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Chen J, Li Q. Emerging role of HDAC11 in skeletal muscle biology. Front Cell Dev Biol 2024; 12:1368171. [PMID: 38859964 PMCID: PMC11163118 DOI: 10.3389/fcell.2024.1368171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/07/2024] [Indexed: 06/12/2024] Open
Abstract
HDAC11 is an epigenetic repressor of gene transcription, acting through its deacetylase activity to remove functional acetyl groups from the lysine residues of histones at genomic loci. It has been implicated in the regulation of different immune responses, metabolic activities, as well as cell cycle progression. Recent studies have also shed lights on the impact of HDAC11 on myogenic differentiation and muscle development, indicating that HDAC11 is important for histone deacetylation at the promoters to inhibit transcription of cell cycle related genes, thereby permitting myogenic activation at the onset of myoblast differentiation. Interestingly, the upstream networks of HDAC11 target genes are mainly associated with cell cycle regulators and the acetylation of histones at the HDAC11 target promoters appears to be residue specific. As such, selective inhibition, or activation of HDAC11 presents a potential therapeutic approach for targeting distinct epigenetic pathways in clinical applications.
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Affiliation(s)
- Jihong Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Qiao Li
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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Schmidt A, Zhang H, Schmitt S, Rausch C, Popp O, Chen J, Cmarko D, Butter F, Dittmar G, Lermyte F, Cardoso MC. The Proteomic Composition and Organization of Constitutive Heterochromatin in Mouse Tissues. Cells 2024; 13:139. [PMID: 38247831 PMCID: PMC10814525 DOI: 10.3390/cells13020139] [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: 11/01/2023] [Revised: 12/13/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Pericentric heterochromatin (PCH) forms spatio-temporarily distinct compartments and affects chromosome organization and stability. Albeit some of its components are known, an elucidation of its proteome and how it differs between tissues in vivo is lacking. Here, we find that PCH compartments are dynamically organized in a tissue-specific manner, possibly reflecting compositional differences. As the mouse brain and liver exhibit very different PCH architecture, we isolated native PCH fractions from these tissues, analyzed their protein compositions using quantitative mass spectrometry, and compared them to identify common and tissue-specific PCH proteins. In addition to heterochromatin-enriched proteins, the PCH proteome includes RNA/transcription and membrane-related proteins, which showed lower abundance than PCH-enriched proteins. Thus, we applied a cut-off of PCH-unspecific candidates based on their abundance and validated PCH-enriched proteins. Amongst the hits, MeCP2 was classified into brain PCH-enriched proteins, while linker histone H1 was not. We found that H1 and MeCP2 compete to bind to PCH and regulate PCH organization in opposite ways. Altogether, our workflow of unbiased PCH isolation, quantitative mass spectrometry, and validation-based analysis allowed the identification of proteins that are common and tissue-specifically enriched at PCH. Further investigation of selected hits revealed their opposing role in heterochromatin higher-order architecture in vivo.
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Affiliation(s)
- Annika Schmidt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Hui Zhang
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Stephanie Schmitt
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Cathia Rausch
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
| | - Oliver Popp
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Jiaxuan Chen
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Dusan Cmarko
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 00 Prague, Czech Republic
| | - Falk Butter
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany
| | - Gunnar Dittmar
- Proteomics Platform, Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, 13125 Berlin, Germany
| | - Frederik Lermyte
- Clemens-Schöpf Institute of Organic Chemistry and Biochemistry, Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - M. Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany (S.S.)
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Li Q, Mach YZ, Hamed M, Khilji S, Chen J. Regulation of HDAC11 gene expression in early myogenic differentiation. PeerJ 2023; 11:e15961. [PMID: 37663282 PMCID: PMC10474826 DOI: 10.7717/peerj.15961] [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: 05/15/2023] [Accepted: 08/03/2023] [Indexed: 09/05/2023] Open
Abstract
Histone acetylation and deacetylation affect the patterns of gene expression in cellular differentiation, playing pivotal roles in tissue development and maintenance. For example, the intrinsic histone acetyltransferase activity of transcriptional coactivator p300 is especially required for the expression of myogenic regulatory factors including Myf5 and MyoD, and consequently for skeletal myogenesis. On the other hand, histone deacetylases (HDACs) remove the acetyl group from histones, which is critical for gene repression in stem cell fate transition. Through integrative omic analyses, we found that while some HDACs were differentially expressed at the early stage of skeletal myoblast differentiation, Hdac11 gene expression was significantly enhanced by nuclear receptor signaling. In addition, p300 and MyoD control Hdac11 expression in milieu of normal and signal-enhanced myoblast differentiation. Thus, HDAC11 may be essential to differential gene expression at the onset of myoblast differentiation.
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Affiliation(s)
- Qiao Li
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Yan Z. Mach
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Munerah Hamed
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Saadia Khilji
- Department of Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Jihong Chen
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
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Hulen J, Kenny D, Black R, Hallgren J, Hammond KG, Bredahl EC, Wickramasekara RN, Abel PW, Stessman HAF. KMT5B is required for early motor development. Front Genet 2022; 13:901228. [PMID: 36035149 PMCID: PMC9411648 DOI: 10.3389/fgene.2022.901228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Disruptive variants in lysine methyl transferase 5B (KMT5B/SUV4-20H1) have been identified as likely-pathogenic among humans with neurodevelopmental phenotypes including motor deficits (i.e., hypotonia and motor delay). However, the role that this enzyme plays in early motor development is largely unknown. Using a Kmt5b gene trap mouse model, we assessed neuromuscular strength, skeletal muscle weight (i.e., muscle mass), neuromuscular junction (NMJ) structure, and myofiber type, size, and distribution. Tests were performed over developmental time (postnatal days 17 and 44) to represent postnatal versus adult structures in slow- and fast-twitch muscle types. Prior to the onset of puberty, slow-twitch muscle weight was significantly reduced in heterozygous compared to wild-type males but not females. At the young adult stage, we identified decreased neuromuscular strength, decreased skeletal muscle weights (both slow- and fast-twitch), increased NMJ fragmentation (in slow-twitch muscle), and smaller myofibers in both sexes. We conclude that Kmt5b haploinsufficiency results in a skeletal muscle developmental deficit causing reduced muscle mass and body weight.
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Affiliation(s)
- Jason Hulen
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
| | - Dorothy Kenny
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
| | - Rebecca Black
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
| | - Jodi Hallgren
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
| | - Kelley G. Hammond
- Department of Exercise Science, College of Arts and Sciences, Creighton University, Omaha, NE, United States
| | - Eric C. Bredahl
- Department of Exercise Science, College of Arts and Sciences, Creighton University, Omaha, NE, United States
| | - Rochelle N. Wickramasekara
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
- Molecular Diagnostic Laboratory, Boys Town National Research Hospital, Omaha, NE, United States
| | - Peter W. Abel
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
| | - Holly A. F. Stessman
- Department of Pharmacology and Neuroscience, School of Medicine, Creighton University, Omaha, NE, United States
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SETDB1-like MET-2 promotes transcriptional silencing and development independently of its H3K9me-associated catalytic activity. Nat Struct Mol Biol 2022; 29:85-96. [PMID: 35102319 PMCID: PMC8850192 DOI: 10.1038/s41594-021-00712-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 12/02/2021] [Indexed: 12/30/2022]
Abstract
Transcriptionally silenced heterochromatin bearing methylation of histone H3 on lysine 9 (H3K9me) is critical for maintaining organismal viability and tissue integrity. Here we show that in addition to ensuring H3K9me, MET-2, the Caenorhabditis elegans homolog of the SETDB1 histone methyltransferase, has a noncatalytic function that contributes to gene repression. Subnuclear foci of MET-2 coincide with H3K9me deposition, yet these foci also form when MET-2 is catalytically deficient and H3K9me is compromised. Whereas met-2 deletion triggers a loss of silencing and increased histone acetylation, foci of catalytically deficient MET-2 maintain silencing of a subset of genes, blocking acetylation on H3K9 and H3K27. In normal development, this noncatalytic MET-2 activity helps to maintain fertility. Under heat stress MET-2 foci disperse, coinciding with increased acetylation and transcriptional derepression. Our study suggests that the noncatalytic, focus-forming function of this SETDB1-like protein and its intrinsically disordered cofactor LIN-65 is physiologically relevant. Genetic and genome-wide analysis of a catalytically deficient SETDB1-like enzyme, MET-2, in Caenorhabditiselegans reveals that MET-2 promotes transcriptional silencing and fertility through both H3K9 methylation and focus formation, which blocks histone acetylation.
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Mihìc P, Hédouin S, Francastel C. Centromeres Transcription and Transcripts for Better and for Worse. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2021; 60:169-201. [PMID: 34386876 DOI: 10.1007/978-3-030-74889-0_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Centromeres are chromosomal regions that are essential for the faithful transmission of genetic material through each cell division. They represent the chromosomal platform on which assembles a protein complex, the kinetochore, which mediates attachment to the mitotic spindle. In most organisms, centromeres assemble on large arrays of tandem satellite repeats, although their DNA sequences and organization are highly divergent among species. It has become evident that centromeres are not defined by underlying DNA sequences, but are instead epigenetically defined by the deposition of the centromere-specific histone H3 variant, CENP-A. In addition, and although long regarded as silent chromosomal loci, centromeres are in fact transcriptionally competent in most species, yet at low levels in normal somatic cells, but where the resulting transcripts participate in centromere architecture, identity, and function. In this chapter, we discuss the various roles proposed for centromere transcription and their transcripts, and the potential molecular mechanisms involved. We also discuss pathological cases in which unscheduled transcription of centromeric repeats or aberrant accumulation of their transcripts are pathological signatures of chromosomal instability diseases. In sum, tight regulation of centromeric satellite repeats transcription is critical for healthy development and tissue homeostasis, and thus prevents the emergence of disease states.
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Affiliation(s)
- Pia Mihìc
- Université De Paris, Epigenetics and Cell Fate, CNRS UMR7216, Paris, France
| | - Sabrine Hédouin
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Claire Francastel
- Université De Paris, Epigenetics and Cell Fate, CNRS UMR7216, Paris, France.
