field, with the aim of providing a foundation for understanding the mechanisms that regulate totipotency.
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Affiliation(s)
- Falong Lu
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115 ; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115 ; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115
| | - Yi Zhang
- Howard Hughes Medical Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115 ; Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115 ; Department of Genetics, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115 ; Harvard Stem Cell Institute, Harvard Medical School, WAB-149G, 200 Longwood Avenue, Boston, MA 02115
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Østrup O, Pedersen HS, Holm HM, Hyttel P. Analysis of nucleolar morphology and protein localization as an indicator of nuclear reprogramming. Methods Mol Biol 2015; 1222:161-174. [PMID: 25287345 DOI: 10.1007/978-1-4939-1594-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
When a cell is reprogrammed to a new phenotype, the nucleolus undergoes more or less dramatic modulations, which can be used as a marker for the occurrence of the reprogramming. This phenomenon is most pronounced when differentiated cells are reprogrammed to totipotency when they are submitted to cloning by somatic cell nuclear transfer. However, when cells are reprogrammed by less fundamental means, as for example treatment by Xenopus extract or expression of pluripotency genes, more subtle nucleolar modulations can also be noted. The monitoring and understanding of the reprogramming-related nucleolar modulations are based upon detailed knowledge about the nucleolar changes that occur during normal development from the developing oocyte over oocyte maturation and fertilization to the activation of the embryonic genome in the early embryo. Below, the ultrastructural and molecular modulations of the nucleolus are summarized in this developmental context, but also as they occur in assisted reproductive technologies such as in vitro fertilization and somatic cell nuclear transfer. Moreover, detailed protocols for monitoring the nucleolar changes by transmission electron microscopy and immunocytochemistry are presented.
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Affiliation(s)
- Olga Østrup
- Department of Tumor Biology, Oslo University Hospital RH, Oslo, Norway,
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44
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Beaujean N. Epigenetics, embryo quality and developmental potential. Reprod Fertil Dev 2015; 27:53-62. [DOI: 10.1071/rd14309] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
It is very important for embryologists to understand how parental inherited genomes are reprogrammed after fertilisation in order to obtain good-quality embryos that will sustain further development. In mammals, it is now well established that important epigenetic modifications occur after fertilisation. Although gametes carry special epigenetic signatures, they should attain embryo-specific signatures, some of which are crucial for the production of healthy embryos. Indeed, it appears that proper establishment of different epigenetic modifications and subsequent scaffolding of the chromatin are crucial steps during the first cleavages. This ‘reprogramming’ is promoted by the intimate contact between the parental inherited genomes and the oocyte cytoplasm after fusion of the gametes. This review introduces two main epigenetic players, namely histone post-translational modifications and DNA methylation, and highlights their importance during early embryonic development.
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45
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Çelik S. Understanding the complexity of antigen retrieval of DNA methylation for immunofluorescence-based measurement and an approach to challenge. J Immunol Methods 2014; 416:1-16. [PMID: 25435341 DOI: 10.1016/j.jim.2014.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Revised: 10/31/2014] [Accepted: 11/21/2014] [Indexed: 12/28/2022]
Abstract
Cytosine methylation (5-methylcytosine, 5meC) in the CpG-rich regions of the mammalian genome is an important epigenetic mechanism playing roles in transcription regulation and genomic stability. The abnormalities in DNA methylation can occur in various types of cancer and some genetic diseases. The measurement of DNA methylation is therefore important and there is a range of methodologies used to detect DNA methylation. Many methods based on bisulfite treatment appeared with a lack of specificity after recent discoveries of various modifications of methylated cytosine, however there are new treatments developed to overcome this limitation. Immunofluorescence is currently known to be able to specifically detect DNA methylation as it uses different antibodies against 5meC and its derivatives, but it is a semi-quantitative method. Immunofluorescence protocols commonly include fixation of cells followed by permeabilisation, antigen retrieval, and treatments with antibodies. Establishing the strategy for antigen retrieval of immunofluorescence is important to unmask epitopes (i.e. 5meC) from other proteins, and therefore to access the antigen of interest. There are many approaches used for antigen retrieval induced by acid, enzyme and/or heat. The selection of antigen retrieval method can depend on a variety of such antigen-based or cell-based conditions, since the dynamic structure of DNA and chromatin accounts for the complexity of involved proteins to mask the epitope. This review aims to specifically focus on the complexity of in situ detection of DNA methylation by immunofluorescence-based methods using antigen retrieval with the current understanding of DNA methylation mechanism, and suggests conditions for antigenic retrieval of 5meC epitope.
