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DNA polymerase epsilon binds histone H3.1-H4 and recruits MORC1 to mediate meiotic heterochromatin condensation. Proc Natl Acad Sci U S A 2022; 119:e2213540119. [PMID: 36260743 PMCID: PMC9618065 DOI: 10.1073/pnas.2213540119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochromatin is essential for genomic integrity and stability in eukaryotes. The mechanisms that regulate meiotic heterochromatin formation remain largely undefined. Here, we show that the catalytic subunit (POL2A) of Arabidopsis DNA polymerase epsilon (POL ε) is required for proper formation of meiotic heterochromatin. The POL2A N terminus interacts with the GHKL adenosine triphosphatase (ATPase) MORC1 (Microrchidia 1), and POL2A is required for MORC1's localization on meiotic heterochromatin. Mutations affecting the POL2A N terminus cause aberrant morphology of meiotic heterochromatin, which is also observed in morc1. Moreover, the POL2A C-terminal zinc finger domain (ZF1) specifically binds to histone H3.1-H4 dimer or tetramer and is important for meiotic heterochromatin condensation. Interestingly, we also found similar H3.1-binding specificity for the mouse counterpart. Together, our results show that two distinct domains of POL2A, ZF1 and N terminus bind H3.1-H4 and recruit MORC1, respectively, to induce a continuous process of meiotic heterochromatin organization. These activities expand the functional repertoire of POL ε beyond its classic role in DNA replication and appear to be conserved in animals and plants.
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2
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Van Esch H, Colnaghi R, Freson K, Starokadomskyy P, Zankl A, Backx L, Abramowicz I, Outwin E, Rohena L, Faulkner C, Leong GM, Newbury-Ecob RA, Challis RC, Õunap K, Jaeken J, Seuntjens E, Devriendt K, Burstein E, Low KJ, O'Driscoll M. Defective DNA Polymerase α-Primase Leads to X-Linked Intellectual Disability Associated with Severe Growth Retardation, Microcephaly, and Hypogonadism. Am J Hum Genet 2019; 104:957-967. [PMID: 31006512 PMCID: PMC6506757 DOI: 10.1016/j.ajhg.2019.03.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 03/04/2019] [Indexed: 12/26/2022] Open
Abstract
Replicating the human genome efficiently and accurately is a daunting challenge involving the duplication of upward of three billion base pairs. At the core of the complex machinery that achieves this task are three members of the B family of DNA polymerases: DNA polymerases α, δ, and ε. Collectively these multimeric polymerases ensure DNA replication proceeds at optimal rates approaching 2 × 103 nucleotides/min with an error rate of less than one per million nucleotides polymerized. The majority of DNA replication of undamaged DNA is conducted by DNA polymerases δ and ε. The DNA polymerase α-primase complex performs limited synthesis to initiate the replication process, along with Okazaki-fragment synthesis on the discontinuous lagging strand. An increasing number of human disorders caused by defects in different components of the DNA-replication apparatus have been described to date. These are clinically diverse and involve a wide range of features, including variable combinations of growth delay, immunodeficiency, endocrine insufficiencies, lipodystrophy, and cancer predisposition. Here, by using various complementary approaches, including classical linkage analysis, targeted next-generation sequencing, and whole-exome sequencing, we describe distinct missense and splice-impacting mutations in POLA1 in five unrelated families presenting with an X-linked syndrome involving intellectual disability, proportionate short stature, microcephaly, and hypogonadism. POLA1 encodes the p180 catalytic subunit of DNA polymerase α-primase. A range of replicative impairments could be demonstrated in lymphoblastoid cell lines derived from affected individuals. Our findings describe the presentation of pathogenic mutations in a catalytic component of a B family DNA polymerase member, DNA polymerase α.
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Affiliation(s)
- Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium; Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium.