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Chromatin and transcriptome changes in human myoblasts show spatio-temporal correlations and demonstrate DPP4 inhibition in differentiated myotubes. Sci Rep 2020; 10:14336. [PMID: 32868771 PMCID: PMC7459101 DOI: 10.1038/s41598-020-70756-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/03/2020] [Indexed: 12/03/2022] Open
Abstract
Although less attention was paid to understanding physical localization changes in cell nuclei recently, depicting chromatin interaction maps is a topic of high interest. Here, we focused on defining extensive physical changes in chromatin organization in the process of skeletal myoblast differentiation. Based on RNA profiling data and 3D imaging of myogenic (NCAM1, DES, MYOG, ACTN3, MYF5, MYF6, ACTN2, and MYH2) and other selected genes (HPRT1, CDH15, DPP4 and VCAM1), we observed correlations between the following: (1) expression change and localization, (2) a gene and its genomic neighbourhood expression and (3) intra-chromosome and microscopical locus-centromere distances. In particular, we demonstrated the negative regulation of DPP4 mRNA (p < 0.001) and protein (p < 0.05) in differentiated myotubes, which coincided with a localization change of the DPP4 locus towards the nuclear lamina (p < 0.001) and chromosome 2 centromere (p < 0.001). Furthermore, we discuss the possible role of DPP4 in myoblasts (supported by an inhibition assay). We also provide positive regulation examples (VCAM1 and MYH2). Overall, we describe for the first time existing mechanisms of spatial gene expression regulation in myoblasts that might explain the issue of heterogenic responses observed during muscle regenerative therapies.
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Golczyk H, Limanówka A, Uchman-Książek A. Pericentromere clustering in Tradescantia section Rhoeo involves self-associations of AT- and GC-rich heterochromatin fractions, is developmentally regulated, and increases during differentiation. Chromosoma 2020; 129:227-242. [PMID: 32681184 PMCID: PMC7666280 DOI: 10.1007/s00412-020-00740-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 06/30/2020] [Accepted: 07/01/2020] [Indexed: 11/30/2022]
Abstract
A spectacular but poorly recognized nuclear repatterning is the association of heterochromatic domains during interphase. Using base-specific fluorescence and extended-depth-of-focus imaging, we show that the association of heterochromatic pericentromeres composed of AT- and GC-rich chromatin occurs on a large scale in cycling meiotic and somatic cells and during development in ring- and bivalent-forming Tradescantia spathacea (section Rhoeo) varieties. The mean number of pericentromere AT-rich domains per root meristem nucleus was ca. half the expected diploid number in both varieties, suggesting chromosome pairing via (peri)centromeric regions. Indeed, regular pairing of AT-rich domains was observed. The AT- and GC-rich associations in differentiated cells contributed to a significant reduction of the mean number of the corresponding foci per nucleus in relation to root meristem. Within the first 10 mm of the root, the pericentromere attraction was in progress, as if it was an active process and involved both AT- and GC-rich associations. Complying with Rabl arrangement, the pericentromeres preferentially located on one nuclear pole, clustered into diverse configurations. Among them, a strikingly regular one with 5-7 ring-arranged pericentromeric AT-rich domains may be potentially engaged in chromosome positioning during mitosis. The fluorescent pattern of pachytene meiocytes and somatic nuclei suggests the existence of a highly prescribed ring/chain type of chromocenter architecture with side-by-side arranged pericentromeric regions. The dynamics of pericentromere associations together with their non-random location within nuclei was compared with nuclear architecture in other organisms, including the widely explored Arabidopsis model.
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Affiliation(s)
- Hieronim Golczyk
- Department of Molecular Biology, Institute of Biological Sciences, John Paul II Catholic University of Lublin, Konstantynów 1i, 20-708, Lublin, Poland.
| | - Arleta Limanówka
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
| | - Anna Uchman-Książek
- Department of Plant Cytology and Embryology, Institute of Botany, Jagiellonian University, Grodzka 52, 31-044, Cracow, Poland
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Epigenetic Factors That Control Pericentric Heterochromatin Organization in Mammals. Genes (Basel) 2020; 11:genes11060595. [PMID: 32481609 PMCID: PMC7349813 DOI: 10.3390/genes11060595] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/17/2020] [Accepted: 05/25/2020] [Indexed: 12/11/2022] Open
Abstract
Pericentric heterochromatin (PCH) is a particular form of constitutive heterochromatin that is localized to both sides of centromeres and that forms silent compartments enriched in repressive marks. These genomic regions contain species-specific repetitive satellite DNA that differs in terms of nucleotide sequences and repeat lengths. In spite of this sequence diversity, PCH is involved in many biological phenomena that are conserved among species, including centromere function, the preservation of genome integrity, the suppression of spurious recombination during meiosis, and the organization of genomic silent compartments in the nucleus. PCH organization and maintenance of its repressive state is tightly regulated by a plethora of factors, including enzymes (e.g., DNA methyltransferases, histone deacetylases, and histone methyltransferases), DNA and histone methylation binding factors (e.g., MECP2 and HP1), chromatin remodeling proteins (e.g., ATRX and DAXX), and non-coding RNAs. This evidence helps us to understand how PCH organization is crucial for genome integrity. It then follows that alterations to the molecular signature of PCH might contribute to the onset of many genetic pathologies and to cancer progression. Here, we describe the most recent updates on the molecular mechanisms known to underlie PCH organization and function.
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Jury N, Abarzua S, Diaz I, Guerra MV, Ampuero E, Cubillos P, Martinez P, Herrera-Soto A, Arredondo C, Rojas F, Manterola M, Rojas A, Montecino M, Varela-Nallar L, van Zundert B. Widespread loss of the silencing epigenetic mark H3K9me3 in astrocytes and neurons along with hippocampal-dependent cognitive impairment in C9orf72 BAC transgenic mice. Clin Epigenetics 2020; 12:32. [PMID: 32070418 PMCID: PMC7029485 DOI: 10.1186/s13148-020-0816-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022] Open
Abstract
Background Hexanucleotide repeat expansions of the G4C2 motif in a non-coding region of the C9ORF72 gene are the most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Tissues from C9ALS/FTD patients and from mouse models of ALS show RNA foci, dipeptide-repeat proteins, and notably, widespread alterations in the transcriptome. Epigenetic processes regulate gene expression without changing DNA sequences and therefore could account for the altered transcriptome profiles in C9ALS/FTD; here, we explore whether the critical repressive marks H3K9me2 and H3K9me3 are altered in a recently developed C9ALS/FTD BAC mouse model (C9BAC). Results Chromocenters that constitute pericentric constitutive heterochromatin were visualized as DAPI- or Nucblue-dense foci in nuclei. Cultured C9BAC astrocytes exhibited a reduced staining signal for H3K9me3 (but not for H3K9me2) at chromocenters that was accompanied by a marked decline in the global nuclear level of this mark. Similar depletion of H3K9me3 at chromocenters was detected in astrocytes and neurons of the spinal cord, motor cortex, and hippocampus of C9BAC mice. The alterations of H3K9me3 in the hippocampus of C9BAC mice led us to identify previously undetected neuronal loss in CA1, CA3, and dentate gyrus, as well as hippocampal-dependent cognitive deficits. Conclusions Our data indicate that a loss of the repressive mark H3K9me3 in astrocytes and neurons in the central nervous system of C9BAC mice represents a signature during neurodegeneration and memory deficit of C9ALS/FTD.
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Affiliation(s)
- Nur Jury
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sebastian Abarzua
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Ivan Diaz
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Miguel V Guerra
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Estibaliz Ampuero
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.,Current address: Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago, Chile
| | - Paula Cubillos
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Pablo Martinez
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrea Herrera-Soto
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile
| | - Cristian Arredondo
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Fabiola Rojas
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Marcia Manterola
- Program of Human Genetics, ICBM, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Adriana Rojas
- Instituto de Genética Humana, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Martín Montecino
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,FONDAP Center for Genome Regulation, Santiago, Chile
| | - Lorena Varela-Nallar
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.
| | - Brigitte van Zundert
- Institute of Biomedical Sciences (ICB), Faculty of Medicine & Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile. .,CARE Biomedical Research Center, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile.
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Choi MH, Palanichamy Kala M, Ow JR, Rao VK, Suriyamurthy S, Taneja R. GLP inhibits heterochromatin clustering and myogenic differentiation by repressing MeCP2. J Mol Cell Biol 2019; 10:161-174. [PMID: 28992061 DOI: 10.1093/jmcb/mjx038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 08/17/2017] [Indexed: 01/07/2023] Open
Abstract
Myogenic differentiation is accompanied by alterations in the chromatin states, which permit or restrict the transcriptional machinery and thus impact distinctive gene expression profiles. The mechanisms by which higher-order chromatin remodeling is associated with gene activation and silencing during differentiation is not fully understood. In this study, we provide evidence that the euchromatic lysine methyltransferase GLP regulates heterochromatin organization and myogenic differentiation. Interestingly, GLP represses expression of the methyl-binding protein MeCP2 that induces heterochromatin clustering during differentiation. Consequently, MeCP2 and HP1γ localization at major satellites are altered upon modulation of GLP expression. In GLP knockdown cells, depletion of MeCP2 restored both chromatin organization and myogenic differentiation. These results identify a novel regulatory axis between a histone methylation writer and DNA methylation reader, which is important for heterochromatin organization during differentiation.
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Affiliation(s)
- Min Hee Choi
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456, Singapore
| | - Monica Palanichamy Kala
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Jin Rong Ow
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456, Singapore
| | - Vinay Kumar Rao
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Sudha Suriyamurthy
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 117597, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 117456, Singapore
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12
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Histone 4 Lysine 20 Methylation: A Case for Neurodevelopmental Disease. BIOLOGY 2019; 8:biology8010011. [PMID: 30832413 PMCID: PMC6466304 DOI: 10.3390/biology8010011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 02/07/2023]
Abstract
Neurogenesis is an elegantly coordinated developmental process that must maintain a careful balance of proliferation and differentiation programs to be compatible with life. Due to the fine-tuning required for these processes, epigenetic mechanisms (e.g., DNA methylation and histone modifications) are employed, in addition to changes in mRNA transcription, to regulate gene expression. The purpose of this review is to highlight what we currently know about histone 4 lysine 20 (H4K20) methylation and its role in the developing brain. Utilizing publicly-available RNA-Sequencing data and published literature, we highlight the versatility of H4K20 methyl modifications in mediating diverse cellular events from gene silencing/chromatin compaction to DNA double-stranded break repair. From large-scale human DNA sequencing studies, we further propose that the lysine methyltransferase gene, KMT5B (OMIM: 610881), may fit into a category of epigenetic modifier genes that are critical for typical neurodevelopment, such as EHMT1 and ARID1B, which are associated with Kleefstra syndrome (OMIM: 610253) and Coffin-Siris syndrome (OMIM: 135900), respectively. Based on our current knowledge of the H4K20 methyl modification, we discuss emerging themes and interesting questions on how this histone modification, and particularly KMT5B expression, might impact neurodevelopment along with current challenges and potential avenues for future research.