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Affiliation(s)
- Selcen Çelik
- Human Reproduction and Development Unit, Kolling Institute for Medical Research, Sydney Medical School, University of Sydney, Sydney 2065, Australia.
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46
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Meglicki M, Teperek-Tkacz M, Borsuk E. Appearance and heterochromatin localization of HP1α in early mouse embryos depends on cytoplasmic clock and H3S10 phosphorylation. Cell Cycle 2014; 11:2189-205. [DOI: 10.4161/cc.20705] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Burton A, Torres-Padilla ME. Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis. Nat Rev Mol Cell Biol 2014; 15:723-34. [PMID: 25303116 DOI: 10.1038/nrm3885] [Citation(s) in RCA: 161] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Following fertilization, gametes undergo epigenetic reprogramming in order to revert to a totipotent state. How embryonic cells subsequently acquire their fate and the role of chromatin dynamics in this process are unknown. Genetic and experimental embryology approaches have identified some of the players and morphological changes that are involved in early mammalian development, but the exact events underlying cell fate allocation in single embryonic cells have remained elusive. Experimental and technological advances have recently provided novel insights into chromatin dynamics and nuclear architecture in single cells; these insights have reshaped our understanding of the mechanisms underlying cell fate allocation and plasticity in early mammalian development.
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Affiliation(s)
- Adam Burton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, F-67404 ILLKIRCH, Cité Universitaire de Strasbourg, France
| | - Maria-Elena Torres-Padilla
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, F-67404 ILLKIRCH, Cité Universitaire de Strasbourg, France
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Kim SY, Kim TS, Park SH, Lee MR, Eun HJ, Baek SK, Ko YG, Kim SW, Seong HH, Campbell KHS, Lee JH. Siberian Sturgeon Oocyte Extract Induces Epigenetic Modifications of Porcine Somatic Cells and Improves Developmental Competence of SCNT Embryos. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2014; 27:266-77. [PMID: 25049951 PMCID: PMC4093206 DOI: 10.5713/ajas.2013.13699] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Revised: 11/29/2013] [Accepted: 11/25/2013] [Indexed: 11/27/2022]
Abstract
Somatic cell nuclear transfer (SCNT) has generally demonstrated that a differentiated cell can convert into a undifferentiated or pluripotent state. In the SCNT experiment, nuclear reprogramming is induced by exposure of introduced donor nuclei to the recipient cytoplasm of matured oocytes. However, because the efficiency of SCNT still remains low, a combination of SCNT technique with the ex-ovo method may improve the normal development of SCNT embryos. Here we hypothesized that treatment of somatic cells with extracts prepared from the germinal vesicle (GV) stage Siberian sturgeon oocytes prior to their use as nuclear donor for SCNT would improve in vitro development. A reversible permeability protocol with 4 μg/mL of digitonin for 2 min at 4°C in order to deliver Siberian sturgeon oocyte extract (SOE) to porcine fetal fibroblasts (PFFs) was carried out. As results, the intensity of H3K9ac staining in PFFs following treatment of SOE for 7 h at 18°C was significantly increased but the intensity of H3K9me3 staining in PFFs was significantly decreased as compared with the control (p<0.05). Additionally, the level of histone acetylation in SCNT embryos at the zygote stage was significantly increased when reconstructed using SOE-treated cells (p<0.05), similar to that of IVF embryos at the zygote stage. The number of apoptotic cells was significantly decreased and pluripotency markers (Nanog, Oct4 and Sox2) were highly expressed in the blastocyst stage of SCNT embryos reconstructed using SOE-treated cells as nuclear donor (p<0.05). And there was observed a better development to the blastocyst stage in the SOE-treated group (p<0.05). Our results suggested that pre-treatment of cells with SOE could improve epigenetic reprogramming and the quality of porcine SCNT embryos.
