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Abstract
Immediately following the discovery of the structure of DNA and the semi-conservative replication of the parental DNA sequence into two new DNA strands, it became apparent that DNA replication is organized in a temporal and spatial fashion during the S phase of the cell cycle, correlated with the large-scale organization of chromatin in the nucleus. After many decades of limited progress, technological advances in genomics, genome engineering, and imaging have finally positioned the field to tackle mechanisms underpinning the temporal and spatial regulation of DNA replication and the causal relationships between DNA replication and other features of large-scale chromosome structure and function. In this review, we discuss these major recent discoveries as well as expectations for the coming decade.
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Affiliation(s)
- Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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2
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Courtot L, Bournique E, Maric C, Guitton-Sert L, Madrid-Mencía M, Pancaldi V, Cadoret JC, Hoffmann JS, Bergoglio V. Low Replicative Stress Triggers Cell-Type Specific Inheritable Advanced Replication Timing. Int J Mol Sci 2021; 22:ijms22094959. [PMID: 34066960 PMCID: PMC8125030 DOI: 10.3390/ijms22094959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 12/27/2022] Open
Abstract
DNA replication timing (RT), reflecting the temporal order of origin activation, is known as a robust and conserved cell-type specific process. Upon low replication stress, the slowing of replication forks induces well-documented RT delays associated to genetic instability, but it can also generate RT advances that are still uncharacterized. In order to characterize these advanced initiation events, we monitored the whole genome RT from six independent human cell lines treated with low doses of aphidicolin. We report that RT advances are cell-type-specific and involve large heterochromatin domains. Importantly, we found that some major late to early RT advances can be inherited by the unstressed next-cellular generation, which is a unique process that correlates with enhanced chromatin accessibility, as well as modified replication origin landscape and gene expression in daughter cells. Collectively, this work highlights how low replication stress may impact cellular identity by RT advances events at a subset of chromosomal domains.
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Affiliation(s)
- Lilas Courtot
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
| | - Elodie Bournique
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
| | - Chrystelle Maric
- Université de Paris, CNRS, Institut Jacques Monod, DNA Replication Pathologies Team, F-75006 Paris, France;
| | - Laure Guitton-Sert
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
| | - Miguel Madrid-Mencía
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
| | - Vera Pancaldi
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
- Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Jean-Charles Cadoret
- Université de Paris, CNRS, Institut Jacques Monod, DNA Replication Pathologies Team, F-75006 Paris, France;
- Correspondence: (J.-C.C.); (J.-S.H.); (V.B.)
| | - Jean-Sébastien Hoffmann
- Laboratoire de pathologie, Laboratoire d’excellence Toulouse Cancer, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irène-Joliot-Curie, CEDEX, 31059 Toulouse, France
- Correspondence: (J.-C.C.); (J.-S.H.); (V.B.)
| | - Valérie Bergoglio
- Centre de Recherches en Cancérologie de Toulouse (CRCT), UMR1037 Inserm, University Paul Sabatier III, ERL5294 CNRS, 2 Avenue Hubert Curien, 31037 Toulouse, France; (L.C.); (E.B.); (L.G.-S.); (M.M.-M.); (V.P.)
- Correspondence: (J.-C.C.); (J.-S.H.); (V.B.)
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3
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Chromosomal coordination and differential structure of asynchronous replicating regions. Nat Commun 2021; 12:1035. [PMID: 33589603 PMCID: PMC7884787 DOI: 10.1038/s41467-021-21348-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/18/2021] [Indexed: 02/05/2023] Open
Abstract
Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development. Most regions of the mammalian genome replicate both alleles in a synchronous manner, but some loci have been found to replicate asynchronously and the time of replication of each allele is different. Here the authors, by employing clonal mouse cells from a hybrid strain chart replication timing over the entire genome, using polymorphisms to distinguish between the paternal and maternal alleles.
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4
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Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol 2019; 20:721-737. [DOI: 10.1038/s41580-019-0162-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
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5
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Sima J, Chakraborty A, Dileep V, Michalski M, Klein KN, Holcomb NP, Turner JL, Paulsen MT, Rivera-Mulia JC, Trevilla-Garcia C, Bartlett DA, Zhao PA, Washburn BK, Nora EP, Kraft K, Mundlos S, Bruneau BG, Ljungman M, Fraser P, Ay F, Gilbert DM. Identifying cis Elements for Spatiotemporal Control of Mammalian DNA Replication. Cell 2019; 176:816-830.e18. [PMID: 30595451 PMCID: PMC6546437 DOI: 10.1016/j.cell.2018.11.036] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 10/01/2018] [Accepted: 11/21/2018] [Indexed: 01/09/2023]
Abstract
The temporal order of DNA replication (replication timing [RT]) is highly coupled with genome architecture, but cis-elements regulating either remain elusive. We created a series of CRISPR-mediated deletions and inversions of a pluripotency-associated topologically associating domain (TAD) in mouse ESCs. CTCF-associated domain boundaries were dispensable for RT. CTCF protein depletion weakened most TAD boundaries but had no effect on RT or A/B compartmentalization genome-wide. By contrast, deletion of three intra-TAD CTCF-independent 3D contact sites caused a domain-wide early-to-late RT shift, an A-to-B compartment switch, weakening of TAD architecture, and loss of transcription. The dispensability of TAD boundaries and the necessity of these "early replication control elements" (ERCEs) was validated by deletions and inversions at additional domains. Our results demonstrate that discrete cis-regulatory elements orchestrate domain-wide RT, A/B compartmentalization, TAD architecture, and transcription, revealing fundamental principles linking genome structure and function.
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Affiliation(s)
- Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | | | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Marco Michalski
- Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Nicolas P Holcomb
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Jesse L Turner
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Michelle T Paulsen
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | | | | | - Daniel A Bartlett
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Brian K Washburn
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Elphège P Nora
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA
| | - Katerina Kraft
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany; Institute for Medical and Human Genetics, Charité Universitäts Medizin Berlin, 13353 Berlin, Germany
| | - Benoit G Bruneau
- Gladstone Institute of Cardiovascular Disease and Roddenberry Center for Stem Cell Biology and Medicine, San Francisco, CA 94158, USA; Department of Pediatrics, Cardiovascular Research Institute, University of California at San Francisco, San Francisco, CA 94158, USA; Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mats Ljungman
- Departments of Radiation Oncology and Environmental Health Sciences, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Peter Fraser
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA; Nuclear Dynamics Program, The Babraham Institute, Cambridge CB22 3AT, UK
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA; UC San Diego, School of Medicine, La Jolla, CA 92037, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.
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6
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Sansam CG, Pietrzak K, Majchrzycka B, Kerlin MA, Chen J, Rankin S, Sansam CL. A mechanism for epigenetic control of DNA replication. Genes Dev 2018; 32:224-229. [PMID: 29483155 DOI: 10.1101/gad.306464.117] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/23/2018] [Indexed: 01/12/2023]
Abstract
DNA replication origins in hyperacetylated euchromatin fire preferentially during early S phase. However, how acetylation controls DNA replication timing is unknown. TICRR/TRESLIN is an essential protein required for the initiation of DNA replication. Here, we report that TICRR physically interacts with the acetyl-histone binding bromodomain (BRD) and extraterminal (BET) proteins BRD2 and BRD4. Abrogation of this interaction impairs TICRR binding to acetylated chromatin and disrupts normal S-phase progression. Our data reveal a novel function for BET proteins and establish the TICRR-BET interaction as a potential mechanism for epigenetic control of DNA replication.
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Affiliation(s)
- Courtney G Sansam
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA
| | - Katarzyna Pietrzak
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA
| | - Blanka Majchrzycka
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA
| | - Maciej A Kerlin
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA
| | - Jingrong Chen
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA
| | - Susannah Rankin
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA.,University of Oklahoma Health Sciences Center, Department of Cell Biology, Oklahoma City, Oklahoma 73104, USA
| | - Christopher L Sansam
- Oklahoma Medical Research Foundation, Cell Cycle and Cancer Biology Research Program, Oklahoma City, Oklahoma 73104, USA.,University of Oklahoma Health Sciences Center, Department of Cell Biology, Oklahoma City, Oklahoma 73104, USA
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7
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Zhang Y, Huang L, Fu H, Smith OK, Lin CM, Utani K, Rao M, Reinhold WC, Redon CE, Ryan M, Kim R, You Y, Hanna H, Boisclair Y, Long Q, Aladjem MI. A replicator-specific binding protein essential for site-specific initiation of DNA replication in mammalian cells. Nat Commun 2016; 7:11748. [PMID: 27272143 PMCID: PMC4899857 DOI: 10.1038/ncomms11748] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 04/26/2016] [Indexed: 12/28/2022] Open
Abstract
Mammalian chromosome replication starts from distinct sites; however, the principles governing initiation site selection are unclear because proteins essential for DNA replication do not exhibit sequence-specific DNA binding. Here we identify a replication-initiation determinant (RepID) protein that binds a subset of replication-initiation sites. A large fraction of RepID-binding sites share a common G-rich motif and exhibit elevated replication initiation. RepID is required for initiation of DNA replication from RepID-bound replication origins, including the origin at the human beta-globin (HBB) locus. At HBB, RepID is involved in an interaction between the replication origin (Rep-P) and the locus control region. RepID-depleted murine embryonic fibroblasts exhibit abnormal replication fork progression and fewer replication-initiation events. These observations are consistent with a model, suggesting that RepID facilitates replication initiation at a distinct group of human replication origins. Origins of mammalian DNA replication are poorly characterised because they lack an Identifiable consensus sequence. Here the authors identify RepID, a protein that binds to a subset of G-rich replication origins and facilitates initiation from those origins.