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Park J, Lee H, Han N, Kwak S, Lee HT, Kim JH, Kang K, Youn BH, Yang JH, Jeong HJ, Kang JS, Kim SY, Han JW, Youn HD, Cho EJ. Long non-coding RNA ChRO1 facilitates ATRX/DAXX-dependent H3.3 deposition for transcription-associated heterochromatin reorganization. Nucleic Acids Res 2018; 46:11759-11775. [PMID: 30335163 PMCID: PMC6294499 DOI: 10.1093/nar/gky923] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 09/20/2018] [Accepted: 10/05/2018] [Indexed: 12/23/2022] Open
Abstract
Constitutive heterochromatin undergoes a dynamic clustering and spatial reorganization during myogenic differentiation. However the detailed mechanisms and its role in cell differentiation remain largely elusive. Here, we report the identification of a muscle-specific long non-coding RNA, ChRO1, involved in constitutive heterochromatin reorganization. ChRO1 is induced during terminal differentiation of myoblasts, and is specifically localized to the chromocenters in myotubes. ChRO1 is required for efficient cell differentiation, with global impacts on gene expression. It influences DNA methylation and chromatin compaction at peri/centromeric regions. Inhibition of ChRO1 leads to defects in the spatial fusion of chromocenters, and mislocalization of H4K20 trimethylation, Suv420H2, HP1, MeCP2 and cohesin. In particular, ChRO1 specifically associates with ATRX/DAXX/H3.3 complex at chromocenters to promote H3.3 incorporation and transcriptional induction of satellite repeats, which is essential for chromocenter clustering. Thus, our results unveil a mechanism involving a lncRNA that plays a role in large-scale heterochromatin reorganization and cell differentiation.
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MESH Headings
- Animals
- CRISPR-Cas Systems
- Carrier Proteins/genetics
- Carrier Proteins/metabolism
- Cell Cycle Proteins/genetics
- Cell Cycle Proteins/metabolism
- Cell Differentiation
- Chromosomal Proteins, Non-Histone/genetics
- Chromosomal Proteins, Non-Histone/metabolism
- Co-Repressor Proteins
- Female
- Gene Editing
- Gene Expression Regulation, Developmental
- HEK293 Cells
- Heterochromatin/chemistry
- Heterochromatin/metabolism
- Histone-Lysine N-Methyltransferase/genetics
- Histone-Lysine N-Methyltransferase/metabolism
- Histones/genetics
- Histones/metabolism
- Humans
- Intracellular Signaling Peptides and Proteins/genetics
- Intracellular Signaling Peptides and Proteins/metabolism
- Male
- Methyl-CpG-Binding Protein 2/genetics
- Methyl-CpG-Binding Protein 2/metabolism
- Mice
- Mice, Inbred C57BL
- Molecular Chaperones
- Muscle Development/genetics
- Muscle, Skeletal/cytology
- Muscle, Skeletal/growth & development
- Muscle, Skeletal/metabolism
- NIH 3T3 Cells
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- RNA, Long Noncoding/antagonists & inhibitors
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Transcription, Genetic
- X-linked Nuclear Protein/genetics
- X-linked Nuclear Protein/metabolism
- Cohesins
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Affiliation(s)
- Jinyoung Park
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Hongmin Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Namshik Han
- Milner Therapeutics Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Sojung Kwak
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Han-Teo Lee
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Jae-Hwan Kim
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Keonjin Kang
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Byoung Ha Youn
- Medical Genome Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jae-Hyun Yang
- Department of Genetics, Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115, USA
| | - Hyeon-Ju Jeong
- College of Medicine, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Jong-Sun Kang
- College of Medicine, Sungkyunkwan University, Suwon, Gyeonggi-do 440-746, Republic of Korea
| | - Seon-Young Kim
- Medical Genome Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Jeung-Whan Han
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
| | - Hong-Duk Youn
- Department of Biomedical Sciences,National Creative Research Center for Epigenome Reprogramming Network, Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
- Department of Molecular Medicine & Biopharmaceutical Sciences, Graduate School of Convergence Science and technology, Seoul National University, Seoul 03080, Republic of Korea
| | - Eun-Jung Cho
- School of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi-do 16419, Republic of Korea
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14
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Cáceres-Gutiérrez R, Herrera LA. Centromeric Non-coding Transcription: Opening the Black Box of Chromosomal Instability? Curr Genomics 2017; 18:227-235. [PMID: 28603453 PMCID: PMC5439370 DOI: 10.2174/1389202917666161102095508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 09/01/2016] [Accepted: 10/27/2016] [Indexed: 02/05/2023] Open
Abstract
In eukaryotes, mitosis is tightly regulated to avoid the generation of numerical chromosome aberrations, or aneuploidies. The aneuploid phenotype is a consequence of chromosomal instability (CIN), i.e., an enhanced rate of chromosome segregation errors, which is frequently found in cancer cells and is associated with tumor aggressiveness and increased tumor cell survival potential. To avoid the generation of aneuploidies, cells rely on the spindle assembly checkpoint (SAC), a widely conserved mechanism that protects the genome against this type of error. This signaling pathway stops mitotic pro-gression before anaphase until all chromosomes are correctly attached to spindle microtubules. Howev-er, impairment of the SAC cannot account for the establishment of CIN because cells bearing this phe-notype have a functional SAC. Hence, in cells with CIN, anaphase is not triggered until all chromo-somes are correctly attached to spindle microtubules and congressed at the metaphase plate. Thus, an in-teresting question arises: What mechanisms actually mediate CIN in cancer cells? Recent research has shown that some pathways involved in chromosome segregation are closely associated to centromere-encoded non-coding RNA (cencRNA) and that these RNAs are deregulated in abnormal conditions, such as cancer. These mechanisms may provide new explanations for chromosome segregation errors. The present review discusses some of these findings and proposes novel mechanisms for the establish-ment of CIN based on regulation by cencRNA.
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Affiliation(s)
- Rodrigo Cáceres-Gutiérrez
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
| | - Luis A Herrera
- Unidad de Investigación Biomédica en Cáncer, Instituto Nacional de Cancerología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexicocity, Mexico
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15
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Salsman J, Rapkin LM, Margam NN, Duncan R, Bazett-Jones DP, Dellaire G. Myogenic differentiation triggers PML nuclear body loss and DAXX relocalization to chromocentres. Cell Death Dis 2017; 8:e2724. [PMID: 28358373 PMCID: PMC5386546 DOI: 10.1038/cddis.2017.151] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 03/05/2017] [Accepted: 03/07/2017] [Indexed: 12/12/2022]
Abstract
The promyelocytic leukemia protein (PML) is expressed in most normal human tissues and forms nuclear bodies (NBs) that have roles in gene regulation and cellular processes such as DNA repair, cell cycle control, and cell fate decisions. Using murine C2C12 myoblasts, we demonstrate that activation of skeletal muscle differentiation results in loss of PML and PML NBs prior to myotube fusion. Myotube formation was associated with marked chromatin reorganization and the relocalization of DAXX from PML NBs to chromocentres. MyoD expression was sufficient to cause PML NB loss, and silencing of PML induced DAXX relocalization. Fusion of C2C12 cells using the reptilian reovirus p14 fusogenic protein failed to disrupt PML NBs yet still promoted DAXX redistribution and loss; whereas ectopic expression of PML in differentiated cells only partially restored PML NB formation and DAXX localization at NBs. Finally, we determined that the C-terminal SUMO-interacting motif of DAXX is required for its colocalization with ATRX in heterochromatin domains during myotube formation. These data support a model in which activation of myogenic differentiation results in PML NB loss, chromatin reorganization and DAXX relocalization, and provides a paradigm for understanding the consequence of PML loss in other cellular contexts, such as during cancer development and progression.