| | - Rita Colnaghi
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Kathleen Freson
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Andreas Zankl
- Department of Clinical Genetics, the Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Children's Hospital Westmead Clinical School, Sydney Medical School, the University of Sydney, Westmead, NSW 2145, Australia; Bone Biology Division and Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Liesbeth Backx
- Laboratory for the Genetics of Cognition, Department of Human Genetics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Iga Abramowicz
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Emily Outwin
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK
| | - Luis Rohena
- Division of Genetics, Department of Pediatrics, San Antonio Military Medical Center, San Antonio, TX 78234, USA
| | - Claire Faulkner
- Bristol Genetics Laboratory, Southmead Hospital, BS10 5NB Bristol, UK
| | - Gary M Leong
- Department of Paediatrics, Nepean Hospital, Nepean Clinical School, the University of Sydney, Kingswood, NSW 2747, Australia
| | - Ruth A Newbury-Ecob
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Rachel C Challis
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, EH4 2XU Edinburgh, UK
| | - Katrin Õunap
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital and Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
| | - Jacques Jaeken
- Center for Metabolic Diseases, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Eve Seuntjens
- Developmental Neurobiology, Department of Biology, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, 3000 Leuven, Belgium
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390 Texas, USA
| | - Karen J Low
- Clinical Genetics, St. Michael's Hospital, University Hospitals NHS Trust, BS2 8HW Bristol, UK
| | - Mark O'Driscoll
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Sussex, UK.
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3
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Coordinated regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. Proc Natl Acad Sci U S A 2017; 114:12524-12529. [PMID: 29109278 DOI: 10.1073/pnas.1712961114] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
During DNA replication, chromatin is disrupted ahead of the replication fork, and epigenetic information must be restored behind the fork. How epigenetic marks are inherited through DNA replication remains poorly understood. Histone H3 lysine 9 (H3K9) methylation and histone hypoacetylation are conserved hallmarks of heterochromatin. We previously showed that the inheritance of H3K9 methylation during DNA replication depends on the catalytic subunit of DNA polymerase epsilon, Cdc20. Here we show that the histone-fold subunit of Pol epsilon, Dpb4, interacts an uncharacterized small histone-fold protein, SPCC16C4.22, to form a heterodimer in fission yeast. We demonstrate that SPCC16C4.22 is nonessential for viability and corresponds to the true ortholog of Dpb3. We further show that the Dpb3-Dpb4 dimer associates with histone deacetylases, chromatin remodelers, and histones and plays a crucial role in the inheritance of histone hypoacetylation in heterochromatin. We solve the 1.9-Å crystal structure of Dpb3-Dpb4 and reveal that they form the H2A-H2B-like dimer. Disruption of Dpb3-Dpb4 dimerization results in loss of heterochromatin silencing. Our findings reveal a link between histone deacetylation and H3K9 methylation and suggest a mechanism for how two processes are coordinated during replication. We propose that the Dpb3-Dpb4 heterodimer together with Cdc20 serves as a platform for the recruitment of chromatin modifiers and remodelers that mediate heterochromatin assembly during DNA replication, and ensure the faithful inheritance of epigenetic marks in heterochromatin.
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4
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Acharya S, Hartmann M, Erhardt S. Chromatin-associated noncoding RNAs in development and inheritance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28840663 DOI: 10.1002/wrna.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sreemukta Acharya
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
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5
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O'Driscoll M. The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. J Pathol 2017; 241:192-207. [PMID: 27757957 DOI: 10.1002/path.4828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022]
Abstract
Accurate and efficient replication of the human genome occurs in the context of an array of constitutional barriers, including regional topological constraints imposed by chromatin architecture and processes such as transcription, catenation of the helical polymer and spontaneously generated DNA lesions, including base modifications and strand breaks. DNA replication is fundamentally important for tissue development and homeostasis; differentiation programmes are intimately linked with stem cell division. Unsurprisingly, impairments of the DNA replication machinery can have catastrophic consequences for genome stability and cell division. Functional impacts on DNA replication and genome stability have long been known to play roles in malignant transformation through a variety of complex mechanisms, and significant further insights have been gained from studying model organisms in this context. Congenital hypomorphic defects in components of the DNA replication machinery have been and continue to be identified in humans. These disorders present with a wide range of clinical features. Indeed, in some instances, different mutations in the same gene underlie different clinical presentations. Understanding the origin and molecular basis of these features opens a window onto the range of developmental impacts of suboptimal DNA replication and genome instability in humans. Here, I will briefly overview the basic steps involved in DNA replication and the key concepts that have emerged from this area of research, before switching emphasis to the pathological consequences of defects within the DNA replication network; the human disorders. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