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Affiliation(s)
- So-Young Kim
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Tae-Suk Kim
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Sang-Hoon Park
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Mi-Ran Lee
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hye-Ju Eun
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Sang-Ki Baek
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Yeoung-Gyu Ko
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Sung-Woo Kim
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Hwan-Hoo Seong
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Keith H S Campbell
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
| | - Joon-Hee Lee
- Department of Animal Bioscience, College of Agriculture and Life Sciences, Gyeongsang National University, Jinju, 660-701, Korea
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Time-lapse dynamics of the mouse oocyte chromatin organisation during meiotic resumption. BIOMED RESEARCH INTERNATIONAL 2014; 2014:207357. [PMID: 24864231 PMCID: PMC4016838 DOI: 10.1155/2014/207357] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 02/25/2014] [Indexed: 12/20/2022]
Abstract
In the mammalian oocyte, distinct patterns of centromeres and pericentromeric heterochromatin localisation correlate with the gamete's developmental competence. Mouse antral oocytes display two main types of chromatin organisation: SN oocytes, with a ring of Hoechst-positive chromatin surrounding the nucleolus, and NSN oocytes lacking this ring. When matured to MII and fertilised, only SN oocytes develop beyond the 2-cell, and reach full term. To give detailed information on the dynamics of the SN or NSN chromatin during meiosis resumption, we performed a 9 hr time-lapse observation. The main significant differences recorded are: (1) reduction of the nuclear area only in SN oocytes; (2) ~17 min delay of GVBD in NSN oocytes; (3) chromatin condensation, after GVBD, in SN oocytes; (4) formation of 4-5 CHCs in SN oocytes; (5) increase of the perivitelline space, ~57 min later in NSN oocytes; (6) formation of a rosette-like disposition of CHCs, ~84 min later in SN oocytes; (7) appearance of the MI plate ~40 min later in NSN oocytes. Overall, we described a pathway of transition from the GV to the MII stage that is punctuated of discrete recordable events showing their specificity and occurring with different time kinetics in the two types of oocytes.
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50
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Jachowicz JW, Santenard A, Bender A, Muller J, Torres-Padilla ME. Heterochromatin establishment at pericentromeres depends on nuclear position. Genes Dev 2014; 27:2427-32. [PMID: 24240232 PMCID: PMC3841731 DOI: 10.1101/gad.224550.113] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Mammalian development begins with fertilization followed by genome-wide epigenetic reprogramming involving de novo formation of pericentromeric heterochromatin. Here, Jachowicz et al. dissect the spatiotemporal kinetics of the first acquisition of heterochromatic signatures. Physically tethering pericentromeric chromatin to the nuclear periphery results in defective silencing and impaired development. This study demonstrates that correct nuclear organization in the early embryo is essential for chromatin reprogramming and developmental progression. Mammalian development begins with fertilization of an oocyte by the sperm followed by genome-wide epigenetic reprogramming. This involves de novo establishment of chromatin domains, including the formation of pericentric heterochromatin. We dissected the spatiotemporal kinetics of the first acquisition of heterochromatic signatures of pericentromeric chromatin and found that the heterochromatic marks follow a temporal order that depends on a specific nuclear localization. We addressed whether nuclear localization of pericentric chromatin is required for silencing by tethering it to the nuclear periphery and show that this results in defective silencing and impaired development. Our results indicate that reprogramming of pericentromeric heterochromatin is functionally linked to its nuclear localization.
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Affiliation(s)
- Joanna W Jachowicz
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, F-67404 Illkirch, France
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