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Affiliation(s)
- Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - Lindsy M Rapkin
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada, M5G 1X8
| | - Nandini N Margam
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - Roy Duncan
- Department of Microbiology & Immunology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
| | - David P Bazett-Jones
- Genetics & Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada, M5G 1X8
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS, Canada, B3H 4R2.,Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS, Canada, B3H 4R2
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16
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Magaraki A, van der Heijden G, Sleddens-Linkels E, Magarakis L, van Cappellen WA, Peters AHFM, Gribnau J, Baarends WM, Eijpe M. Silencing markers are retained on pericentric heterochromatin during murine primordial germ cell development. Epigenetics Chromatin 2017; 10:11. [PMID: 28293300 PMCID: PMC5346203 DOI: 10.1186/s13072-017-0119-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 03/02/2017] [Indexed: 12/14/2022] Open
Abstract
Background In the nuclei of most mammalian cells, pericentric heterochromatin is characterized by DNA methylation, histone modifications such as H3K9me3 and H4K20me3, and specific binding proteins like heterochromatin-binding protein 1 isoforms (HP1 isoforms). Maintenance of this specialized chromatin structure is of great importance for genome integrity and for the controlled repression of the repetitive elements within the pericentric DNA sequence. Here we have studied histone modifications at pericentric heterochromatin during primordial germ cell (PGC) development using different fixation conditions and fluorescent immunohistochemical and immunocytochemical protocols. Results We observed that pericentric heterochromatin marks, such as H3K9me3, H4K20me3, and HP1 isoforms, were retained on pericentric heterochromatin throughout PGC development. However, the observed immunostaining patterns varied, depending on the fixation method, explaining previous findings of a general loss of pericentric heterochromatic features in PGCs. Also, in contrast to the general clustering of multiple pericentric regions and associated centromeres in DAPI-dense regions in somatic cells, the pericentric regions of PGCs were more frequently organized as individual entities. We also observed a transient enrichment of the chromatin remodeler ATRX in pericentric regions in embryonic day 11.5 (E11.5) PGCs. At this stage, a similar and low level of major satellite repeat RNA transcription was detected in both PGCs and somatic cells. Conclusions These results indicate that in pericentric heterochromatin of mouse PGCs, only minor reductions in levels of some chromatin-associated proteins occur, in association with a transient increase in ATRX, between E11.5 and E13.5. These pericentric heterochromatin regions more frequently contain only a single centromere in PGCs compared to the surrounding soma, indicating a difference in overall organization, but there is no de-repression of major satellite transcription. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0119-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aristea Magaraki
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Godfried van der Heijden
- Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Erasmus MC, Rotterdam, The Netherlands
| | - Esther Sleddens-Linkels
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Leonidas Magarakis
- Division of Reproductive Medicine, Department of Obstetrics and Gynecology, Central Hospital of Karlstad, Karlstad, Värmland Sweden
| | | | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), Basel, Switzerland.,Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Maureen Eijpe
- Department of Developmental Biology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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17
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Lomonte P. Herpesvirus Latency: On the Importance of Positioning Oneself. ADVANCES IN ANATOMY, EMBRYOLOGY, AND CELL BIOLOGY 2017; 223:95-117. [PMID: 28528441 DOI: 10.1007/978-3-319-53168-7_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nucleus is composed of multiple compartments and domains, which directly or indirectly influence many cellular processes including gene expression, RNA splicing and maturation, protein post-translational modifications, and chromosome segregation. Nuclear-replicating viruses, especially herpesviruses, have co-evolved with the cell, adopting strategies to counteract and eventually hijack this hostile environment for their own benefit. This allows them to persist in the host for the entire life of an individual and to ensure their maintenance in the target species. Herpesviruses establish latency in dividing or postmitotic cells from which they can efficiently reactivate after sometimes years of a seemingly dormant state. Therefore, herpesviruses circumvent the threat of permanent silencing by reactivating their dormant genomes just enough to escape extinction, but not too much to avoid life-threatening damage to the host. In addition, herpesviruses that establish latency in dividing cells must adopt strategies to maintain their genomes in the daughter cells to avoid extinction by dilution of their genomes following multiple cell divisions. From a biochemical point of view, reactivation and maintenance of viral genomes in dividing cells occur successfully because the viral genomes interact with the nuclear architecture in a way that allows the genomes to be transmitted faithfully and to benefit from the nuclear micro-environments that allow reactivation following specific stimuli. Therefore, spatial positioning of the viral genomes within the nucleus is likely to be essential for the success of the latent infection and, beyond that, for the maintenance of herpesviruses in their respective hosts.
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Affiliation(s)
- Patrick Lomonte
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS UMR-5310, INSERM U-1217, LabEx DEVweCAN, Institut NeuroMyoGène (INMG), team Chromatin Assembly, Nuclear Domains, Virus, 69008, Lyon, France.
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18
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Satellite RNAs promote pancreatic oncogenic processes via the dysfunction of YBX1. Nat Commun 2016; 7:13006. [PMID: 27667193 PMCID: PMC5052683 DOI: 10.1038/ncomms13006] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 08/23/2016] [Indexed: 01/01/2023] Open
Abstract
Highly repetitive tandem arrays at the centromeric and pericentromeric regions in chromosomes, previously considered silent, are actively transcribed, particularly in cancer. This aberrant expression occurs even in K-ras-mutated pancreatic intraepithelial neoplasia (PanIN) tissues, which are precancerous lesions. To examine the biological roles of the satellite RNAs in carcinogenesis, we construct mouse PanIN-derived cells expressing major satellite (MajSAT) RNA and show increased malignant properties. We find an increase in frequency of chromosomal instability and point mutations in both genomic and mitochondrial DNA. We identify Y-box binding protein 1 (YBX1) as a protein that binds to MajSAT RNA. MajSAT RNA inhibits the nuclear translocation of YBX1 under stress conditions, thus reducing its DNA-damage repair function. The forced expression of YBX1 significantly decreases the aberrant phenotypes. These findings indicate that during the early stage of cancer development, satellite transcripts may act as 'intrinsic mutagens' by inducing YBX1 dysfunction, which may be crucial in oncogenic processes.
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19
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20
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Becker JS, Nicetto D, Zaret KS. H3K9me3-Dependent Heterochromatin: Barrier to Cell Fate Changes. Trends Genet 2015; 32:29-41. [PMID: 26675384 DOI: 10.1016/j.tig.2015.11.001] [Citation(s) in RCA: 306] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 01/26/2023]
Abstract
Establishing and maintaining cell identity depends on the proper regulation of gene expression, as specified by transcription factors and reinforced by epigenetic mechanisms. Among the epigenetic mechanisms, heterochromatin formation is crucial for the preservation of genome stability and the cell type-specific silencing of genes. The heterochromatin-associated histone mark H3K9me3, although traditionally associated with the noncoding portions of the genome, has emerged as a key player in repressing lineage-inappropriate genes and shielding them from activation by transcription factors. Here we describe the role of H3K9me3 heterochromatin in impeding the reprogramming of cell identity and the mechanisms by which H3K9me3 is reorganized during development and cell fate determination.
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Affiliation(s)
- Justin S Becker
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Dario Nicetto
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine, Epigenetics Program, and Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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21
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22
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Rapkin LM, Ahmed K, Dulev S, Li R, Kimura H, Ishov AM, Bazett-Jones DP. The histone chaperone DAXX maintains the structural organization of heterochromatin domains. Epigenetics Chromatin 2015; 8:44. [PMID: 26500702 PMCID: PMC4617904 DOI: 10.1186/s13072-015-0036-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 10/07/2015] [Indexed: 12/20/2022] Open
Abstract
Background The death domain-associated protein (DAXX) collaborates with accessory proteins to deposit the histone variant H3.3 into mouse telomeric and pericentromeric repeat DNA. Pericentromeric repeats are the main genetic contributor to spatially discrete, compact, constitutive heterochromatic structures called chromocentres. Chromocentres are enriched in the H3K9me3 histone modification and serve as integral, functionally important components of nuclear organization. To date, the role of DAXX as an H3.3-specific histone chaperone has been investigated primarily using biochemical approaches which provide genome-wide views on cell populations and information on changes in local chromatin structures. However, the global chromatin and subnuclear reorganization events that coincide with these changes remain to be investigated. Results Using electron spectroscopic imagine (ESI), a specialized form of energy-filtered transmission electron microscopy that allows us to visualize chromatin domains in situ with high contrast and spatial resolution, we show that in the absence of DAXX, H3K9me3-enriched domains are structurally altered and become uncoupled from major satellite DNA. In addition, the structural integrity of nucleoli and the organization of ribosomal DNA (rDNA) are disrupted. Moreover, the absence of DAXX leads to chromatin that is more sensitive, on a global level, to micrococcal nuclease digestion. Conclusions We identify a novel role of DAXX as a major regulator of subnuclear organization through the maintenance of the global heterochromatin structural landscape. As well, we show, for the first time, that the loss of a histone chaperone can have severe consequences for global nuclear organization. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0036-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lindsy M Rapkin
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4 Canada ; Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8 Canada
| | - Kashif Ahmed
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4 Canada
| | - Stanimir Dulev
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4 Canada
| | - Ren Li
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4 Canada
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-Ku, Yokohama 226-8501 Japan
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, and University of Florida Cancer Center, Gainesville, FL 32610 USA
| | - David P Bazett-Jones
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON M5G 0A4 Canada ; Department of Biochemistry, The University of Toronto, Toronto, ON M5S 1A8 Canada
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23
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Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. Nat Struct Mol Biol 2015; 22:662-71. [PMID: 26237512 DOI: 10.1038/nsmb.3066] [Citation(s) in RCA: 227] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/09/2015] [Indexed: 12/30/2022]
Abstract
Cellular plasticity is essential for early embryonic cells. Unlike pluripotent cells, which form embryonic tissues, totipotent cells can generate a complete organism including embryonic and extraembryonic tissues. Cells resembling 2-cell-stage embryos (2C-like cells) arise at very low frequency in embryonic stem (ES) cell cultures. Although induced reprogramming to pluripotency is well established, totipotent cells remain poorly characterized, and whether reprogramming to totipotency is possible is unknown. We show that mouse 2C-like cells can be induced in vitro through downregulation of the chromatin-assembly activity of CAF-1. Endogenous retroviruses and genes specific to 2-cell embryos are the highest-upregulated genes upon CAF-1 knockdown. Emerging 2C-like cells exhibit molecular characteristics of 2-cell embryos and higher reprogrammability than ES cells upon nuclear transfer. Our results suggest that early embryonic-like cells can be induced by modulating chromatin assembly and that atypical histone deposition may trigger the emergence of totipotent cells.
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24
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Ollion J, Loll F, Cochennec J, Boudier T, Escudé C. Proliferation-dependent positioning of individual centromeres in the interphase nucleus of human lymphoblastoid cell lines. Mol Biol Cell 2015; 26:2550-60. [PMID: 25947134 PMCID: PMC4571307 DOI: 10.1091/mbc.e14-05-1002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 04/27/2015] [Indexed: 01/01/2023] Open
Abstract
Centromeres are not randomly distributed in interphase nuclei. High-throughput imaging provides an accurate characterization of how their organization varies as a function of the proliferation state in human lymphoblastoid cells. The results suggest the existence of mechanisms that drive the nuclear positioning of centromeres. The cell nucleus is a highly organized structure and plays an important role in gene regulation. Understanding the mechanisms that sustain this organization is therefore essential for understanding genome function. Centromeric regions (CRs) of chromosomes have been known for years to adopt specific nuclear positioning patterns, but the significance of this observation is not yet completely understood. Here, using a combination of fluorescence in situ hybridization and immunochemistry on fixed human cells and high-throughput imaging, we directly and quantitatively investigated the nuclear positioning of specific human CRs. We observe differential attraction of individual CRs toward both the nuclear border and the nucleoli, the former being enhanced in nonproliferating cells and the latter being enhanced in proliferating cells. Similar positioning patterns are observed in two different lymphoblastoid cell lines. Moreover, the positioning of CRs differs from that of noncentromeric regions, and CRs display specific orientations within chromosome territories. These results suggest the existence of not-yet-characterized mechanisms that drive the nuclear positioning of CRs and therefore pave the way toward a better understanding of how CRs affect nuclear organization.