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Affiliation(s)
- Ya Zhang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Liang Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Owen K Smith
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Chii Mei Lin
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Koichi Utani
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Mishal Rao
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William C Reinhold
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Christophe E Redon
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Michael Ryan
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - RyangGuk Kim
- In Silico Solutions, Fairfax, Virginia 22033, USA
| | - Yang You
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Harlington Hanna
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yves Boisclair
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Qiaoming Long
- Department of Animal Science, Cornell University, Ithaca, New York 14853-4801, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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8
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Almouzni G, Cedar H. Maintenance of Epigenetic Information. Cold Spring Harb Perspect Biol 2016; 8:8/5/a019372. [PMID: 27141050 DOI: 10.1101/cshperspect.a019372] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genome is subject to a diverse array of epigenetic modifications from DNA methylation to histone posttranslational changes. Many of these marks are somatically stable through cell division. This article focuses on our knowledge of the mechanisms governing the inheritance of epigenetic marks, particularly, repressive ones, when the DNA and chromatin template are duplicated in S phase. This involves the action of histone chaperones, nucleosome-remodeling enzymes, histone and DNA methylation binding proteins, and chromatin-modifying enzymes. Last, the timing of DNA replication is discussed, including the question of whether this constitutes an epigenetic mark that facilitates the propagation of epigenetic marks.
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Affiliation(s)
- Geneviève Almouzni
- Department of Nuclear Dynamics and Genome Plasticity, Institut Curie, Section de recherche, 75231 Paris Cedex 05, France
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel 91120
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9
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Rivera-Mulia JC, Gilbert DM. Replication timing and transcriptional control: beyond cause and effect-part III. Curr Opin Cell Biol 2016; 40:168-178. [PMID: 27115331 DOI: 10.1016/j.ceb.2016.03.022] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 03/24/2016] [Accepted: 03/29/2016] [Indexed: 11/17/2022]
Abstract
DNA replication is essential for faithful transmission of genetic information and is intimately tied to chromosome structure and function. Genome duplication occurs in a defined temporal order known as the replication-timing (RT) program, which is regulated during the cell cycle and development in discrete units referred to as replication domains (RDs). RDs correspond to topologically-associating domains (TADs) and are spatio-temporally compartmentalized in the nucleus. While improvements in experimental tools have begun to reveal glimpses of causality, they have also unveiled complex context-dependent relationships that challenge long recognized correlations of RT to chromatin organization and gene regulation. In particular, RDs/TADs that switch RT during development march to the beat of a different drummer.
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Affiliation(s)
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4295, USA; Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, FL, USA.
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10
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Dileep V, Rivera-Mulia JC, Sima J, Gilbert DM. Large-Scale Chromatin Structure-Function Relationships during the Cell Cycle and Development: Insights from Replication Timing. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2015; 80:53-63. [PMID: 26590169 DOI: 10.1101/sqb.2015.80.027284] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromosome architecture has received a lot of attention since the recent development of genome-scale methods to measure chromatin interactions (Hi-C), enabling the first sequence-based models of chromosome tertiary structure. A view has emerged of chromosomes as a string of structural units (topologically associating domains; TADs) whose boundaries persist through the cell cycle and development. TADs with similar chromatin states tend to aggregate, forming spatially segregated chromatin compartments. However, high-resolution Hi-C has revealed substructure within TADs (subTADs) that poses a challenge for models that attribute significance to structural units at any given scale. More than 20 years ago, the DNA replication field independently identified stable structural (and functional) units of chromosomes (replication foci) as well as spatially segregated chromatin compartments (early and late foci), but lacked the means to link these units to genomic map units. Genome-wide studies of replication timing (RT) have now merged these two disciplines by identifying individual units of replication regulation (replication domains; RDs) that correspond to TADs and are arranged in 3D to form spatiotemporally segregated subnuclear compartments. Furthermore, classifying RDs/TADs by their constitutive versus developmentally regulated RT has revealed distinct classes of chromatin organization, providing unexpected insight into the relationship between large-scale chromosome structure and function.
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Affiliation(s)
- Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | | | - Jiao Sima
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306-4295 Center for Genomics and Personalized Medicine, Florida State University, Tallahassee, Florida 32306-4295
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11
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Dolgushin KV, Iudinkova ES, Petrova NV, Razin SV, Iarovaia OV. Joint locus of a/b-globin genes in Danio rerio is segregated into structural subdomains active at different stages of development. Mol Biol 2015. [DOI: 10.1134/s0026893315030048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Fritz A, Sinha S, Marella N, Berezney R. Alterations in replication timing of cancer-related genes in malignant human breast cancer cells. J Cell Biochem 2013; 114:1074-83. [PMID: 23161755 DOI: 10.1002/jcb.24447] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 01/13/2023]
Abstract
The replication timing of nine genes commonly involved in cancer was investigated in the MCF10 cell lines for human breast cancer progression. Six of these nine genes are part of a constellation of tumor suppressor genes that play a major role in familial human breast cancer (TP53, ATM, PTEN, CHK2, BRCA1, and BRCA2). Three other genes are involved in a large number of human cancers including breast as either tumor suppressors (RB1 and RAD51) or as an oncogene (cMYC). Five of these nine genes (TP53, RAD51, ATM, PTEN, and cMYC) show significant differences (P < 0.05) in replication timing between MCF10A normal human breast cells and the corresponding malignant MCF10CA1a cells. These differences are specific to the malignant state of the MCF10CA1a cells since there were no significant differences in the replication timing of these genes between normal MCF10A cells and the non-malignant cancer MCF10AT1 cells. Microarray analysis further demonstrated that three of these five genes (TP53, RAD51, and cMYC) showed significant changes in gene expression (≥2-fold) between normal and malignant cells. Our findings demonstrate an alteration in the replication timing of a small subset of cancer-related genes in malignant breast cancer cells. These alterations partially correlate with the major transcriptional changes characteristic of the malignant state in these cells.
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Affiliation(s)
- Andrew Fritz
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
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13
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Lo Sardo F, Lanzuolo C, Comoglio F, De Bardi M, Paro R, Orlando V. PcG-mediated higher-order chromatin structures modulate replication programs at the Drosophila BX-C. PLoS Genet 2013; 9:e1003283. [PMID: 23437006 PMCID: PMC3578750 DOI: 10.1371/journal.pgen.1003283] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2012] [Accepted: 12/14/2012] [Indexed: 12/03/2022] Open
Abstract
Polycomb group proteins (PcG) exert conserved epigenetic functions that convey maintenance of repressed transcriptional states, via post-translational histone modifications and high order structure formation. During S-phase, in order to preserve cell identity, in addition to DNA information, PcG-chromatin-mediated epigenetic signatures need to be duplicated requiring a tight coordination between PcG proteins and replication programs. However, the interconnection between replication timing control and PcG functions remains unknown. Using Drosophila embryonic cell lines, we find that, while presence of specific PcG complexes and underlying transcription state are not the sole determinants of cellular replication timing, PcG-mediated higher-order structures appear to dictate the timing of replication and maintenance of the silenced state. Using published datasets we show that PRC1, PRC2, and PhoRC complexes differently correlate with replication timing of their targets. In the fully repressed BX-C, loss of function experiments revealed a synergistic role for PcG proteins in the maintenance of replication programs through the mediation of higher-order structures. Accordingly, replication timing analysis performed on two Drosophila cell lines differing for BX-C gene expression states, PcG distribution, and chromatin domain conformation revealed a cell-type-specific replication program that mirrors lineage-specific BX-C higher-order structures. Our work suggests that PcG complexes, by regulating higher-order chromatin structure at their target sites, contribute to the definition and the maintenance of genomic structural domains where genes showing the same epigenetic state replicate at the same time. DNA replication is a tightly orchestrated process that precisely duplicates the entire genome during cell division to ensure that daughter cells inherit the same genetic information. The genome is replicated following a specific temporal program, where different segments replicate in distinct moments of the S phase correlating with active (early) and repressed (late) transcriptional state of resident genes. Moreover, replicating chromosomal domains are organized in the nuclear space, perhaps to guarantee the conservation of the same topological order in daughter cells. Epigenetic mechanisms, acting via chromatin organization, determine transcriptional states and must be maintained through cell division. Here, we analyzed in detail the link between Polycomb Group (PcG) proteins, higher-order chromatin structure, and replication timing in Drosophila. By using bioinformatic analyses combined with functional experiments, we show that Polycomb Repressive Complex 1 (PRC1), PRC2, and PhoRC differently correlate with replication timing of their targets and that transcription per se does not determine replication timing. Strikingly, by analyzing the PcG-regulated Bithorax Complex, where PRC1, PRC2, and PhoRC complexes are bound to repressed targets, we provide evidence for a synergistic role of PcG proteins in the modulation and maintenance of replication timing through the definition of specific, topologically distinct genomic domains.