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6
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Cenci G, Ciapponi L, Marzullo M, Raffa GD, Morciano P, Raimondo D, Burla R, Saggio I, Gatti M. The Analysis of Pendolino (peo) Mutants Reveals Differences in the Fusigenic Potential among Drosophila Telomeres. PLoS Genet 2015; 11:e1005260. [PMID: 26110638 PMCID: PMC4481407 DOI: 10.1371/journal.pgen.1005260] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 05/04/2015] [Indexed: 01/08/2023] Open
Abstract
Drosophila telomeres are sequence-independent structures that are maintained by transposition to chromosome ends of three specialized retroelements (HeT-A, TART and TAHRE; collectively designated as HTT) rather than telomerase activity. Fly telomeres are protected by the terminin complex (HOAP-HipHop-Moi-Ver) that localizes and functions exclusively at telomeres and by non-terminin proteins that do not serve telomere-specific functions. Although all Drosophila telomeres terminate with HTT arrays and are capped by terminin, they differ in the type of subtelomeric chromatin; the Y, XR, and 4L HTT are juxtaposed to constitutive heterochromatin, while the XL, 2L, 2R, 3L and 3R HTT are linked to the TAS repetitive sequences; the 4R HTT is associated with a chromatin that has features common to both euchromatin and heterochromatin. Here we show that mutations in pendolino (peo) cause telomeric fusions (TFs). The analysis of several peo mutant combinations showed that these TFs preferentially involve the Y, XR and 4th chromosome telomeres, a TF pattern never observed in the other 10 telomere-capping mutants so far characterized. peo encodes a non-terminin protein homologous to the E2 variant ubiquitin-conjugating enzymes. The Peo protein directly interacts with the terminin components, but peo mutations do not affect telomeric localization of HOAP, Moi, Ver and HP1a, suggesting that the peo-dependent telomere fusion phenotype is not due to loss of terminin from chromosome ends. peo mutants are also defective in DNA replication and PCNA recruitment. However, our results suggest that general defects in DNA replication are unable to induce TFs in Drosophila cells. We thus hypothesize that DNA replication in Peo-depleted cells results in specific fusigenic lesions concentrated in heterochromatin-associated telomeres. Alternatively, it is possible that Peo plays a dual function being independently required for DNA replication and telomere capping. Telomeres are specialized structures that protect chromosome ends from incomplete replication, degradation and end-to-end fusion. Abnormalities in telomere structure or maintenance can promote a variety of human diseases including premature aging and cancer. Although all human telomeres contain the same DNA sequences, they differ from each other in the subtelomeric regions or subtelomeres. Recent work has shown that human subtelomeres control telomere replication and that abnormalities in these structures can lead to localized chromosome instability and disease. However, the relationships between subtelomeres and telomeres are currently poorly understood. Here, we have addressed this problem using the fruit fly Drosophila melanogaster as model system. Drosophila subtelomers are very different from each other as they contain different types of chromatin. We have found that mutations in a gene we called pendolino (peo) cause telomeric fusions (TFs) and that these fusions preferentially involve the telomeres associated with a tightly packed form of chromatin called heterochromatin. Interestingly, none of the 10 mutants with TFs so far described in Drosophila shows the pattern of TFs observed in peo mutants. Thus, our data provide the first demonstration that subtelomeres can affect telomere fusion. We believe that these results will stimulate further studies on the role of subtelomeres in the maintenance of genome stability.
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Affiliation(s)
- Giovanni Cenci
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Laura Ciapponi
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Marta Marzullo
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Grazia D. Raffa
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Patrizia Morciano
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | | | - Romina Burla
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
| | - Isabella Saggio
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
- IBPM CNR, Sapienza—Università di Roma, Roma, Italy
| | - Maurizio Gatti
- Dipartimento di Biologia e Biotecnologie, Sapienza—Università di Roma, Roma, Italy
- Istituto Pasteur Fondazione Cenci Bolognetti, Sapienza—Università di Roma, Roma, Italy
- IBPM CNR, Sapienza—Università di Roma, Roma, Italy
- * E-mail:
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7
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Belyayev A. Bursts of transposable elements as an evolutionary driving force. J Evol Biol 2014; 27:2573-84. [PMID: 25290698 DOI: 10.1111/jeb.12513] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 09/17/2014] [Accepted: 09/17/2014] [Indexed: 12/25/2022]
Abstract
A burst of transposable elements (TEs) is a massive outbreak that may cause radical genomic rebuilding. This phenomenon has been reported in connection with the formation of taxonomic groups and species and has therefore been associated with major evolutionary events in the past. Over the past few years, several research groups have discovered recent stress-induced bursts of different TEs. The events for which bursts of TEs have been recorded include domestication, polyploidy, changes in mating systems, interspecific and intergeneric hybridization and abiotic stress. Cases involving abiotic stress, particularly bursts of TEs in natural populations driven by environmental change, are of special interest because this phenomenon may underlie micro- and macro-evolutionary events and ultimately support the maintenance and generation of biological diversity. This study reviews the known cases of bursts of TEs and their possible consequences, with particular emphasis on the speciation process.