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Affiliation(s)
- Jean Ollion
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - François Loll
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Julien Cochennec
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
| | - Thomas Boudier
- Université Pierre et Marie Curie, Sorbonne Universités, 75005 Paris, France
| | - Christophe Escudé
- Institut National de la Santé et de la Recherche Médicale U1154, Centre National de la Recherche Scientifique UMR7196, Muséum National d'Histoire Naturelle, 75231 Paris, France
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25
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Yang M, Yuan ZM. A novel role of PRR14 in the regulation of skeletal myogenesis. Cell Death Dis 2015; 6:e1734. [PMID: 25906157 PMCID: PMC4650536 DOI: 10.1038/cddis.2015.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 12/11/2022]
Abstract
Dysregulation of genes involved in organizing and maintaining nuclear structures, such as SYNE1, SYNE2, TREM43, EMD and LMNA is frequently associated with diverse diseases termed laminopathies, which often affect the muscle tissue. The PRR14 protein was recently reported to tether heterochromatin to nuclear lamina but its function remains largely unknown. Here, we present several lines of evidence demonstrating a critical role of PRR14 in regulation of myoblast differentiation. We found that Prr14 expression was upregulated during skeletal myogenesis. Knockdown of Prr14 impeded, whereas overexpression of PRR14 enhanced C2C12 differentiation. The pro-myogenesis activity of PRR14 seemed to correlate with its ability to support cell survival and to maintain the stability and structure of lamin A/C. In addition, PRR14 stimulated the activity of MyoD via binding to heterochromatin protein 1 alpha (HP1α). The results altogether support a model in which PRR14 promotes skeletal myogenesis via supporting nuclear lamina structure and enhancing the activity of MyoD.
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Affiliation(s)
- M Yang
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Z-M Yuan
- Department of Genetics and Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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26
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Saksouk N, Simboeck E, Déjardin J. Constitutive heterochromatin formation and transcription in mammals. Epigenetics Chromatin 2015; 8:3. [PMID: 25788984 PMCID: PMC4363358 DOI: 10.1186/1756-8935-8-3] [Citation(s) in RCA: 341] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 12/16/2014] [Indexed: 12/17/2022] Open
Abstract
Constitutive heterochromatin, mainly formed at the gene-poor regions of pericentromeres, is believed to ensure a condensed and transcriptionally inert chromatin conformation. Pericentromeres consist of repetitive tandem satellite repeats and are crucial chromosomal elements that are responsible for accurate chromosome segregation in mitosis. The repeat sequences are not conserved and can greatly vary between different organisms, suggesting that pericentromeric functions might be controlled epigenetically. In this review, we will discuss how constitutive heterochromatin is formed and maintained at pericentromeres in order to ensure their integrity. We will describe the biogenesis and the function of main epigenetic pathways that are involved and how they are interconnected. Interestingly, recent findings suggest that alternative pathways could substitute for well-established pathways when disrupted, suggesting that constitutive heterochromatin harbors much more plasticity than previously assumed. In addition, despite of the heterochromatic nature of pericentromeres, there is increasing evidence for active and regulated transcription at these loci, in a multitude of organisms and under various biological contexts. Thus, in the second part of this review, we will address this relatively new aspect and discuss putative functions of pericentromeric expression.
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Affiliation(s)
- Nehmé Saksouk
- INSERM AVENIR Team, Institute of Human Genetics, CNRS UPR 1142, Montpellier, France
| | - Elisabeth Simboeck
- INSERM AVENIR Team, Institute of Human Genetics, CNRS UPR 1142, Montpellier, France
| | - Jérôme Déjardin
- INSERM AVENIR Team, Institute of Human Genetics, CNRS UPR 1142, Montpellier, France
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Cebrià-Costa JP, Millanes-Romero A, de Herreros AG, Peiró S. The Epithelial-to-Mesenchymal Transition (EMT), a Particular Case. Mol Cell Oncol 2014; 1:e960770. [PMID: 27308335 PMCID: PMC4905179 DOI: 10.4161/23723548.2014.960770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 07/25/2014] [Accepted: 08/01/2014] [Indexed: 01/05/2023]
Abstract
Constitutive heterochromatin, an essential structure that has been conserved throughout evolution, is required to maintain genome stability. Although heterochromatin is enriched for repressive traits, it can be actively transcribed to generate thousands of noncoding RNAs that are required for correct chromatin assembly. Despite the importance of this structure, how and why heterochromatin transcription is regulated, and the proteins responsible for this regulation, remain poorly understood. Here, we summarize recent findings in heterochromatin transcription regulation during different cellular processes with a focus on the epithelial–mesenchymal transition (EMT), which elicits important changes in cell behavior, has a key role in early development, and is involved in cancer progression.
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Affiliation(s)
- Joan Pau Cebrià-Costa
- Programa de Recerca en Càncer; IMIM (Institut Hospital del Mar d'Investigacions Mèdiques) ; Barcelona, Spain
| | | | - Antonio García de Herreros
- Programa de Recerca en Càncer; IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Barcelona, Spain; Departament de Ciències Experimentals i de la Salut; Universitat Pompeu Fabra; Barcelona, Spain
| | - Sandra Peiró
- Programa de Recerca en Càncer; IMIM (Institut Hospital del Mar d'Investigacions Mèdiques) ; Barcelona, Spain
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Boyarchuk E, Filipescu D, Vassias I, Cantaloube S, Almouzni G. The histone variant composition of centromeres is controlled by the pericentric heterochromatin state during the cell cycle. J Cell Sci 2014; 127:3347-59. [PMID: 24906798 DOI: 10.1242/jcs.148189] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Correct chromosome segregation requires a unique chromatin environment at centromeres and in their vicinity. Here, we address how the deposition of canonical H2A and H2A.Z histone variants is controlled at pericentric heterochromatin (PHC). Whereas in euchromatin newly synthesized H2A and H2A.Z are deposited throughout the cell cycle, we reveal two discrete waves of deposition at PHC - during mid to late S phase in a replication-dependent manner for H2A and during G1 phase for H2A.Z. This G1 cell cycle restriction is lost when heterochromatin features are altered, leading to the accumulation of H2A.Z at the domain. Interestingly, compromising PHC integrity also impacts upon neighboring centric chromatin, increasing the amount of centromeric CENP-A without changing the timing of its deposition. We conclude that the higher-order chromatin structure at the pericentric domain influences dynamics at the nucleosomal level within centromeric chromatin. The two different modes of rearrangement of the PHC during the cell cycle provide distinct opportunities to replenish one or the other H2A variant, highlighting PHC integrity as a potential signal to regulate the deposition timing and stoichiometry of histone variants at the centromere.
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Affiliation(s)
- Ekaterina Boyarchuk
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Dan Filipescu
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Isabelle Vassias
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Sylvain Cantaloube
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
| | - Geneviève Almouzni
- Institut Curie, Centre de Recherche, Paris, 75248 France CNRS, UMR3664, Paris, 75248 France Equipe Labellisée Ligue contre le Cancer, UMR3664, Paris, 75248 France UPMC, UMR3664, Paris, 75248 France Sorbonne University, PSL, 75006 Paris, France
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Heterochromatin reorganization during early mouse development requires a single-stranded noncoding transcript. Cell Rep 2013; 4:1156-67. [PMID: 24055057 DOI: 10.1016/j.celrep.2013.08.015] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/02/2013] [Accepted: 08/08/2013] [Indexed: 02/05/2023] Open
Abstract
The equalization of pericentric heterochromatin from distinct parental origins following fertilization is essential for genome function and development. The recent implication of noncoding transcripts in this process raises questions regarding the connection between RNA and the nuclear organization of distinct chromatin environments. Our study addresses the interrelationship between replication and transcription of the two parental pericentric heterochromatin (PHC) domains and their reorganization during early embryonic development. We demonstrate that the replication of PHC is dispensable for its clustering at the late two-cell stage. In contrast, using parthenogenetic embryos, we show that pericentric transcripts are essential for this reorganization independent of the chromatin marks associated with the PHC domains. Finally, our discovery that only reverse pericentric transcripts are required for both the nuclear reorganization of PHC and development beyond the two-cell stage challenges current views on heterochromatin organization.
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Characterisation of nuclear architectural alterations during in vitro differentiation of human stem cells of myogenic origin. PLoS One 2013; 8:e73231. [PMID: 24019912 PMCID: PMC3760906 DOI: 10.1371/journal.pone.0073231] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 07/18/2013] [Indexed: 01/06/2023] Open
Abstract
Cell differentiation is based on a synchronised orchestra of complex pathways of intrinsic and extrinsic signals that manifest in the induced expression of specific transcription factors and pivotal genes within the nucleus. One cannot ignore the epigenetic status of differentiating cells, comprising not only histones and DNA modifications but also the spatial and temporal intranuclear chromatin organisation, which is an important regulator of nuclear processes. In the present study, we investigated the nuclear architecture of human primary myoblasts and myocytes in an in vitro culture, with reference to global changes in genomic expression. Repositioning of the chromosomal centromeres, along with alterations in the nuclear shape and volume, was observed as a consequence of myotube formation. Moreover, the microarray data showed that during in vitro myogenesis cells tend to silence rather than induce gene expression. The creation of a chromosome map marked with gene expression changes that were at least 2-fold confirmed the observation. Additionally, almost all of the chromosomal centromeres in the differentiated cells preferentially localised near the nuclear periphery when compared to the undifferentiated cells. The exceptions were chromosomes 7 and 11, in which we were unable to confirm the centromere repositioning. In our opinion, this is the first reported observation of the movement of chromosomal centromeres along differentiating myogenic cells. Based on these data we can conclude that the myogenic differentiation with global gene expression changes is accompanied by the spatial repositioning of chromosomes and chromatin remodelling, which are important processes that regulate cell differentiation.