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Affiliation(s)
- Federica Lo Sardo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Chiara Lanzuolo
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- CNR Institute of Cellular Biology and Neurobiology, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Federico Comoglio
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
| | - Marco De Bardi
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
| | - Renato Paro
- Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology Zürich, Basel, Switzerland
- Faculty of Science, University of Basel, Basel, Switzerland
| | - Valerio Orlando
- Dulbecco Telethon Institute, IRCCS Santa Lucia Foundation, Rome, Italy
- Neuroimmunology Unit, IRCCS Santa Lucia Foundation, Rome, Italy
- * E-mail:
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14
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Petrakis TG, Vougas K, Gorgoulis VG. Cdc6: a multi-functional molecular switch with critical role in carcinogenesis. Transcription 2012; 3:124-9. [PMID: 22771947 DOI: 10.4161/trns.20301] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Research in the last decade revealed an additional role for the Replication Licensing Factor Cdc6 in transcriptional regulation. This novel function has been linked to human cancer development. Here, we summarize all the findings arguing over a role of Cdc6 as a transcriptional repressor and shed light toward new research directions for this field.
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Affiliation(s)
- Thodoris G Petrakis
- Molecular Carcinogenesis Group, Department of Histology and Embryology, School of Medicine, University of Athens, Athens, Greece
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15
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Pope BD, Chandra T, Buckley Q, Hoare M, Ryba T, Wiseman FK, Kuta A, Wilson MD, Odom DT, Gilbert DM. Replication-timing boundaries facilitate cell-type and species-specific regulation of a rearranged human chromosome in mouse. Hum Mol Genet 2012; 21:4162-70. [PMID: 22736031 PMCID: PMC3441118 DOI: 10.1093/hmg/dds232] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 06/07/2012] [Accepted: 06/11/2012] [Indexed: 01/04/2023] Open
Abstract
In multicellular organisms, developmental changes to replication timing occur in 400-800 kb domains across half the genome. While examples of epigenetic control of replication timing have been described, a role for DNA sequence in mammalian replication-timing regulation has not been substantiated. To assess the role of DNA sequences in directing developmental changes to replication timing, we profiled replication timing in mice carrying a genetically rearranged Human Chromosome 21 (Hsa21). In two distinct mouse cell types, Hsa21 sequences maintained human-specific replication timing, except at points of Hsa21 rearrangement. Changes in replication timing at rearrangements extended up to 900 kb and consistently reconciled with the wild-type replication pattern at developmental boundaries of replication-timing domains. Our results are consistent with DNA sequence-driven regulation of Hsa21 replication timing during development and provide evidence that mammalian chromosomes consist of multiple independent units of replication-timing regulation.
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Affiliation(s)
- Benjamin D. Pope
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Tamir Chandra
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - Quinton Buckley
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Matthew Hoare
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
| | - Tyrone Ryba
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
| | - Frances K. Wiseman
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Anna Kuta
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Michael D. Wilson
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - Duncan T. Odom
- Cancer Research UK, Cambridge Research Institute, Cambridge CB2 0RE, UK
- Department of Oncology, Hutchison/MRC Research Centre, University of Cambridge, Cambridge CB2 0XZ, UK and
| | - David M. Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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16
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Comprehensive identification and annotation of cell type-specific and ubiquitous CTCF-binding sites in the human genome. PLoS One 2012; 7:e41374. [PMID: 22829947 PMCID: PMC3400636 DOI: 10.1371/journal.pone.0041374] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/20/2012] [Indexed: 12/17/2022] Open
Abstract
Chromatin insulators are DNA elements that regulate the level of gene expression either by preventing gene silencing through the maintenance of heterochromatin boundaries or by preventing gene activation by blocking interactions between enhancers and promoters. CCCTC-binding factor (CTCF), a ubiquitously expressed 11-zinc-finger DNA-binding protein, is the only protein implicated in the establishment of insulators in vertebrates. While CTCF has been implicated in diverse regulatory functions, CTCF has only been studied in a limited number of cell types across human genome. Thus, it is not clear whether the identified cell type-specific differences in CTCF-binding sites are functionally significant. Here, we identify and characterize cell type-specific and ubiquitous CTCF-binding sites in the human genome across 38 cell types designated by the Encyclopedia of DNA Elements (ENCODE) consortium. These cell type-specific and ubiquitous CTCF-binding sites show uniquely versatile transcriptional functions and characteristic chromatin features. In addition, we confirm the insulator barrier function of CTCF-binding and explore the novel function of CTCF in DNA replication. These results represent a critical step toward the comprehensive and systematic understanding of CTCF-dependent insulators and their versatile roles in the human genome.
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The chromatin backdrop of DNA replication: lessons from genetics and genome-scale analyses. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1819:794-801. [PMID: 22342530 DOI: 10.1016/j.bbagrm.2012.01.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/27/2012] [Accepted: 01/31/2012] [Indexed: 01/04/2023]
Abstract
The entire cellular genome must replicate during each cell cycle, but it is yet unclear how replication proceeds along with chromatin condensation and remodeling while ensuring the fidelity of the replicated genome. Mapping replication initiation sites can provide clues for the coordination of DNA replication and transcription on a whole-genome scale. Here we discuss recent insights obtained from genome-scale analyses of replication initiation sites and transcription in mammalian cells and ask how transcription and chromatin modifications affect the frequency of replication initiation events. We also discuss DNA sequences, such as insulators and replicators, which modulate replication and transcription of target genes, and use genome-wide maps of replication initiation sites to evaluate possible commonalities between replicators and chromatin insulators. This article is part of a Special Issue entitled: Chromatin in time and space.
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A key commitment step in erythropoiesis is synchronized with the cell cycle clock through mutual inhibition between PU.1 and S-phase progression. PLoS Biol 2010; 8. [PMID: 20877475 PMCID: PMC2943437 DOI: 10.1371/journal.pbio.1000484] [Citation(s) in RCA: 132] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 08/04/2010] [Indexed: 11/19/2022] Open
Abstract
Hematopoietic progenitors undergo differentiation while navigating several cell division cycles, but it is unknown whether these two processes are coupled. We addressed this question by studying erythropoiesis in mouse fetal liver in vivo. We found that the initial upregulation of cell surface CD71 identifies developmentally matched erythroblasts that are tightly synchronized in S-phase. We show that DNA replication within this but not subsequent cycles is required for a differentiation switch comprising rapid and simultaneous committal transitions whose precise timing was previously unknown. These include the onset of erythropoietin dependence, activation of the erythroid master transcriptional regulator GATA-1, and a switch to an active chromatin conformation at the β-globin locus. Specifically, S-phase progression is required for the formation of DNase I hypersensitive sites and for DNA demethylation at this locus. Mechanistically, we show that S-phase progression during this key committal step is dependent on downregulation of the cyclin-dependent kinase p57(KIP2) and in turn causes the downregulation of PU.1, an antagonist of GATA-1 function. These findings therefore highlight a novel role for a cyclin-dependent kinase inhibitor in differentiation, distinct to their known function in cell cycle exit. Furthermore, we show that a novel, mutual inhibition between PU.1 expression and S-phase progression provides a "synchromesh" mechanism that "locks" the erythroid differentiation program to the cell cycle clock, ensuring precise coordination of critical differentiation events.
