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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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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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Baicalin hydrate inhibits cancer progression in nasopharyngeal carcinoma by affecting genome instability and splicing. Oncotarget 2017; 9:901-914. [PMID: 29416665 PMCID: PMC5787522 DOI: 10.18632/oncotarget.22868] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023] Open
Abstract
Baicalin hydrate (BH), a natural compound, has been investigated for many years because of its traditional medicinal properties. However, the anti-tumor activities of BH and its epigenetic role in NPC have not been elucidated. In this study, we identified that BH inhibits NPC cell growth in vivo and in vitro by inducing apoptosis and cell cycle arrest. BH epigenetically regulated genome instability by up-regulating the expression of satellite 2 (Sat2), alpha satellite (α-Sat), and major satellite (Major-Sat). BH also increased the level of IKKα, Suv39H1, and H3K9me3 and decreased LSH expression. Interestingly, BH promoted the splicing of Suv39H1 via the enhancement of m6A RNA methylation, rather than DNA methylation. Taken together, our results demonstrated that BH has an anti-tumor role in NPC and revealed a unique role of BH in genome instability and splicing in response to DNA damage.
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de Castro IJ, Budzak J, Di Giacinto ML, Ligammari L, Gokhan E, Spanos C, Moralli D, Richardson C, de las Heras JI, Salatino S, Schirmer EC, Ullman KS, Bickmore WA, Green C, Rappsilber J, Lamble S, Goldberg MW, Vinciotti V, Vagnarelli P. Repo-Man/PP1 regulates heterochromatin formation in interphase. Nat Commun 2017; 8:14048. [PMID: 28091603 PMCID: PMC5241828 DOI: 10.1038/ncomms14048] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2016] [Accepted: 11/23/2016] [Indexed: 12/28/2022] Open
Abstract
Repo-Man is a protein phosphatase 1 (PP1) targeting subunit that regulates mitotic progression and chromatin remodelling. After mitosis, Repo-Man/PP1 remains associated with chromatin but its function in interphase is not known. Here we show that Repo-Man, via Nup153, is enriched on condensed chromatin at the nuclear periphery and at the edge of the nucleopore basket. Repo-Man/PP1 regulates the formation of heterochromatin, dephosphorylates H3S28 and it is necessary and sufficient for heterochromatin protein 1 binding and H3K27me3 recruitment. Using a novel proteogenomic approach, we show that Repo-Man is enriched at subtelomeric regions together with H2AZ and H3.3 and that depletion of Repo-Man alters the peripheral localization of a subset of these regions and alleviates repression of some polycomb telomeric genes. This study shows a role for a mitotic phosphatase in the regulation of the epigenetic landscape and gene expression in interphase.
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Affiliation(s)
- Inês J. de Castro
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - James Budzak
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Maria L. Di Giacinto
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Lorena Ligammari
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Ezgi Gokhan
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Christos Spanos
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
| | - Daniela Moralli
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Silvia Salatino
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | - Katharine S. Ullman
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Wendy A. Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Catherine Green
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology, Edinburgh EH9 3BF, UK
- Technische Universitat Berlin, 13355 Berlin, Germany
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Martin W. Goldberg
- School of Biological and Medical Science, Durham University, Durham DH1 3LE, UK
| | - Veronica Vinciotti
- College of Engineering, Design and Technology, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
| | - Paola Vagnarelli
- College of Health and Life Science, Research Institute for Environment Health and Society, Brunel University London, London UB8 3PH, UK
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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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Leonard PH, Grzenda A, Mathison A, Morbeck DE, Fredrickson JR, de Assuncao TM, Christensen T, Salisbury J, Calvo E, Iovanna J, Coddington CC, Urrutia R, Lomberk G. The Aurora A-HP1γ pathway regulates gene expression and mitosis in cells from the sperm lineage. BMC DEVELOPMENTAL BIOLOGY 2015; 15:23. [PMID: 26021315 PMCID: PMC4448908 DOI: 10.1186/s12861-015-0073-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 05/12/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND HP1γ, a well-known regulator of gene expression, has been recently identified to be a target of Aurora A, a mitotic kinase which is important for both gametogenesis and embryogenesis. The purpose of this study was to define whether the Aurora A-HP1γ pathway supports cell division of gametes and/or early embryos, using western blot, immunofluorescence, immunohistochemistry, electron microscopy, shRNA-based knockdown, site-directed mutagenesis, and Affymetrix-based genome-wide expression profiles. RESULTS We find that the form of HP1γ phosphorylated by Aurora A, P-Ser83 HP1γ, is a passenger protein, which localizes to the spermatozoa centriole and axoneme. In addition, disruption in this pathway causes centrosomal abnormalities and aberrations in cell division. Expression profiling of male germ cell lines demonstrates that HP1γ phosphorylation is critical for the regulation of mitosis-associated gene expression networks. In female gametes, we observe that P-Ser83-HP1γ is not present in meiotic centrosomes of M2 oocytes, but after syngamy, it becomes detectable during cleavage divisions, coinciding with early embryonic genome activation. CONCLUSIONS These results support the idea that phosphorylation of HP1γ by Aurora A plays a role in the regulation of gene expression and mitotic cell division in cells from the sperm lineage and in early embryos. Combined, this data is relevant to better understanding the function of HP1γ in reproductive biology.