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Neguembor MV, Xynos A, Onorati MC, Caccia R, Bortolanza S, Godio C, Pistoni M, Corona DF, Schotta G, Gabellini D. FSHD muscular dystrophy region gene 1 binds Suv4-20h1 histone methyltransferase and impairs myogenesis. J Mol Cell Biol 2013; 5:294-307. [DOI: 10.1093/jmcb/mjt018] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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Fadloun A, Eid A, Torres-Padilla ME. Mechanisms and dynamics of heterochromatin formation during mammalian development: closed paths and open questions. Curr Top Dev Biol 2013; 104:1-45. [PMID: 23587237 DOI: 10.1016/b978-0-12-416027-9.00001-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Early embryonic development in mammals is characterized by major changes in the components of the chromatin and its remodeling. The embryonic chromatin and the nuclear organization in the mouse preimplantation embryo display particular features that are dramatically different from somatic cells. These include the highly specific organization of the pericentromeric heterochromatin within the nucleus and the suggested lack of conventional heterochromatin. We postulate that the plasticity of the cells in the early embryo relies on the distinctive heterochromatin features that prevail during early embryogenesis. Here, we review some of these features and discuss recent findings on the mechanisms driving heterochromatin formation after fertilization, in particular, the emerging role of RNA as a regulator of heterochromatic loci also in mammals. Finally, we believe that there are at least three major avenues that should be addressed in the coming years: (i) Is heterochromatin a driving force in development? (ii) Does it have a role in lineage allocation? (iii) How can heterochromatin "regulate" epigenetic reprogramming?
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Affiliation(s)
- Anas Fadloun
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM U964, Université de Strasbourg, Illkirch, France
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MeCP2 dependent heterochromatin reorganization during neural differentiation of a novel Mecp2-deficient embryonic stem cell reporter line. PLoS One 2012; 7:e47848. [PMID: 23112857 PMCID: PMC3480415 DOI: 10.1371/journal.pone.0047848] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/21/2012] [Indexed: 01/17/2023] Open
Abstract
The X-linked Mecp2 is a known interpreter of epigenetic information and mutated in Rett syndrome, a complex neurological disease. MeCP2 recruits HDAC complexes to chromatin thereby modulating gene expression and, importantly regulates higher order heterochromatin structure. To address the effects of MeCP2 deficiency on heterochromatin organization during neural differentiation, we developed a versatile model for stem cell in vitro differentiation. Therefore, we modified murine Mecp2 deficient (Mecp2−/y) embryonic stem cells to generate cells exhibiting green fluorescent protein expression upon neural differentiation. Subsequently, we quantitatively analyzed heterochromatin organization during neural differentiation in wild type and in Mecp2 deficient cells. We found that MeCP2 protein levels increase significantly during neural differentiation and accumulate at constitutive heterochromatin. Statistical analysis of Mecp2 wild type neurons revealed a significant clustering of heterochromatin per nuclei with progressing differentiation. In contrast we found Mecp2 deficient neurons and astroglia cells to be significantly impaired in heterochromatin reorganization. Our results (i) introduce a new and manageable cellular model to study the molecular effects of Mecp2 deficiency, and (ii) support the view of MeCP2 as a central protein in heterochromatin architecture in maturating cells, possibly involved in stabilizing their differentiated state.
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Gross S, Catez F, Masumoto H, Lomonte P. Centromere architecture breakdown induced by the viral E3 ubiquitin ligase ICP0 protein of herpes simplex virus type 1. PLoS One 2012; 7:e44227. [PMID: 23028505 PMCID: PMC3447814 DOI: 10.1371/journal.pone.0044227] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2012] [Accepted: 07/30/2012] [Indexed: 01/20/2023] Open
Abstract
The viral E3 ubiquitin ligase ICP0 protein has the unique property to temporarily localize at interphase and mitotic centromeres early after infection of cells by the herpes simplex virus type 1 (HSV-1). As a consequence ICP0 induces the proteasomal degradation of several centromeric proteins (CENPs), namely CENP-A, the centromeric histone H3 variant, CENP-B and CENP-C. Following ICP0-induced centromere modification cells trigger a specific response to centromeres called interphase Centromere Damage Response (iCDR). The biological significance of the iCDR is unknown; so is the degree of centromere structural damage induced by ICP0. Interphase centromeres are complex structures made of proximal and distal protein layers closely associated to CENP-A-containing centromeric chromatin. Using several cell lines constitutively expressing GFP-tagged CENPs, we investigated the extent of the centromere destabilization induced by ICP0. We show that ICP0 provokes the disappearance from centromeres, and the proteasomal degradation of several CENPs from the NAC (CENP-A nucleosome associated) and CAD (CENP-A Distal) complexes. We then investigated the nucleosomal occupancy of the centromeric chromatin in ICP0-expressing cells by micrococcal nuclease (MNase) digestion analysis. ICP0 expression either following infection or in cell lines constitutively expressing ICP0 provokes significant modifications of the centromeric chromatin structure resulting in higher MNase accessibility. Finally, using human artificial chromosomes (HACs), we established that ICP0-induced iCDR could also target exogenous centromeres. These results demonstrate that, in addition to the protein complexes, ICP0 also destabilizes the centromeric chromatin resulting in the complete breakdown of the centromere architecture, which consequently induces iCDR.
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Affiliation(s)
- Sylvain Gross
- Virus and Centromere Team, Centre de Génétique et de Physiologie Moléculaire et Cellulaire CNRS, UMR5534, Villeurbanne, France
- Université de Lyon 1, Lyon, France
- Laboratoire d'excellence, Labex DEVweCAN, Lyon, France
| | - Frédéric Catez
- Virus and Centromere Team, Centre de Génétique et de Physiologie Moléculaire et Cellulaire CNRS, UMR5534, Villeurbanne, France
- Université de Lyon 1, Lyon, France
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Kazusa DNA Research Institute, Chiba, Japan
| | - Patrick Lomonte
- Virus and Centromere Team, Centre de Génétique et de Physiologie Moléculaire et Cellulaire CNRS, UMR5534, Villeurbanne, France
- Université de Lyon 1, Lyon, France
- Laboratoire d'excellence, Labex DEVweCAN, Lyon, France
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HSV-1 genome subnuclear positioning and associations with host-cell PML-NBs and centromeres regulate LAT locus transcription during latency in neurons. PLoS Pathog 2012; 8:e1002852. [PMID: 22912575 PMCID: PMC3415458 DOI: 10.1371/journal.ppat.1002852] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Accepted: 06/26/2012] [Indexed: 02/04/2023] Open
Abstract
Major human pathologies are caused by nuclear replicative viruses establishing life-long latent infection in their host. During latency the genomes of these viruses are intimately interacting with the cell nucleus environment. A hallmark of herpes simplex virus type 1 (HSV-1) latency establishment is the shutdown of lytic genes expression and the concomitant induction of the latency associated (LAT) transcripts. Although the setting up and the maintenance of the latent genetic program is most likely dependent on a subtle interplay between viral and nuclear factors, this remains uninvestigated. Combining the use of in situ fluorescent-based approaches and high-resolution microscopic analysis, we show that HSV-1 genomes adopt specific nuclear patterns in sensory neurons of latently infected mice (28 days post-inoculation, d.p.i.). Latent HSV-1 genomes display two major patterns, called “Single” and “Multiple”, which associate with centromeres, and with promyelocytic leukemia nuclear bodies (PML-NBs) as viral DNA-containing PML-NBs (DCP-NBs). 3D-image reconstruction of DCP-NBs shows that PML forms a shell around viral genomes and associated Daxx and ATRX, two PML partners within PML-NBs. During latency establishment (6 d.p.i.), infected mouse TGs display, at the level of the whole TG and in individual cells, a substantial increase of PML amount consistent with the interferon-mediated antiviral role of PML. “Single” and “Multiple” patterns are reminiscent of low and high-viral genome copy-containing neurons. We show that LAT expression is significantly favored within the “Multiple” pattern, which underlines a heterogeneity of LAT expression dependent on the viral genome copy number, pattern acquisition, and association with nuclear domains. Infection of PML-knockout mice demonstrates that PML/PML-NBs are involved in virus nuclear pattern acquisition, and negatively regulate the expression of the LAT. This study demonstrates that nuclear domains including PML-NBs and centromeres are functionally involved in the control of HSV-1 latency, and represent a key level of host/virus interaction. After an initial lytic infection, many viruses establish a lifelong latent infection that hides them from the host immune system activity until reactivation. To understand the resurgence of the associated diseases, it is indispensable to acquire a better knowledge of the different mechanisms involved in the antiviral defense. During latency, viral genomes of nuclear-replicative viruses, such as herpes simplex virus type 1 (HSV-1), are stored in the nucleus of host cells in a non-integrated form. Latency establishment is associated with a drastic change in HSV-1 gene expression program that is maintained until reactivation occurs. The last two decades of research has revealed that the functional organization of the cell nucleus, so-called nuclear architecture, is a major factor of regulation of cellular genes expression. Nonetheless, the role of nuclear architecture on HSV-1 gene expression has been widely overlooked. Here we describe that the genome of HSV-1 selectively interacts with two major nuclear structures, the promyelocytic nuclear bodies (PMLNBs or ND10) and the centromeres. We provide evidence supporting that these nuclear domains directly influence the behavior of latent viral genomes and their transcriptional activity. Overall, this study demonstrates that nuclear architecture is a major parameter driving the highly complex HSV-1 latency process.
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36
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Pezer Z, Ugarkovic D. Satellite DNA-associated siRNAs as mediators of heat shock response in insects. RNA Biol 2012; 9:587-95. [PMID: 22647527 DOI: 10.4161/rna.20019] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Conversion of environmental signals into epigenetic information is thought to occur widely but has been poorly studied as yet. It is proposed that changes in the expression of molecules involved in chromatin modifications might play a role in this process. Here we study the expression of abundant satellite DNA TCAST that makes up 35% of genome of the red flour beetle Tribolium castaneum and is located within the constitutive pericentromeric heterochromatin. RNA polymerase II promotes the transcription of TCAST satellite DNA from both strands, and long primary transcripts are rapidly processed into 21-30 nt siRNAs. Expression of TCAST satellite DNA-associated siRNAs is developmentally regulated, the most intense being at specific stages of embryogenesis. Moreover, the expression is strongly induced following heat shock and is accompanied by increase in repressive epigenetic modifications of histones at TCAST regions. Upon recovery from heat stress, the expression of satellite DNA-associated siRNAs as well as histone modifications is quickly restored. Our results indicate that satellite DNA-associated siRNAs, transiently activated after heat shock, affect epigenetic state of constitutive heterochromatin in Tribolium. It can be hypothesized that transient remodeling of heterochromatin is part of a physiological gene expression program activated under stress conditions in insects.