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Affiliation(s)
- A Belyayev
- Institute of Botany, Czech Academy of Sciences, Pruhonice near Prague, Czech Republic
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8
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Chang LL, Wun WSA, Wang PS. Recovery from developmental nonylphenol exposure is possible for female rats. Chem Biol Interact 2014; 221:52-60. [DOI: 10.1016/j.cbi.2014.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/04/2014] [Accepted: 07/25/2014] [Indexed: 11/25/2022]
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9
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Wyse BA, Oshidari R, Jeffery DC, Yankulov KY. Parasite epigenetics and immune evasion: lessons from budding yeast. Epigenetics Chromatin 2013; 6:40. [PMID: 24252437 PMCID: PMC3843538 DOI: 10.1186/1756-8935-6-40] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/11/2013] [Indexed: 11/23/2022] Open
Abstract
The remarkable ability of many parasites to evade host immunity is the key to their success and pervasiveness. The immune evasion is directly linked to the silencing of the members of extended families of genes that encode for major parasite antigens. At any time only one of these genes is active. Infrequent switches to other members of the gene family help the parasites elude the immune system and cause prolonged maladies. For most pathogens, the detailed mechanisms of gene silencing and switching are poorly understood. On the other hand, studies in the budding yeast Saccharomyces cerevisiae have revealed similar mechanisms of gene repression and switching and have provided significant insights into the molecular basis of these phenomena. This information is becoming increasingly relevant to the genetics of the parasites. Here we summarize recent advances in parasite epigenetics and emphasize the similarities between S. cerevisiae and pathogens such as Plasmodium, Trypanosoma, Candida, and Pneumocystis. We also outline current challenges in the control and the treatment of the diseases caused by these parasites and link them to epigenetics and the wealth of knowledge acquired from budding yeast.
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Affiliation(s)
| | | | | | - Krassimir Y Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2 W1, Canada.
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10
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Jeffery DCB, Wyse BA, Rehman MA, Brown GW, You Z, Oshidari R, Masai H, Yankulov KY. Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation. Nucleic Acids Res 2013; 41:8475-88. [PMID: 23863839 PMCID: PMC3794585 DOI: 10.1093/nar/gkt623] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state. Consequently, the active state then persists with occasional conversions to the repressed state. These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively. In this study, we have addressed an important but often neglected aspect of PEV: the frequency of conversions at such loci. We have developed a model and have projected various PEV scenarios based on various rates of conversions. We have also enhanced two existing assays for gene silencing in Saccharomyces cerevisiae to measure the rate of switches from repressed to active state and vice versa. We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing. The assays have revealed that the histone chaperone Chromatin Assembly Factor I is involved in the control of epigenetic conversions. Together, our model and assays provide a comprehensive methodology for further investigation of epigenetic stability and position effects.
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Affiliation(s)
- Daniel C B Jeffery
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada, Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, Ontario, Canada and Department of Genome Medicine, Genome Dynamics Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
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11
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Yankulov K. Dynamics and stability: epigenetic conversions in position effect variegation. Biochem Cell Biol 2013; 91:6-13. [DOI: 10.1139/bcb-2012-0048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Position effect variegation (PEV) refers to quasi-stable patterns of gene expression that are observed at specific loci throughout the genomes of eukaryotes. The genes subjected to PEV can be completely silenced or fully active. Stochastic conversions between these 2 states are responsible for the variegated phenotypes. Positional variegation is used by human pathogens (Trypanosoma, Plasmodium, and Candida) to evade the immune system or adapt to the host environment. In the yeasts Saccharomyces cerevisiae and S accharomyces pombe, telomeric PEV aids the adaptation to a changing environment. In metazoans, similar epigenetic conversions are likely to accompany cell differentiation and the setting of tissue-specific gene expression programs. Surprisingly, we know very little about the mechanisms of epigenetic conversions. In this article, earlier models on the nature of PEV are revisited and recent advances on the dynamic nature of chromatin are reviewed. The normal dynamic histone turnover during transcription and DNA replication and its perturbation at transcription and replication pause sites are discussed. It is proposed that such perturbations play key roles in epigenetic conversions and in PEV.