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Karmakar S, Mahajan MC, Schulz V, Boyapaty G, Weissman SM. A multiprotein complex necessary for both transcription and DNA replication at the β-globin locus. EMBO J 2010; 29:3260-71. [PMID: 20808282 DOI: 10.1038/emboj.2010.204] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 07/29/2010] [Indexed: 12/17/2022] Open
Abstract
DNA replication, repair, transcription and chromatin structure are intricately associated nuclear processes, but the molecular links between these events are often obscure. In this study, we have surveyed the protein complexes that bind at β-globin locus control region, and purified and characterized the function of one such multiprotein complex from human erythroleukemic K562 cells. We further validated the existence of this complex in human CD34+ cell-derived normal erythroid cells. This complex contains ILF2/ILF3 transcription factors, p300 acetyltransferase and proteins associated with DNA replication, transcription and repair. RNAi knockdown of ILF2, a DNA-binding component of this complex, abrogates the recruitment of the complex to its cognate DNA sequence and inhibits transcription, histone acetylation and usage of the origin of DNA replication at the β-globin locus. These results imply a direct link between mammalian DNA replication, transcription and histone acetylation mediated by a single multiprotein complex.
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Affiliation(s)
- Subhradip Karmakar
- Department of Genetics, The Anlyan Center, Yale University School of Medicine, New Haven, CT, USA
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20
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Gene density profile reveals the marking of late replicated domains in the Drosophila melanogaster genome. Chromosoma 2010; 119:589-600. [PMID: 20602235 DOI: 10.1007/s00412-010-0280-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Revised: 06/04/2010] [Accepted: 06/07/2010] [Indexed: 10/19/2022]
Abstract
Regulation of replication timing has been a focus of many studies. It has been shown that numerous chromosomal regions switch their replication timing on cell differentiation in Drosophila and mice. However, it is not clear which features of these regions are essential for such regulation. In this study, we examined the organization of late underreplicated regions (URs) of the Drosophila melanogaster genome. When compared with their flanks, these regions showed decreased gene density. A detailed view revealed that these regions originate from unusual combination of short genes and long intergenic spacers. Furthermore, gene expression study showed that this pattern is mostly contributed by short testis-specific genes abundant in the URs. Based on these observations, we developed a genome scanning algorithm and identified 110 regions possessing similar gene density and transcriptional profiles. According to the published data, replication of these regions has been significantly shifted towards late S-phase in two Drosophila cell lines and in polytene chromosomes. Our results suggest that genomic organization of the underreplicated areas of Drosophila polytene chromosomes may be associated with the regulation of their replication timing.
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21
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Masai H, Matsumoto S, You Z, Yoshizawa-Sugata N, Oda M. Eukaryotic chromosome DNA replication: where, when, and how? Annu Rev Biochem 2010; 79:89-130. [PMID: 20373915 DOI: 10.1146/annurev.biochem.052308.103205] [Citation(s) in RCA: 370] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA replication is central to cell proliferation. Studies in the past six decades since the proposal of a semiconservative mode of DNA replication have confirmed the high degree of conservation of the basic machinery of DNA replication from prokaryotes to eukaryotes. However, the need for replication of a substantially longer segment of DNA in coordination with various internal and external signals in eukaryotic cells has led to more complex and versatile regulatory strategies. The replication program in higher eukaryotes is under a dynamic and plastic regulation within a single cell, or within the cell population, or during development. We review here various regulatory mechanisms that control the replication program in eukaryotes and discuss future directions in this dynamic field.
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Affiliation(s)
- Hisao Masai
- Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan.
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22
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Abstract
Studies of replication timing provide a handle into previously impenetrable higher-order levels of chromosome organization and their plasticity during development. Although mechanisms regulating replication timing are not clear, novel genome-wide studies provide a thorough survey of the extent to which replication timing is regulated during most of the early cell fate transitions in mammals, revealing coordinated changes of a defined set of 400-800 kb chromosomal segments that involve at least half the genome. Furthermore, changes in replication time are linked to changes in sub-nuclear organization and domain-wide transcriptional potential, and tissue-specific replication timing profiles are conserved from mouse to human, suggesting that the program has developmental significance. Hence, these studies have provided a solid foundation for linking megabase level chromosome structure to function, and suggest a central role for replication in domain-level genome organization.
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23
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Differences in the epigenetic and reprogramming properties of pluripotent and extra-embryonic stem cells implicate chromatin remodelling as an important early event in the developing mouse embryo. Epigenetics Chromatin 2010; 3:1. [PMID: 20157423 PMCID: PMC2821315 DOI: 10.1186/1756-8935-3-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Accepted: 01/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND During early mouse development, two extra-embryonic lineages form alongside the future embryo: the trophectoderm (TE) and the primitive endoderm (PrE). Epigenetic changes known to take place during these early stages include changes in DNA methylation and modified histones, as well as dynamic changes in gene expression. RESULTS In order to understand the role and extent of chromatin-based changes for lineage commitment within the embryo, we examined the epigenetic profiles of mouse embryonic stem (ES), trophectoderm stem (TS) and extra-embryonic endoderm (XEN) stem cell lines that were derived from the inner cell mass (ICM), TE and PrE, respectively. As an initial indicator of the chromatin state, we assessed the replication timing of a cohort of genes in each cell type, based on data that expressed genes and acetylated chromatin domains, generally, replicate early in S-phase, whereas some silent genes, hypoacetylated or condensed chromatin tend to replicate later. We found that many lineage-specific genes replicate early in ES, TS and XEN cells, which was consistent with a broadly 'accessible' chromatin that was reported previously for multiple ES cell lines. Close inspection of these profiles revealed differences between ES, TS and XEN cells that were consistent with their differing lineage affiliations and developmental potential. A comparative analysis of modified histones at the promoters of individual genes showed that in TS and ES cells many lineage-specific regulator genes are co-marked with modifications associated with active (H4ac, H3K4me2, H3K9ac) and repressive (H3K27me3) chromatin. However, in XEN cells several of these genes were marked solely by repressive modifications (such as H3K27me3, H4K20me3). Consistent with TS and XEN having a restricted developmental potential, we show that these cells selectively reprogramme somatic cells to induce the de novo expression of genes associated with extraembryonic differentiation. CONCLUSIONS These data provide evidence that the diversification of defined embryonic and extra-embryonic lineages is accompanied by chromatin remodelling at specific loci. Stem cell lines from the ICM, TE and PrE can each dominantly reprogramme somatic cells but reset gene expression differently, reflecting their separate lineage identities and increasingly restricted developmental potentials.
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24
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Yeshaya J, Amir I, Rimon A, Freedman J, Shohat M, Avivi L. Microdeletion syndromes disclose replication timing alterations of genes unrelated to the missing DNA. Mol Cytogenet 2009; 2:11. [PMID: 19284877 PMCID: PMC2660353 DOI: 10.1186/1755-8166-2-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/14/2009] [Indexed: 11/26/2022] Open
Abstract
Background The temporal order of allelic replication is interrelated to the epigenomic profile. A significant epigenetic marker is the asynchronous replication of monoallelically-expressed genes versus the synchronous replication of biallelically-expressed genes. The present study sought to determine whether a microdeletion in the genome affects epigenetic profiles of genes unrelated to the missing segment. In order to test this hypothesis, we checked the replication patterns of two genes – SNRPN, a normally monoallelically expressed gene (assigned to 15q11.13), and the RB1, an archetypic biallelically expressed gene (assigned to 13.q14) in the genomes of patients carrying the 22q11.2 deletion (DiGeorge/Velocardiofacial syndrome) and those carrying the 7q11.23 deletion (Williams syndrome). Results The allelic replication timing was determined by fluorescence in situ hybridization (FISH) technology performed on peripheral blood cells. As expected, in the cells of normal subjects the frequency of cells showing asynchronous replication for SNRPN was significantly (P < 10-12) higher than the corresponding value for RB1. In contrast, cells of the deletion-carrying patients exhibited a reversal in this replication pattern: there was a significantly lower frequency of cells engaging in asynchronous replication for SNRPN than for RB1 (P < 10-4 and P < 10-3 for DiGeorge/Velocardiofacial and Williams syndromes, respectively). Accordingly, the significantly lower frequency of cells showing asynchronous replication for SNRPN than for RB1 is a new epigenetic marker distinguishing these deletion syndrome genotypes from normal ones. Conclusion In cell samples of each deletion-carrying individual, an aberrant, reversed pattern of replication is delineated, namely, where a monoallelic gene replicates more synchronously than a biallelic gene. This inverted pattern, which appears to be non-deletion-specific, clearly distinguishes cells of deletion-carriers from normal ones. As such, it offers a potential epigenetic marker for suspecting a hidden microdeletion that is too small to be detected by conventional karyotyping methods.