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Affiliation(s)
- Zeljka Pezer
- Department of Molecular Biology, Ruđer Bošković Institute, Bijenička, Zagreb, Croatia
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37
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Probst AV, Almouzni G. Heterochromatin establishment in the context of genome-wide epigenetic reprogramming. Trends Genet 2011; 27:177-85. [PMID: 21497937 DOI: 10.1016/j.tig.2011.02.002] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 02/09/2011] [Accepted: 02/11/2011] [Indexed: 01/08/2023]
Abstract
Heterochromatin at pericentric satellites, characterized by a specific chromatin signature and chromocenter organization, is of paramount importance for genome function. Re-establishment of this organization after fertilization takes place in the context of genome-wide epigenetic reprogramming. We review how the asymmetry in histone variants and post-translational modifications between paternal and maternal genomes and their respective pericentric heterochromatin domains evolve during early cleavage stages in mouse. We draw a parallel between these data and the burst of pericentric satellite transcription that occurs concomitantly with the dynamic reorganization of the pericentric domains into chromocenters in two-cell stage embryos. Based on this new angle, we propose that a crucial developmental transition at the two-cell stage allows chromocenter formation by involving non-coding satellite transcripts to trigger specific chromatin changes.
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Affiliation(s)
- Aline V Probst
- Centre National de la Recherche Scientifique Unité Mixte de Recherche 6247 and Institut National de la Santé et de la Recherche Médicale Unité 931 - Genetics, Reproduction and Development, Clermont University, 24 avenue des Landais, 63177 Aubière CEDEX, France
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38
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SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin. Nat Genet 2011; 43:220-7. [PMID: 21317888 DOI: 10.1038/ng.765] [Citation(s) in RCA: 175] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2010] [Accepted: 01/18/2011] [Indexed: 12/13/2022]
Abstract
HP1 enrichment at pericentric heterochromatin is considered important for centromere function. Although HP1 binding to H3K9me3 can explain its accumulation at pericentric heterochromatin, how it is initially targeted there remains unclear. Here, in mouse cells, we reveal the presence of long nuclear noncoding transcripts corresponding to major satellite repeats at the periphery of pericentric heterochromatin. Furthermore, we find that major transcripts in the forward orientation specifically associate with SUMO-modified HP1 proteins. We identified this modification as SUMO-1 and mapped it in the hinge domain of HP1α. Notably, the hinge domain and its SUMOylation proved critical to promote the initial targeting of HP1α to pericentric domains using de novo localization assays, whereas they are dispensable for maintenance of HP1 domains. We propose that SUMO-HP1, through a specific association with major forward transcript, is guided at the pericentric heterochromatin domain to seed further HP1 localization.
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39
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Balakrishnan L, Milavetz B. Decoding the histone H4 lysine 20 methylation mark. Crit Rev Biochem Mol Biol 2011; 45:440-52. [PMID: 20735237 DOI: 10.3109/10409238.2010.504700] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The molecular biology of histone H4 lysine 20 (H4K20) methylation, like many other post-translational modifications of histones, has been the subject of intensive interest in recent years. While there is an emerging consensus linking H4K20me1, H4K20me2, and H4K20me3 to transcription, repair, and constitutive heterochromatin, respectively, the specific details of these associations and the biological mechanisms by which the methylated histones are introduced and function are now the subject of active investigation. Although a large number of methylases capable of methylating H4K20 have been identified and characterized; there is no known demethylase of H4K20, though the search is ongoing. Additionally, many recent studies have been directed at understanding the role of methylated H4K20 and other histone modifications associated with different biological processes in the context of a combinatorial histone code. It seems likely that continued study of the methylation of H4K20 will yield extremely valuable insights concerning the regulation of histone modifications before and during cell division and the impact of these modifications on subsequent gene expression.
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Affiliation(s)
- Lata Balakrishnan
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY, USA
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40
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Rosati J, Spallotta F, Nanni S, Grasselli A, Antonini A, Vincenti S, Presutti C, Colussi C, D'Angelo C, Biroccio A, Farsetti A, Capogrossi MC, Illi B, Gaetano C. Smad-interacting protein-1 and microRNA 200 family define a nitric oxide-dependent molecular circuitry involved in embryonic stem cell mesendoderm differentiation. Arterioscler Thromb Vasc Biol 2011; 31:898-907. [PMID: 21233447 DOI: 10.1161/atvbaha.110.214478] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
OBJECTIVE Smad-interacting protein-1 (Sip1/ZEB2) is a transcriptional repressor of the telomerase reverse transcriptase catalytic subunit (Tert) and has recently been identified as a key regulator of embryonic cell fate with a phenotypic effect similar, in our opinion, to that reported for nitric oxide (NO). Remarkably, SIP1/ZEB2 is a known target of the microRNA 200 (miR-200) family. In this light, we postulated that Sip1/ZEB2 and the miR-200 family could play a role during the NO-dependent differentiation of mES. METHODS AND RESULTS The results of the present study show that Sip1/ZEB2 expression is downregulated during the NO-dependent expression of mesendoderm and early cardiovascular precursor markers, including Flk1 and CXCR4 in mES. Coincidently, members of the miR-200 family, namely miR-429, -200a, -200b, and -200c, were transcriptionally induced in parallel to mouse Tert. This regulation occurred at the level of chromatin. Remarkably, miR-429/miR-200a overexpression or Sip1/ZEB2 knockdown by short hairpin RNA interference elicited a gene expression pattern similar to that of NO regardless of the presence of leukemia inhibitory factor. CONCLUSIONS These results are the first demonstrating that the miR-200 family and Sip1/ZEB2 transcription factor are regulated by NO, indicating an unprecedented molecular circuitry important for telomerase regulation and early differentiation of mES.
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Affiliation(s)
- Jessica Rosati
- Laboratorio di Patologia Vascolare, Istituto Dermopatico dell'Immacolata-IRCCS, Rome, Italy
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Vourc'h C, Biamonti G. Transcription of Satellite DNAs in Mammals. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2011; 51:95-118. [PMID: 21287135 DOI: 10.1007/978-3-642-16502-3_5] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Centromeric and pericentric regions have long been regarded as transcriptionally inert portions of chromosomes. A number of studies in the past 10 years disproved this dogma and provided convincing evidence that centromeric and pericentric sequences are transcriptionally active in several biological contexts.In this chapter, we provide a comprehensive picture of the various contexts (cell growth and differentiation, stress, effect of chromatin organization) in which these sequences are expressed in mouse and human cells and discuss the possible functional implications of centromeric and pericentric sequences activation and/or of the resulting noncoding RNAs. Moreover, we provide an overview of the molecular mechanisms underlying the activation of centromeric and pericentromeric sequences as well as the structural features of encoded RNAs.
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Affiliation(s)
- Claire Vourc'h
- INSERM U823; Institut Albert Bonniot, Université Joseph Fourier-Grenoble, La Tronche BP170, 38042, Grenoble cedex 9, France,
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42
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Probst AV, Okamoto I, Casanova M, El Marjou F, Le Baccon P, Almouzni G. A strand-specific burst in transcription of pericentric satellites is required for chromocenter formation and early mouse development. Dev Cell 2010; 19:625-38. [PMID: 20951352 DOI: 10.1016/j.devcel.2010.09.002] [Citation(s) in RCA: 242] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 07/01/2010] [Accepted: 08/18/2010] [Indexed: 01/21/2023]
Abstract
At the time of fertilization, the paternal genome lacks the typical configuration and marks characteristic of pericentric heterochromatin. It is thus essential to understand the dynamics of this region during early development, its importance during that time period and how a somatic configuration is attained. Here, we show that pericentric satellites undergo a transient peak in expression precisely at the time of chromocenter formation. This transcription is regulated in a strand-specific manner in time and space and is strongly biased by the parental asymmetry. The transcriptional upregulation follows a developmental clock, yet when replication is blocked chromocenter formation is impeded. Furthermore, interference with major satellite transcripts using locked nucleic acid (LNA)-DNA gapmers results in developmental arrest before completion of chromocenter formation. We conclude that the exquisite strand-specific expression dynamics at major satellites during the 2-cell stage, with both up and downregulation, are necessary events for proper chromocenter organization and developmental progression.
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Affiliation(s)
- Aline V Probst
- Laboratory of Nuclear Dynamics and Genome Plasticity, Unité Mixte de Recherche, 218 Centre National de la Recherche Scientifique/Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 05, France
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43
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Bulchand S, Menon SD, George SE, Chia W. Muscle wasted: a novel component of the Drosophila histone locus body required for muscle integrity. J Cell Sci 2010; 123:2697-707. [DOI: 10.1242/jcs.063172] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Skeletal muscles arise by cellular differentiation and regulated gene expression. Terminal differentiation programmes such as muscle growth, extension and attachment to the epidermis, lead to maturation of the muscles. These events require changes in chromatin organization as genes are differentially regulated. Here, we identify and characterise muscle wasted (mute), a novel component of the Drosophila histone locus body (HLB). We demonstrate that a mutation in mute leads to severe loss of muscle mass and an increase in levels of normal histone transcripts. Importantly, Drosophila Myocyte enhancer factor 2 (Mef2), a central myogenic differentiation factor, and how, an RNA binding protein required for muscle and tendon cell differentiation, are downregulated. Mef2 targets are, in turn, misregulated. Notably, the degenerating muscles in mute mutants show aberrant localisation of heterochromatin protein 1 (HP1). We further show a genetic interaction between mute and the Stem-loop binding protein (Slbp) and a loss of muscle striations in Lsm11 mutants. These data demonstrate a novel role of HLB components and histone processing factors in the maintenance of muscle integrity. We speculate that mute regulates terminal muscle differentiation possibly through heterochromatic reorganisation.