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Affiliation(s)
- Krassimir Yankulov
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G2W1, Canada
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12
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Guerrero-Bosagna C, Covert TR, Haque MM, Settles M, Nilsson EE, Anway MD, Skinner MK. Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers. Reprod Toxicol 2012; 34:694-707. [PMID: 23041264 PMCID: PMC3513496 DOI: 10.1016/j.reprotox.2012.09.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 01/20/2023]
Abstract
The endocrine disruptor vinclozolin has previously been shown to promote epigenetic transgenerational inheritance of adult onset disease in the rat. The current study was designed to investigate the transgenerational actions of vinclozolin on the mouse. Transient exposure of the F0 generation gestating female during gonadal sex determination promoted transgenerational adult onset disease in F3 generation male and female mice, including spermatogenic cell defects, testicular abnormalities, prostate abnormalities, kidney abnormalities and polycystic ovarian disease. Pathology analysis demonstrated 75% of the vinclozolin lineage animals developed disease with 34% having two or more different disease states. Interestingly, the vinclozolin induced transgenerational disease was observed in the outbred CD-1 strain, but not the inbred 129 mouse strain. Analysis of the F3 generation sperm epigenome identified differential DNA methylation regions that can potentially be utilized as epigenetic biomarkers for transgenerational exposure and disease.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States
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13
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Guerrero-Bosagna C, Skinner MK. Environmentally induced epigenetic transgenerational inheritance of phenotype and disease. Mol Cell Endocrinol 2012; 354:3-8. [PMID: 22020198 PMCID: PMC3312615 DOI: 10.1016/j.mce.2011.10.004] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Revised: 10/03/2011] [Accepted: 10/05/2011] [Indexed: 12/15/2022]
Abstract
Environmental epigenetics has an important role in regulating phenotype formation or disease etiology. The ability of environmental factors and exposures early in life to alter somatic cell epigenomes and subsequent development is a critical factor in how environment affects biology. Environmental epigenetics provides a molecular mechanism to explain long term effects of environment on the development of altered phenotypes and "emergent" properties, which the "genetic determinism" paradigm cannot. When environmental factors permanently alter the germ line epigenome, then epigenetic transgenerational inheritance of these environmentally altered phenotypes and diseases can occur. This environmental epigenetic transgenerational inheritance of phenotype and disease is reviewed with a systems biology perspective.
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Affiliation(s)
- Carlos Guerrero-Bosagna
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA.
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14
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Gavin DP, Akbarian S. Epigenetic and post-transcriptional dysregulation of gene expression in schizophrenia and related disease. Neurobiol Dis 2012; 46:255-62. [DOI: 10.1016/j.nbd.2011.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Revised: 11/10/2011] [Accepted: 12/04/2011] [Indexed: 12/22/2022] Open
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15
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Sallé J, Campbell SD, Gho M, Audibert A. CycA is involved in the control of endoreplication dynamics in the Drosophila bristle lineage. Development 2012; 139:547-57. [PMID: 22223681 DOI: 10.1242/dev.069823] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Endocycles, which are characterised by repeated rounds of DNA replication without intervening mitosis, are involved in developmental processes associated with an increase in metabolic cell activity and are part of terminal differentiation. Endocycles are currently viewed as a restriction of the canonical cell cycle. As such, mitotic cyclins have been omitted from the endocycle mechanism and their role in this process has not been specifically analysed. In order to study such a role, we focused on CycA, which has been described to function exclusively during mitosis in Drosophila. Using developing mechanosensory organs as model system and PCNA::GFP to follow endocycle dynamics, we show that (1) CycA proteins accumulate during the last period of endoreplication, (2) both CycA loss and gain of function induce changes in endoreplication dynamics and reduce the number of endocycles, and (3) heterochromatin localisation of ORC2, a member of the Pre-RC complex, depends on CycA. These results show for the first time that CycA is involved in endocycle dynamics in Drosophila. As such, CycA controls the final ploidy that cells reached during terminal differentiation. Furthermore, our data suggest that the control of endocycles by CycA involves the subnuclear relocalisation of pre-RC complex members. Our work therefore sheds new light on the mechanism underlying endocycles, implicating a process that involves remodelling of the entire cell cycle network rather than simply a restriction of the canonical cell cycle.