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Affiliation(s)
- Josepha Yeshaya
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Itay Amir
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ayelet Rimon
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Jane Freedman
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel
| | - Mordechai Shohat
- Raphael Recanati Genetic Institute, Rabin Medical Center Beilinson Campus, Petah-Tikva, Israel.,Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Pediatrics C, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Lydia Avivi
- Department of Human Molecular Genetics & Biochemistry, Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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25
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Abstract
Although early replication has long been associated with accessible chromatin, replication timing is not included in most discussions of epigenetic marks. This is partly due to a lack of understanding of the mechanisms behind this association but the issue has also been confounded by studies concluding that there are very few changes in replication timing during development. Recently, the first genome-wide study of replication timing during the course of differentiation revealed extensive changes that were strongly associated with changes in transcriptional activity and subnuclear organization. Domains of temporally coordinate replication delineate discrete units of chromosome structure and function that are characteristic of particular differentiation states. Hence, although we are still a long way from understanding the functional significance of replication timing, it is clear that replication timing is a distinct epigenetic signature of cell differentiation state.
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Affiliation(s)
- Ichiro Hiratani
- Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA
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26
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Dotan ZA, Dotan A, Ramon J, Avivi L. Aberrant allele-specific replication, independent of parental origin, in blood cells of cancer patients. BMC Cancer 2008; 8:390. [PMID: 19109880 PMCID: PMC2629776 DOI: 10.1186/1471-2407-8-390] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2008] [Accepted: 12/25/2008] [Indexed: 11/10/2022] Open
Abstract
Background Allelic counterparts of biallelically expressed genes display an epigenetic symmetry normally manifested by synchronous replication, different from genes subjected to monoallelic expression, which normally are characterized by an asynchronous mode of replication (well exemplified by the SNRPN imprinted locus). Malignancy was documented to be associated with gross modifications in the inherent replication-timing coordination between allelic counterparts of imprinted genes as well as of biallelically expressed loci. The cancer-related allelic replication timing aberrations are non-disease specific and appear in peripheral blood cells of cancer patients, including those with solid tumors. As such they offer potential blood markers for non-invasive cancer test. The present study was aimed to gain some insight into the mechanism leading to the replication timing alterations of genes in blood lymphocytes of cancer patients. Methods Peripheral blood samples derived from patients with prostate cancer were chosen to represent the cancerous status, and samples taken from patients with no cancer but with benign prostate hyperplasia were used to portray the normal status. Fluorescence In Situ Hybridization (FISH) replication assay, applied to phytohemagglutinin (PHA)-stimulated blood lymphocytes, was used to evaluate the temporal order (either synchronous or asynchronous) of genes in the patients' cells. Results We demonstrated that: (i) the aberrant epigenetic profile, as delineated by the cancer status, is a reversible modification, evidenced by our ability to restore the normal patterns of replication in three unrelated loci (CEN15, SNRPN and RB1) by introducing an archetypical demethylating agent, 5-azacytidine; (ii) following the rehabilitating effect of demethylation, an imprinted gene (SNRPN) retains its original parental imprint; and (iii) the choice of an allele between early or late replication in the aberrant asynchronous replication, delineated by the cancer status, is not random but is independent of the parental origin. Conclusion The non-disease specific aberrant epigenetic profile displayed in peripheral blood cells of patients with a solid tumour (unlike genetic aberrations) can be reversed, by an epigenetic drug applied in vitro, to the normal. It appears that the cancerous status differentiates between two allelic counterparts in a non-random manner, but independent of the parental origin
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Affiliation(s)
- Zohar A Dotan
- Department of Urology, Sheba Medical Center, Tel-Hashomer 52621, Israel.
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27
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Farkash-Amar S, Lipson D, Polten A, Goren A, Helmstetter C, Yakhini Z, Simon I. Global organization of replication time zones of the mouse genome. Genome Res 2008; 18:1562-70. [PMID: 18669478 DOI: 10.1101/gr.079566.108] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The division of genomes into distinct replication time zones has long been established. However, an in-depth understanding of their organization and their relationship to transcription is incomplete. Taking advantage of a novel synchronization method ("baby machine") and of genomic DNA microarrays, we have, for the first time, mapped replication times of the entire mouse genome at a high temporal resolution. Our data revealed that although most of the genome has a distinct time of replication either early, middle, or late S phase, a significant portion of the genome is replicated asynchronously. Analysis of the replication map revealed the genomic scale organization of the replication time zones. We found that the genomic regions between early and late replication time zones often consist of extremely large replicons. Analysis of the relationship between replication and transcription revealed that early replication is frequently correlated with the transcription potential of a gene and not necessarily with its actual transcriptional activity. These findings, along with the strong conservation found between replication timing in human and mouse genomes, emphasize the importance of replication timing in transcription regulation.
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Affiliation(s)
- Shlomit Farkash-Amar
- Department of Molecular Biology, Hebrew University Medical School Jerusalem 91120, Israel
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28
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Goren A, Tabib A, Hecht M, Cedar H. DNA replication timing of the human beta-globin domain is controlled by histone modification at the origin. Genes Dev 2008; 22:1319-24. [PMID: 18443145 DOI: 10.1101/gad.468308] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The human beta-globin genes constitute a large chromosomal domain that is developmentally regulated. In nonerythroid cells, these genes replicate late in S phase, while in erythroid cells, replication is early. The replication origin is packaged with acetylated histones in erythroid cells, yet is associated with deacetylated histones in nonerythroid cells. Recruitment of histone acetylases to this origin brings about a transcription-independent shift to early replication in lymphocytes. In contrast, tethering of a histone deacetylase in erythroblasts causes a shift to late replication. These results suggest that histone modification at the origin serves as a binary switch for controlling replication timing.
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Affiliation(s)
- Alon Goren
- Department of Cellular Biochemistry and Human Genetics, Hebrew University Medical School, Ein Kerem, Jerusalem 91120, Israel
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29
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Karnani N, Taylor C, Malhotra A, Dutta A. Pan-S replication patterns and chromosomal domains defined by genome-tiling arrays of ENCODE genomic areas. Genome Res 2007; 17:865-76. [PMID: 17568004 PMCID: PMC1891345 DOI: 10.1101/gr.5427007] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In eukaryotes, accurate control of replication time is required for the efficient completion of S phase and maintenance of genome stability. We present a high-resolution genome-tiling array-based profile of replication timing for approximately 1% of the human genome studied by The ENCODE Project Consortium. Twenty percent of the investigated segments replicate asynchronously (pan-S). These areas are rich in genes and CpG islands, features they share with early-replicating loci. Interphase FISH showed that pan-S replication is a consequence of interallelic variation in replication time and is not an artifact derived from a specific cell cycle synchronization method or from aneuploidy. The interallelic variation in replication time is likely due to interallelic variation in chromatin environment, because while the early- or late-replicating areas were exclusively enriched in activating or repressing histone modifications, respectively, the pan-S areas had both types of histone modification. The replication profile of the chromosomes identified contiguous chromosomal segments of hundreds of kilobases separated by smaller segments where the replication time underwent an acute transition. Close examination of one such segment demonstrated that the delay of replication time was accompanied by a decrease in level of gene expression and appearance of repressive chromatin marks, suggesting that the transition segments are boundary elements separating chromosomal domains with different chromatin environments.
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Affiliation(s)
- Neerja Karnani
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Christopher Taylor
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Department of Computer Science, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Ankit Malhotra
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Department of Computer Science, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
- Corresponding author.E-mail ; fax (434) 924-5069
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30
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Aladjem MI. Replication in context: dynamic regulation of DNA replication patterns in metazoans. Nat Rev Genet 2007; 8:588-600. [PMID: 17621316 DOI: 10.1038/nrg2143] [Citation(s) in RCA: 153] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Replication in eukaryotes initiates from discrete genomic regions according to a strict, often tissue-specific temporal programme. However, the locations of initiation events within initiation regions vary, show sequence disparity and are affected by interactions with distal elements. Increasing evidence suggests that specification of replication sites and the timing of replication are dynamic processes that are regulated by tissue-specific and developmental cues, and are responsive to epigenetic modifications. Dynamic specification of replication patterns might serve to prevent or resolve possible spatial and/or temporal conflicts between replication, transcription and chromatin assembly, and facilitate subtle or extensive changes of gene expression during differentiation and development.
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Affiliation(s)
- Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, National Institutes of Health, Building 37, Room 5056, 37 Convent Drive, Bethesda, Maryland 20892-4255, USA.