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Affiliation(s)
- Phoebe H Leonard
- Division of Reproductive Endocrinology and Infertility, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Adrienne Grzenda
- Department of Medicine, Mayo Clinic, Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Guggenheim 10, 200 First Street SW, Rochester, MN, 55905, USA. .,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Angela Mathison
- Department of Medicine, Mayo Clinic, Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Guggenheim 10, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Dean E Morbeck
- Division of Reproductive Endocrinology and Infertility, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jolene R Fredrickson
- Division of Reproductive Endocrinology and Infertility, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Thiago M de Assuncao
- Department of Medicine, Mayo Clinic, Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Guggenheim 10, 200 First Street SW, Rochester, MN, 55905, USA.
| | - Trace Christensen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Jeffrey Salisbury
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Ezequiel Calvo
- Molecular Endocrinology and Oncology Research Center, Centre Hospitalier de l'Universite Laval (CHUL) Research Center, Quebec, QC, G1V 4G2, Canada.
| | - Juan Iovanna
- Centre de Recherché en Cancérologie de Marseille (CRCM), Institut National de la Santé et de la Recherche Médicale (INSERM), Unité 624, Stress Cellulaire, 163 Avenue de Luminy, Case 915, Parc Scientifique et Technologique de Luminy, Marseille Cedex 9, 13288, France.
| | - Charles C Coddington
- Division of Reproductive Endocrinology and Infertility, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Raul Urrutia
- Department of Medicine, Mayo Clinic, Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Guggenheim 10, 200 First Street SW, Rochester, MN, 55905, USA. .,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA. .,Translational Epigenomics Program, Center for Individualized Medicine, Rochester, MN, 55905, USA.
| | - Gwen Lomberk
- Department of Medicine, Mayo Clinic, Laboratory of Epigenetics and Chromatin Dynamics, Gastroenterology Research Unit, Guggenheim 10, 200 First Street SW, Rochester, MN, 55905, USA. .,Translational Epigenomics Program, Center for Individualized Medicine, Rochester, MN, 55905, USA. .,Department of Obstetrics and Gynecology, Mayo Clinic, Rochester, MN, 55905, USA.
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Tardat M, Albert M, Kunzmann R, Liu Z, Kaustov L, Thierry R, Duan S, Brykczynska U, Arrowsmith CH, Peters AHFM. Cbx2 targets PRC1 to constitutive heterochromatin in mouse zygotes in a parent-of-origin-dependent manner. Mol Cell 2015; 58:157-71. [PMID: 25801166 DOI: 10.1016/j.molcel.2015.02.013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 12/22/2014] [Accepted: 02/05/2015] [Indexed: 11/17/2022]
Abstract
Polycomb repressive complexes PRC1 and PRC2 regulate expression of genes involved in proliferation and development. In mouse early embryos, however, canonical PRC1 localizes to paternal pericentric heterochromatin (pat-PCH), where it represses transcription of major satellite repeats. In contrast, maternal PCH (mat-PCH) is enriched for H3 lysine 9 tri-methylation (H3K9me3) and Hp1β. How PRC1 is targeted to pat-PCH, yet excluded from mat-PCH, has remained elusive. Here, we identify a PRC1 targeting mechanism that relies on Cbx2 and Hp1β. Cbx2 directs catalytically active PRC1 to PCH via its chromodomain (CD(Cbx2)) and neighboring AT-hook (AT(Cbx2)) binding to H3K27me3 and AT-rich major satellites, respectively. CD(Cbx2) prevents AT(Cbx2) from interacting with DNA at PCH marked by H3K9me3 and Hp1β. Loss-of-function studies show that Hp1β and not H3K9me3 prevents PRC1 targeting to mat-PCH. Our findings indicate that CD(Cbx2) and AT(Cbx2) separated by a short linker function together to integrate H3K9me3/HP1 and H3K27me3 states.