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Affiliation(s)
- Sarada Bulchand
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - Sree Devi Menon
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - Simi Elizabeth George
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
| | - William Chia
- Temasek Lifesciences Laboratory, National University of Singapore, 1 Research Link, 117604, Singapore
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44
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Andrey P, Kiêu K, Kress C, Lehmann G, Tirichine L, Liu Z, Biot E, Adenot PG, Hue-Beauvais C, Houba-Hérin N, Duranthon V, Devinoy E, Beaujean N, Gaudin V, Maurin Y, Debey P. Statistical analysis of 3D images detects regular spatial distributions of centromeres and chromocenters in animal and plant nuclei. PLoS Comput Biol 2010; 6:e1000853. [PMID: 20628576 PMCID: PMC2900307 DOI: 10.1371/journal.pcbi.1000853] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Accepted: 06/03/2010] [Indexed: 12/16/2022] Open
Abstract
In eukaryotes, the interphase nucleus is organized in morphologically and/or functionally distinct nuclear "compartments". Numerous studies highlight functional relationships between the spatial organization of the nucleus and gene regulation. This raises the question of whether nuclear organization principles exist and, if so, whether they are identical in the animal and plant kingdoms. We addressed this issue through the investigation of the three-dimensional distribution of the centromeres and chromocenters. We investigated five very diverse populations of interphase nuclei at different differentiation stages in their physiological environment, belonging to rabbit embryos at the 8-cell and blastocyst stages, differentiated rabbit mammary epithelial cells during lactation, and differentiated cells of Arabidopsis thaliana plantlets. We developed new tools based on the processing of confocal images and a new statistical approach based on G- and F- distance functions used in spatial statistics. Our original computational scheme takes into account both size and shape variability by comparing, for each nucleus, the observed distribution against a reference distribution estimated by Monte-Carlo sampling over the same nucleus. This implicit normalization allowed similar data processing and extraction of rules in the five differentiated nuclei populations of the three studied biological systems, despite differences in chromosome number, genome organization and heterochromatin content. We showed that centromeres/chromocenters form significantly more regularly spaced patterns than expected under a completely random situation, suggesting that repulsive constraints or spatial inhomogeneities underlay the spatial organization of heterochromatic compartments. The proposed technique should be useful for identifying further spatial features in a wide range of cell types.
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Affiliation(s)
- Philippe Andrey
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
- UPMC, Université Paris 06, France
| | - Kiên Kiêu
- INRA, UR341, Mathématiques et Informatique Appliquées, Jouy-en-Josas, France
| | - Clémence Kress
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Gaëtan Lehmann
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Leïla Tirichine
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Zichuan Liu
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Eric Biot
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Pierre-Gaël Adenot
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Cathy Hue-Beauvais
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Nicole Houba-Hérin
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Véronique Duranthon
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Eve Devinoy
- INRA, UR1196 Génomique et Physiologie de la Lactation, Jouy-en-Josas, France
| | - Nathalie Beaujean
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
| | - Valérie Gaudin
- INRA, Institut J.-P. Bourgin, UMR1318 INRA-AgroParisTech, Versailles, France
| | - Yves Maurin
- INRA, UMR1197 Neurobiologie de l'Olfaction et de la Prise Alimentaire, Jouy-en-Josas, France
- Université Paris-Sud 11, UMR 1197, Orsay, France
- IFR144 Neuro-Sud Paris, France
| | - Pascale Debey
- INRA, UMR1198 Biologie du Développement et Reproduction, Jouy-en-Josas, France
- ENVA, Maisons Alfort, France
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Comparison of chromosome centromere topology in differentiating cells with myogenic potential. Folia Histochem Cytobiol 2010; 47:377-83. [PMID: 20164021 DOI: 10.2478/v10042-009-0037-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Chromosome territories (CT's) constitute the critical element of the intranuclear architecture. Position of these compartmentalized structures plays an important role in functioning of entire genome. Present study was to examine whether the centromeres position of chromosomes 4, X and Y can be changed during differentiation from myoblasts to myotubes. Topological analysis of these centromeres was based on two-dimensional fluorescent hybridization in situ (2D-FISH). During differentiation process the majority of X chromosome centromeres analyzed shifted to the peripheral part of a nucleus and similar phenomenon was observed with one of the chromosome 4 centromeres. Completely different tendency was noticed when investigating the location of the chromosome Y centromeres. Centromeres of this chromosome migrated to the centre of a nucleus. The results obtained demonstrated visible changes in chromosome topology along the myogenic stem cells differentiation.
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46
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Massé J, Laurent A, Nicol B, Guerrier D, Pellerin I, Deschamps S. Involvement of ZFPIP/Zfp462 in chromatin integrity and survival of P19 pluripotent cells. Exp Cell Res 2010; 316:1190-201. [DOI: 10.1016/j.yexcr.2010.02.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 02/18/2010] [Accepted: 02/23/2010] [Indexed: 01/27/2023]
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47
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Kress C, Ballester M, Devinoy E, Rijnkels M. Epigenetic modifications in 3D: nuclear organization of the differentiating mammary epithelial cell. J Mammary Gland Biol Neoplasia 2010; 15:73-83. [PMID: 20143138 DOI: 10.1007/s10911-010-9169-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 01/21/2010] [Indexed: 10/19/2022] Open
Abstract
During the development of tissues, complex programs take place to reach terminally differentiated states with specific gene expression profiles. Epigenetic regulations such as histone modifications and chromatin condensation have been implicated in the short and long-term control of transcription. It has recently been shown that the 3D spatial organization of chromosomes in the nucleus also plays a role in genome function. Indeed, the eukaryotic interphase nucleus contains sub-domains that are characterized by their enrichment in specific factors such as RNA Polymerase II, splicing machineries or heterochromatin proteins which render portions of the genome differentially permissive to gene expression. The positioning of individual genes relative to these sub-domains is thought to participate in the control of gene expression as an epigenetic mechanism acting in the nuclear space. Here, we review what is known about the sub-nuclear organization of mammary epithelial cells in connection with gene expression and epigenetics. Throughout differentiation, global changes in nuclear architecture occur, notably with respect to heterochromatin distribution. The positions of mammary-specific genes relative to nuclear sub-compartments varies in response to hormonal stimulation. The contribution of tissue architecture to cell differentiation in the mammary gland is also seen at the level of nuclear organization, which is sensitive to microenvironmental stimuli such as extracellular matrix signaling. In addition, alterations in nuclear organization are concomitant with immortalization and carcinogenesis. Thus, the fate of cells appears to be controlled by complex pathways connecting external signal integration, gene expression, epigenetic modifications and chromatin organization in the nucleus.
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Affiliation(s)
- Clémence Kress
- UR1196 Génomique et Physiologie de la Lactation, INRA, Domaine de Vilvert, F-78352, Jouy-en-Josas, France.
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48
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Marella NV, Seifert B, Nagarajan P, Sinha S, Berezney R. Chromosomal rearrangements during human epidermal keratinocyte differentiation. J Cell Physiol 2009; 221:139-46. [PMID: 19626667 DOI: 10.1002/jcp.21855] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Undifferentiated human epidermal keratinocytes are self-renewing stem cells that can be induced to undergo a program of differentiation by varying the calcium chloride concentration in the culture media. We utilize this model of cell differentiation and a 3D chromosome painting technique to document significant changes in the radial arrangement, morphology, and interchromosomal associations between the gene poor chromosome 18 and the gene rich chromosome 19 territories at discrete stages during keratinocyte differentiation. We suggest that changes observed in chromosomal territorial organization provides an architectural basis for genomic function during cell differentiation and provide further support for a chromosome territory code that contributes to gene expression at the global level.
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Affiliation(s)
- Narasimharao V Marella
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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49
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Snykers S, De Kock J, Rogiers V, Vanhaecke T. In vitro differentiation of embryonic and adult stem cells into hepatocytes: state of the art. Stem Cells 2009; 27:577-605. [PMID: 19056906 PMCID: PMC2729674 DOI: 10.1634/stemcells.2008-0963] [Citation(s) in RCA: 190] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Stem cells are a unique source of self-renewing cells within the human body. Before the end of the last millennium, adult stem cells, in contrast to their embryonic counterparts, were considered to be lineage-restricted cells or incapable of crossing lineage boundaries. However, the unique breakthrough of muscle and liver regeneration by adult bone marrow stem cells at the end of the 1990s ended this long-standing paradigm. Since then, the number of articles reporting the existence of multipotent stem cells in skin, neuronal tissue, adipose tissue, and bone marrow has escalated, giving rise, both in vivo and in vitro, to cell types other than their tissue of origin. The phenomenon of fate reprogrammation and phenotypic diversification remains, though, an enigmatic and rare process. Understanding how to control both proliferation and differentiation of stem cells and their progeny is a challenge in many fields, going from preclinical drug discovery and development to clinical therapy. In this review, we focus on current strategies to differentiate embryonic, mesenchymal(-like), and liver stem/progenitor cells into hepatocytes in vitro. Special attention is paid to intracellular and extracellular signaling, genetic modification, and cell-cell and cell-matrix interactions. In addition, some recommendations are proposed to standardize, optimize, and enrich the in vitro production of hepatocyte-like cells out of stem/progenitor cells.
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Affiliation(s)
- Sarah Snykers
- Department of Toxicology, Vrije Universiteit Brussel, Belgium.
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50
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Snykers S, Henkens T, De Rop E, Vinken M, Fraczek J, De Kock J, De Prins E, Geerts A, Rogiers V, Vanhaecke T. Role of epigenetics in liver-specific gene transcription, hepatocyte differentiation and stem cell reprogrammation. J Hepatol 2009; 51:187-211. [PMID: 19457566 DOI: 10.1016/j.jhep.2009.03.009] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Controlling both growth and differentiation of stem cells and their differentiated somatic progeny is a challenge in numerous fields, from preclinical drug development to clinical therapy. Recently, new insights into the underlying molecular mechanisms have unveiled key regulatory roles of epigenetic marks driving cellular pluripotency, differentiation and self-renewal/proliferation. Indeed, the transcription of genes, governing cell-fate decisions during development and maintenance of a cell's differentiated status in adult life, critically depends on the chromatin accessibility of transcription factors to genomic regulatory and coding regions. In this review, we discuss the epigenetic control of (liver-specific) gene-transcription and the intricate interplay between chromatin modulation, including histone (de)acetylation and DNA (de)methylation, and liver-enriched transcription factors. Special attention is paid to their role in directing hepatic differentiation of primary hepatocytes and stem cells in vitro.
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Affiliation(s)
- Sarah Snykers
- Department of Toxicology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium.
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