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31
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Abstract
Pluripotent stem cells, similar to more restricted stem cells, are able to both self-renew and generate differentiated progeny. Although this dual functionality has been much studied, the search for molecular signatures of 'stemness' and pluripotency is only now beginning to gather momentum. While the focus of much of this work has been on the transcriptional features of embryonic stem cells, recent studies have indicated the importance of unique epigenetic profiles that keep key developmental genes 'poised' in a repressed but activatable state. Determining how these epigenetic features relate to the transcriptional signatures of ES cells, and whether they are also important in other types of stem cell, is a key challenge for the future.
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Affiliation(s)
- Mikhail Spivakov
- Lymphocyte Development Group, MRC Clinical Sciences Centre, Imperial College School of Medicine, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
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32
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Goren A, Simchen G, Fibach E, Szabo PE, Tanimoto K, Chakalova L, Pfeifer GP, Fraser PJ, Engel JD, Cedar H. Fine tuning of globin gene expression by DNA methylation. PLoS One 2006; 1:e46. [PMID: 17183675 PMCID: PMC1762317 DOI: 10.1371/journal.pone.0000046] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2006] [Accepted: 10/13/2006] [Indexed: 11/18/2022] Open
Abstract
Expression patterns in the globin gene cluster are subject to developmental regulation in vivo. While the γA and γG genes are expressed in fetal liver, both are silenced in adult erythrocytes. In order to decipher the role of DNA methylation in this process, we generated a YAC transgenic mouse system that allowed us to control γA methylation during development. DNA methylation causes a 20-fold repression of γA both in non-erythroid and adult erythroid cells. In erythroid cells this modification works as a dominant mechanism to repress γ gene expression, probably through changes in histone acetylation that prevent the binding of erythroid transcription factors to the promoter. These studies demonstrate that DNA methylation serves as an elegant in vivo fine-tuning device for selecting appropriate genes in the globin locus. In addition, our findings provide a mechanism for understanding the high levels of γ-globin transcription seen in patients with Hereditary Persistence of Fetal Hemoglobin, and help explain why 5azaC and butyrate compounds stimulate γ-globin expression in patients with β-hemoglobinopathies.
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Affiliation(s)
- Alon Goren
- Department of Cellular Biochemistry and Human Genetics, Hebrew UniversityJerusalem, Israel
| | - Giora Simchen
- Department of Genetics, Hebrew UniversityJerusalem, Israel
| | - Eitan Fibach
- Department of Hematology, Hebrew UniversityJerusalem, Israel
| | - Piroska E. Szabo
- Division of Biology, Beckman Research Institute of the City of HopeDuarte, California, United States of America
| | - Keiji Tanimoto
- Graduate School of Life and Environmental Sciences, University of TsukubaTsukuba, Japan
| | - Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham InstituteCambridge, United Kingdom
| | - Gerd P. Pfeifer
- Division of Biology, Beckman Research Institute of the City of HopeDuarte, California, United States of America
| | - Peter J. Fraser
- Laboratory of Chromatin and Gene Expression, The Babraham InstituteCambridge, United Kingdom
| | - James D. Engel
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann ArborMichigan, United States of America
| | - Howard Cedar
- Department of Cellular Biochemistry and Human Genetics, Hebrew UniversityJerusalem, Israel
- * To whom correspondence should be addressed. E-mail:
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33
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Holmquist GP, Ashley T. Chromosome organization and chromatin modification: influence on genome function and evolution. Cytogenet Genome Res 2006; 114:96-125. [PMID: 16825762 DOI: 10.1159/000093326] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2005] [Accepted: 12/15/2005] [Indexed: 11/19/2022] Open
Abstract
Histone modifications of nucleosomes distinguish euchromatic from heterochromatic chromatin states, distinguish gene regulation in eukaryotes from that of prokaryotes, and appear to allow eukaryotes to focus recombination events on regions of highest gene concentrations. Four additional epigenetic mechanisms that regulate commitment of cell lineages to their differentiated states are involved in the inheritance of differentiated states, e.g., DNA methylation, RNA interference, gene repositioning between interphase compartments, and gene replication time. The number of additional mechanisms used increases with the taxon's somatic complexity. The ability of siRNA transcribed from one locus to target, in trans, RNAi-associated nucleation of heterochromatin in distal, but complementary, loci seems central to orchestration of chromatin states along chromosomes. Most genes are inactive when heterochromatic. However, genes within beta-heterochromatin actually require the heterochromatic state for their activity, a property that uniquely positions such genes as sources of siRNA to target heterochromatinization of both the source locus and distal loci. Vertebrate chromosomes are organized into permanent structures that, during S-phase, regulate simultaneous firing of replicon clusters. The late replicating clusters, seen as G-bands during metaphase and as meiotic chromomeres during meiosis, epitomize an ontological utilization of all five self-reinforcing epigenetic mechanisms to regulate the reversible chromatin state called facultative (conditional) heterochromatin. Alternating euchromatin/heterochromatin domains separated by band boundaries, and interphase repositioning of G-band genes during ontological commitment can impose constraints on both meiotic interactions and mammalian karyotype evolution.
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Affiliation(s)
- G P Holmquist
- Biology Department, City of Hope Medical Center, Duarte, CA, USA.
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34
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Feng YQ, Desprat R, Fu H, Olivier E, Lin CM, Lobell A, Gowda SN, Aladjem MI, Bouhassira EE. DNA methylation supports intrinsic epigenetic memory in mammalian cells. PLoS Genet 2006; 2:e65. [PMID: 16683039 PMCID: PMC1449906 DOI: 10.1371/journal.pgen.0020065] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 03/17/2006] [Indexed: 12/31/2022] Open
Abstract
We have investigated the role of DNA methylation in the initiation and maintenance of silenced chromatin in somatic mammalian cells. We found that a mutated transgene, in which all the CpG dinucleotides have been eliminated, underwent transcriptional silencing to the same extent as the unmodified transgene. These observations demonstrate that DNA methylation is not required for silencing. The silenced CpG-free transgene exhibited all the features of heterochromatin, including silencing of transcriptional activity, delayed DNA replication, lack of histone H3 and H4 acetylation, lack of H3-K4 methylation, and enrichment in tri-methyl-H3-K9. In contrast, when we tested for transgene reactivation using a Cre recombinase-mediated inversion assay, we observed a marked difference between a CpG-free and an unmodified transgene: the CpG-free transgene resumed transcription and did not exhibit markers of heterochromatin whereas the unmodified transgene remained silenced. These data indicate that methylation of CpG residues conferred epigenetic memory in this system. These results also suggest that replication delay, lack of histone H3 and H4 acetylation, H3-K4 methylation, and enrichment in tri-methyl-H3-K9 are not sufficient to confer epigenetic memory. We propose that DNA methylation within transgenes serves as an intrinsic epigenetic memory to permanently silence transgenes and prevent their reactivation.
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Affiliation(s)
- Yong-Qing Feng
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Romain Desprat
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Haiqing Fu
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Emmanuel Olivier
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Chii Mei Lin
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Amanda Lobell
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
| | - Shilpa N Gowda
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Mirit I Aladjem
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Eric E Bouhassira
- Department of Medicine, Division of Hematology, and Department of Cell Biology, Albert Einstein College Of Medicine, Bronx, New York, New York, United States of America
- * To whom correspondence should be addressed. E-mail:
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35
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Fu H, Wang L, Lin CM, Singhania S, Bouhassira EE, Aladjem MI. Preventing gene silencing with human replicators. Nat Biotechnol 2006; 24:572-6. [PMID: 16604060 DOI: 10.1038/nbt1202] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2005] [Accepted: 02/09/2006] [Indexed: 11/09/2022]
Abstract
Transcriptional silencing, one of the major impediments to gene therapy in humans, is often accompanied by replication during late S-phase. We report that transcriptional silencing and late replication were prevented by DNA sequences that can initiate DNA replication (replicators). When replicators were included in silencing-prone transgenes, they did not undergo transcriptional silencing, replicated early and maintained histone acetylation patterns characteristic of euchromatin. A mutant replicator, which could not initiate replication, could not prevent gene silencing and replicated late when included in identical transgenes and inserted at identical locations. These observations suggest that replicators introduce epigenetic chromatin changes that facilitate initiation of DNA replication and affect gene silencing. Inclusion of functional replicators in gene therapy vectors may provide a tool for stabilizing gene expression patterns.