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Affiliation(s)
- Mathieu Tardat
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Mareike Albert
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Rico Kunzmann
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Zichuan Liu
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Lilia Kaustov
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Raphael Thierry
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Shili Duan
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Urszula Brykczynska
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON M5S 1A8, Canada; Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; Faculty of Sciences, University of Basel, 4056 Basel, Switzerland.
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Zhang G, Pradhan S. Mammalian epigenetic mechanisms. IUBMB Life 2014; 66:240-56. [PMID: 24706538 DOI: 10.1002/iub.1264] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/19/2014] [Indexed: 12/31/2022]
Abstract
The mammalian genome is packaged into chromatin that is further compacted into three-dimensional structures consisting of distinct functional domains. The higher order structure of chromatin is in part dictated by enzymatic DNA methylation and histone modifications to establish epigenetic layers controlling gene expression and cellular functions, without altering the underlying DNA sequences. Apart from DNA and histone modifications, non-coding RNAs can also regulate the dynamics of the mammalian gene expression and various physiological functions including cell division, differentiation, and apoptosis. Aberrant epigenetic signatures are associated with abnormal developmental processes and diseases such as cancer. In this review, we will discuss the different layers of epigenetic regulation, including writer enzymes for DNA methylation, histone modifications, non-coding RNA, and chromatin conformation. We will highlight the combinatorial role of these structural and chemical modifications along with their partners in various cellular processes in mammalian cells. We will also address the cis and trans interacting "reader" proteins that recognize these modifications and "eraser" enzymes that remove these marks. Furthermore, an attempt will be made to discuss the interplay between various epigenetic writers, readers, and erasures in the establishment of mammalian epigenetic mechanisms.
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Vogt EJ, Meglicki M, Hartung KI, Borsuk E, Behr R. Importance of the pluripotency factor LIN28 in the mammalian nucleolus during early embryonic development. Development 2013; 139:4514-23. [PMID: 23172912 PMCID: PMC3912245 DOI: 10.1242/dev.083279] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The maternal nucleolus is required for proper activation of the embryonic genome (EGA) and early embryonic development. Nucleologenesis is characterized by the transformation of a nucleolar precursor body (NPB) to a mature nucleolus during preimplantation development. However, the function of NPBs and the involved molecular factors are unknown. We uncover a novel role for the pluripotency factor LIN28, the biological significance of which was previously demonstrated in the reprogramming of human somatic cells to induced pluripotent stem (iPS) cells. Here, we show that LIN28 accumulates at the NPB and the mature nucleolus in mouse preimplantation embryos and embryonic stem cells (ESCs), where it colocalizes with the nucleolar marker B23 (nucleophosmin 1). LIN28 has nucleolar localization in non-human primate (NHP) preimplantation embryos, but is cytoplasmic in NHP ESCs. Lin28 transcripts show a striking decline before mouse EGA, whereas LIN28 protein localizes to NPBs at the time of EGA. Following knockdown with a Lin28 morpholino, the majority of embryos arrest between the 2- and 4-cell stages and never develop to morula or blastocyst. Lin28 morpholino-injected embryos arrested at the 2-cell stage were not enriched with nucleophosmin at presumptive NPB sites, indicating that functional NPBs were not assembled. Based on these results, we propose that LIN28 is an essential factor of nucleologenesis during early embryonic development.
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Affiliation(s)
- Edgar J Vogt
- German Primate Center, Stem Cell Biology Unit, Kellnerweg 4, 37077 Goettingen, Germany.
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