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Affiliation(s)
- Haiqing Fu
- Laboratory of Molecular Pharmacology, NCI, Bethesda, Maryland 20892, USA
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36
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Schwaiger M, Schübeler D. A question of timing: emerging links between transcription and replication. Curr Opin Genet Dev 2006; 16:177-83. [PMID: 16503127 DOI: 10.1016/j.gde.2006.02.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2005] [Accepted: 02/13/2006] [Indexed: 11/28/2022]
Abstract
The coordination of transcription and timing of DNA replication during the S phase of the cell cycle has recently been studied chromosome-wide in high resolution. This revealed that in the complex genome of higher eukaryotes actively transcribed genes are more likely to replicate early in S phase. Dynamic changes in chromatin structure and nuclear organization appear to provide the underlying mechanism to link transcription and replication. A possible evolutionary benefit for this connection might result from differential replication fidelity during S phase, and comparisons of the human and chimpanzee genomes are compatible with this hypothesis.
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Affiliation(s)
- Michaela Schwaiger
- Friedrich-Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland
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37
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Chakalova L, Debrand E, Mitchell JA, Osborne CS, Fraser P. Replication and transcription: shaping the landscape of the genome. Nat Rev Genet 2006; 6:669-77. [PMID: 16094312 DOI: 10.1038/nrg1673] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
As the relationship between nuclear structure and function begins to unfold, a picture is emerging of a dynamic landscape that is centred on the two main processes that execute the regulated use and propagation of the genome. Rather than being subservient enzymatic activities, the replication and transcriptional machineries provide potent forces that organize the genome in three-dimensional nuclear space. Their activities provide opportunities for epigenetic changes that are required for differentiation and development. In addition, they impose physical constraints on the genome that might help to shape its evolution.
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Affiliation(s)
- Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge CB2 4AT, United Kingdom
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38
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Dean A. On a chromosome far, far away: LCRs and gene expression. Trends Genet 2005; 22:38-45. [PMID: 16309780 DOI: 10.1016/j.tig.2005.11.001] [Citation(s) in RCA: 134] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2005] [Revised: 09/29/2005] [Accepted: 11/09/2005] [Indexed: 11/20/2022]
Abstract
Transcription activation of a gene involves the ordered recruitment of components of the basal transcription machinery in concert with alterations in chromatin structure, including nucleosome remodeling and post-translational modification of histones. Enhancers and locus control regions (LCRs) that are remote from the genes they activate, recruit the complexes that carry out these alterations and, sometimes, recruit RNA polymerase II. The question of how these distant activators interact with their target genes has been of long-standing interest. Recent data indicate that LCRs mediate contact with their coordinate genes through the formation of domains of histone modification and of intra- and inter-chromosomal loops and that they might localize genes within nuclear regions that favor transcription.
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Affiliation(s)
- Ann Dean
- Laboratory of Cellular and Developmental Biology, NIDDK, NIH, Bethesda, MD 20892, USA.
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39
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Abstract
A large fraction of genes in the mammalian genome is repressed in every cell throughout development. Here, we propose that this long-term silencing is carried out by distinct molecular mechanisms that operate in a global manner and, once established, can be maintained autonomously through DNA replication. Both individually and in combination these mechanisms bring about repression, mainly by lowering gene accessibility through closed chromatin structures.
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Affiliation(s)
- Laura Lande-Diner
- Department of Cellular Biochemistry and Human Genetics, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel
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40
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Rodin SN, Parkhomchuk DV, Riggs AD. Epigenetic changes and repositioning determine the evolutionary fate of duplicated genes. BIOCHEMISTRY (MOSCOW) 2005; 70:559-67. [PMID: 15948709 DOI: 10.1007/s10541-005-0149-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Consideration of epigenetic silencing, perhaps by DNA methylation, led to an epigenetic complementation (EC) model for evolution by gene duplication (Rodin and Riggs (2003) J. Mol. Evol., 56, 718-729). This and subsequent work on genome-wide analyses of gene duplicates in several eukaryotic species pointed to a fundamental link between localization in the genome, epigenetic regulation of expression, and the evolutionary fate of new redundant gene copies, which can be either non- or neo-functionalization. Our main message in this report is that repositioning of a new duplicate to an ectopic site epigenetically alters its expression pattern, and concomitantly the rate and direction of mutations. Furthermore, comparison of syntenic vs. non-syntenic pairs of gene duplicates of different age unambiguously indicates that repositioning saves redundant gene duplicates from pseudogenization and hastens their evolution towards a new development-time and tissue-specific pattern of function.
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Affiliation(s)
- S N Rodin
- Department of Theoretical Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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41
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Buzina A, Aladjem MI, Kolman JL, Wahl GM, Ellis J. Initiation of DNA replication at the human beta-globin 3' enhancer. Nucleic Acids Res 2005; 33:4412-24. [PMID: 16085752 PMCID: PMC1183104 DOI: 10.1093/nar/gki747] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The origin of DNA replication in the human β-globin gene contains an initiation region (IR) and two flanking auxiliary elements. Two replicator modules are located within the upstream auxiliary sequence and the IR core, but the functional sequences in the downstream auxiliary element are unknown. Here, we use a combination of benzoylated-naphthoylated DEAE (BND) cellulose purification and nascent strand abundance assays to show that replication initiation occurs at the β-globin 3′ enhancer on human chromosome 11 in the Hu11 hybrid murine erythroleukemia (MEL) cell line. To examine replicator function, 3′ enhancer fragments were inserted into an ectopic site in MEL cells via an optimized FRT/EGFP-FLP integration system. These experiments demonstrate that the 1.6 kb downstream auxiliary element is a third replicator module called bGRep-E in erythroid cells. The minimal 260 bp 3′ enhancer is required but not sufficient to initiate efficient replication, suggesting cooperation with adjacent sequences. The minimal 3′ enhancer also cooperates with elements in an expressing HS3β/γ-globin construct to initiate replication. These data indicate that the β-globin replicator has multiple initiation sites in three closely spaced replicator modules. We conclude that a mammalian enhancer can cooperate with adjacent sequences to create an efficient replicator module.
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Affiliation(s)
- Alla Buzina
- Developmental Biology Program, Hospital for Sick ChildrenToronto, Ontario, Canada
| | | | - John L. Kolman
- Gene Expression Laboratory, The Salk InstituteSan Diego, CA
| | | | - James Ellis
- Developmental Biology Program, Hospital for Sick ChildrenToronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of TorontoToronto, Ontario, Canada
- To whom correspondence should be addressed. Tel: 416 813 7295; Fax: 416 813 8883;
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42
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Mesner LD, Hamlin JL. Specific signals at the 3' end of the DHFR gene define one boundary of the downstream origin of replication. Genes Dev 2005; 19:1053-66. [PMID: 15879555 PMCID: PMC1091740 DOI: 10.1101/gad.1307105] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The Chinese hamster dihydrofolate reductase (DHFR) origin of replication consists of a 55-kb zone of potential initiation sites lying between the convergently transcribed DHFR and 2BE2121 genes. Two subregions within this zone (ori-beta/ori-beta' and ori-gamma) are preferred. In the DHFR-deficient variant, DR8, which has deleted a 14-kb sequence straddling the 3' end of the DHFR gene, early-firing origin activity in the downstream ori-beta/ori-beta' and ori-gamma regions is completely suppressed. We show that the critical deleted sequences reside within a 168-bp segment encompassing the intron 5/exon 6 boundary, exon 6, 54 bp of the 3' untranslated region (UTR), but not the three natural polyA sites. In wild-type cells, this sequence efficiently arrests transcription in a region a few kilobases downstream, which coincides with the 5' boundary of the replication initiation zone. In DR8, DHFR-specific transcripts efficiently use an alternative sixth exon (6c) and polyA signals near the middle of the former intergenic region to process primary transcripts. However, transcription proceeds to a position almost 35 kb downstream from these signals, and replication initiation can only be detected beyond this point. When the wild-type 168-bp 3' element is inserted into DR8 at the same position as alternative exon 6c, transcription is arrested efficiently and initiations occur almost immediately downstream. Thus, the normal 3' end of the DHFR gene constitutes a boundary element not only for the gene but also for the local origin of replication.
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Affiliation(s)
- Larry D Mesner
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22908-0073, USA
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43
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Feng YQ, Warin R, Li T, Olivier E, Besse A, Lobell A, Fu H, Lin CM, Aladjem MI, Bouhassira EE. The human beta-globin locus control region can silence as well as activate gene expression. Mol Cell Biol 2005; 25:3864-74. [PMID: 15870261 PMCID: PMC1087713 DOI: 10.1128/mcb.25.10.3864-3874.2005] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Using recombinase-mediated cassette exchange to test multiple transgenes at the same site of integration, we demonstrate a novel chromatin context-dependent silencer activity of the beta-globin locus control region (LCR). This silencer activity requires DNase I hypersensitive sites HS2 and HS3 but not HS4. After silencing, the silenced cassettes adopt a typical closed chromatin conformation (histone H3 and H4 deacetylation, histone H3-K4 methylation, DNA methylation, and replication in late S phase). In the absence of the LCR at the same site of integration, the chromatin remains decondensed. We demonstrate that the LCR is necessary but not sufficient to trigger these chromatin changes. We also provide evidence that this novel silencing activity is caused by transcriptional interference triggered by activation of transcription in the flanking sequences by the LCR.
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Affiliation(s)
- Yong-Qing Feng
- Division of Hematology, Department of Medicine, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, USA
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44
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Jeon Y, Bekiranov S, Karnani N, Kapranov P, Ghosh S, MacAlpine D, Lee C, Hwang DS, Gingeras TR, Dutta A. Temporal profile of replication of human chromosomes. Proc Natl Acad Sci U S A 2005; 102:6419-24. [PMID: 15845769 PMCID: PMC1088349 DOI: 10.1073/pnas.0405088102] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Chromosomes in human cancer cells are expected to initiate replication from predictably localized origins, firing reproducibly at discrete times in S phase. Replication products obtained from HeLa cells at different stages of S phase were hybridized to cDNA and genome tiling oligonucleotide microarrays to determine the temporal profile of replication of human chromosomes on a genome-wide scale. About 1,000 genes and chromosomal segments were identified as sites containing efficient origins that fire reproducibly. Early replication was correlated with high gene density. An acute transition of gene density from early to late replicating areas suggests that discrete chromatin states dictate early versus late replication. Surprisingly, at least 60% of the interrogated chromosomal segments replicate equally in all quarters of S phase, suggesting that large stretches of chromosomes are replicated by inefficient, variably located and asynchronous origins and forks, producing a pan-S phase pattern of replication. Thus, at least for aneuploid cancer cells, a typical discrete time of replication in S phase is not seen for large segments of the chromosomes.
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Affiliation(s)
- Yesu Jeon
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
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45
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Abstract
The chromosomes of eukaryotic cells possess many potential DNA replication origins, of which a subset is selected in response to the cellular environment, such as the developmental stage, to act as active replication start sites. The mechanism of origin selection is not yet fully understood. In this review, we summarize recent observations regarding replication origins and initiator proteins in various organisms. These studies suggest that the DNA-binding specificities of the initiator proteins that bind to the replication origins and promote DNA replication are primarily responsible for origin selection. We particularly focus on the importance of transcription factors in the origin selection process. We propose that transcription factors are general regulators of the formation of functional complexes on the chromosome, including the replication initiation complex. We discuss the possible mechanisms by which transcription factors influence the selection of particular origins.
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Affiliation(s)
- Hidetsugu Kohzaki
- Department of Viral Oncology, Institute for Virus Research, Kyoto University, Japan.
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46
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Fields PE, Lee GR, Kim ST, Bartsevich VV, Flavell RA. Th2-specific chromatin remodeling and enhancer activity in the Th2 cytokine locus control region. Immunity 2004; 21:865-76. [PMID: 15589174 DOI: 10.1016/j.immuni.2004.10.015] [Citation(s) in RCA: 148] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2004] [Revised: 10/20/2004] [Accepted: 10/27/2004] [Indexed: 11/26/2022]
Abstract
We recently identified a 3' region of the rad50 gene possessing strong enhancer activity as well as activity consistent with function as a locus control region (LCR) for the flanking Th2 cytokine genes. In this study, we identify several functional elements within this region by examining chromatin changes as well as activity in transgenic mice. We find within this region four DNase I hypersensitive clusters, three of which are highly conserved and predominantly expressed in Th2 cells. Histone acetylation of this region is elevated in Th2 cells. Further, one of the hypersensitive sites (RHS7) is rapidly demethylated in Th2, but not Th1, cells. In transgenic mice, these hypersensitive sites impart strong, Th2-specific enhancer activity as well as copy number-dependent expression of the reporter gene, recapitulating LCR function. We postulate that these sites function alone or in combination with other regulatory elements to coordinate gene expression in the Th2 cytokine locus.
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Affiliation(s)
- Patrick E Fields
- Section of Immunobiology and Yale University School of Medicine, New Haven, CT 06520, USA
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47
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Abstract
Eukaryotic genomes are distributed on linear chromosomes that are grouped together in the nucleus, an organelle separated from the cytoplasm by a characteristic double membrane studded with large proteinaceous pores. The chromatin within chromosomes has an as yet poorly characterized higher-order structure, but in addition to this, chromosomes and specific subchromosomal domains are nonrandomly positioned in nuclei. This review examines functional implications of the long-range organization of the genome in interphase nuclei. A rigorous test of the physiological importance of nuclear architecture is achieved by introducing mutations that compromise both structure and function. Focussing on such genetic approaches, we address general concepts of interphase nuclear order, the role of the nuclear envelope (NE) and lamins, and finally the importance of spatial organization for DNA replication and heritable gene expression.
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Affiliation(s)
- Angela Taddei
- University of Geneva, Department of Molecular Biology, CH-1211 Geneva 4, Switzerland
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48
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Gómez M, Brockdorff N. Heterochromatin on the inactive X chromosome delays replication timing without affecting origin usage. Proc Natl Acad Sci U S A 2004; 101:6923-8. [PMID: 15105447 PMCID: PMC406443 DOI: 10.1073/pnas.0401854101] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
DNA replication origins (ORIs) map close to promoter regions in many organisms, including mammals. However, the relationship between initiation of replication and transcription is not well understood. To address this issue, we have analyzed replication timing and activity of several CpG island-associated ORIs on the transcriptionally active and silent X chromosomes. We find equivalent ORI usage and efficiency of both alleles at sites that are replicated late on the inactive X chromosome. Thus, in contrast to its repressive effect on transcription, heterochromatin does not influence ORI activity. These findings suggest that the relationship between sites of transcription and replication initiation at CpG island regions is restricted to early development, and that subsequent gene silencing and heterochromatin formation influence only the timing of ORI activation.
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Affiliation(s)
- María Gómez
- X Inactivation Group, Medical Research Council Clinical Sciences Centre, Faculty of Medicine, Imperial College for Science, Technology, and Medicine, Hammersmith Hospital, DuCane Road, London W12 0NN, United Kingdom
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49
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Biamonti G, Paixão S, Montecucco A, Peverali FA, Riva S, Falaschi A. Is DNA sequence sufficient to specify DNA replication origins in metazoan cells? Chromosome Res 2004; 11:403-12. [PMID: 12971717 DOI: 10.1023/a:1024910307162] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
DNA replication occupies a central position in the cell cycle and, therefore, in the development and life of multicellular organisms. During the last 10 years, our comprehension of this important process has considerably improved. Although the mechanisms that coordinate DNA replication with the other moments of the cell cycle are not yet fully understood, it is known that they mainly operate through DNA replication origins and the protein complexes bound to them. In eukaryotes, the packaging status of chromatin seems to be part of the mechanism that controls whether or not and when during the S-phase a particular origin will be activated. Intriguingly, the protein complexes bound to DNA replication origins appear to be directly involved in controlling chromatin packaging. In this manner they can also affect gene expression. In this review we focus on DNA replication origins in metazoan cells and on the relationship between these elements and the structural and functional organization of the genome.
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Affiliation(s)
- Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, Via Abbiategrasso 207, 27100 Pavia, Italy.
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50
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Razin SV, Farrell CM, Recillas-Targa F. Genomic domains and regulatory elements operating at the domain level. INTERNATIONAL REVIEW OF CYTOLOGY 2004; 226:63-125. [PMID: 12921236 DOI: 10.1016/s0074-7696(03)01002-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The sequencing of the complete genomes of several organisms, including humans, has so far not contributed much to our understanding of the mechanisms regulating gene expression in the course of realization of developmental programs. In this so-called "postgenomic" era, we still do not understand how (if at all) the long-range organization of the genome is related to its function. The domain hypothesis of the eukaryotic genome organization postulates that the genome is subdivided into a number of semiindependent functional units (domains) that may include one or several functionally related genes, with these domains having well-defined borders, and operate under the control of special (domain-level) regulatory systems. This hypothesis was extensively discussed in the literature over the past 15 years. Yet it is still unclear whether the hypothesis is valid or not. There is evidence both supporting and questioning this hypothesis. The most conclusive data supporting the domain hypothesis come from studies of avian and mammalian beta-globin domains. In this review we will critically discuss the present state of the studies on these and other genomic domains, paying special attention to the domain-level regulatory systems known as locus control regions (LCRs). Based on this discussion, we will try to reevaluate the domain hypothesis of the organization of the eukaryotic genome.
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Affiliation(s)
- Sergey V Razin
- Laboratory of Structural and Functional Organization of Chromosomes, Institute of Gene Biology of the Russian Academy of Sciences, 117334 Moscow, Russia
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