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Affiliation(s)
- Jérémy Sallé
- Université Pierre et Marie Curie-Paris 6, UMR 7622, Paris, France
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16
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Finalism in Darwinian and Lamarckian Evolution: Lessons from Epigenetics and Developmental Biology. Evol Biol 2012. [DOI: 10.1007/s11692-012-9163-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Abstract
The origin recognition complex (ORC) was first discovered in the baker's yeast in 1992. Identification of ORC opened up a path for subsequent molecular level investigations on how eukaryotic cells initiate and control genome duplication each cell cycle. Twenty years after the first biochemical isolation, ORC is now taking on a three-dimensional shape, although a very blurry shape at the moment, thanks to the recent electron microscopy and image reconstruction efforts. In this chapter, we outline the current biochemical knowledge about ORC from several eukaryotic systems, with emphasis on the most recent structural and biochemical studies. Despite many species-specific properties, an emerging consensus is that ORC is an ATP-dependent machine that recruits other key proteins to form pre-replicative complexes (pre-RCs) at many origins of DNA replication, enabling the subsequent initiation of DNA replication in S phase.
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Affiliation(s)
- Huilin Li
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA, And, Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA, , Tel: 631-344-2931, Fax: 631-344-3407
| | - Bruce Stillman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA, , Tel: 516-367-8383
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18
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Abstract
Epigenetic marks, such as histone methylation, play a central role in chromatin structure and gene expression. During DNA replication, chromatin undergoes a wave of disruption and reassembly. Little is known about how the epigenetic marks are faithfully inherited from one generation to the next. In fission yeast, the hallmark of heterochromatin, a condensed chromatin structure, is H3K9 methylation. This conserved epigenetic mark is mediated by small interference RNAs (siRNAs) in a cell cycle-dependent manner: at S phase, heterochromatin is briefly transcribed by RNAP II and the transcripts are subsequently processed into siRNAs. These small RNAs, together with other key silencing factors, including Dos1/Raf1/Clr8/Cmc1, Dos2/Raf2/Clr7/Cmc2 and Rik1, mediate H3K9 methylation by the histone H3K9 methyltransferase Clr4. Our recent findings indicate that the ε subunit of DNA polymerase, Cdc20, associates with the Dos2-Rik1 complex and is essential for H3K9 methylation and heterochromatin function. Moreover, Cdc20 regulates siRNA generation by promoting RNAP II transcription of heterochromatin. These data suggest that DNA polymerase components may play a key role in the inheritance of histone methylation by coordinating DNA replication, RNAi and histone methylation, and explain previously observed cell cycle-regulated RNAi-dependent heterochromatin silencing. We propose a model in which, at DNA replication forks, DNA polymerase subunits mediate the recruitment of epigenetic factors required for RNAi and histone modification to heterochromatin to promote the faithful transmission of histone methylation.
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Affiliation(s)
- Marlyn Gonzalez
- Department of Biology, New York University, New York, NY, USA
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19
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Coordination of DNA replication and histone modification by the Rik1-Dos2 complex. Nature 2011; 475:244-8. [PMID: 21725325 PMCID: PMC3163161 DOI: 10.1038/nature10161] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Accepted: 05/03/2011] [Indexed: 12/13/2022]
Abstract
Histone modification marks play an important role in many chromatin processes1,2. During DNA replication, both heterochromatin and euchromatin are disrupted ahead of the replication fork and then reassembled into their original epigenetic states behind the fork3,4. How the histone marks are faithfully inherited during each generation is still poorly understood. In fission yeast RNA interference (RNAi)-mediated histone methylation is cell-cycle regulated. Centromere repeats are transiently transcribed at S phase and processed into small interference RNAs (siRNAs) by RITS and RDRC complexes5-7. The small RNAs, in concert with silencing factors, including Dos1/Clr8, Dos2/Clr7, Rik1 and Lid2, promote heterochromatic H3K9 methylation by a histone methyltransferase, Clr48-13. H3K9 methylation serves as a binding site for Swi6, a structural and functional homolog of metazoan Heterochromatin Protein 1 (HP1)14. Here we characterize a silencing complex, which contains Dos2, Rik1, Mms19, and Cdc20 (DNA polymerase epsilon). The complex regulates RNA Pol II activity in heterochromatin, and is required for DNA replication and heterochromatin assembly. Our findings provide a molecular link between DNA replication and histone methylation, shedding light on how epigenetic marks are transmitted during each cell cycle.
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20
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Margueron R, Reinberg D. Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 2011; 11:285-96. [PMID: 20300089 DOI: 10.1038/nrg2752] [Citation(s) in RCA: 506] [Impact Index Per Article: 38.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although it is widely accepted that the regulation of the chromatin landscape is pivotal to conveying the epigenetic program, it is still unclear how a defined chromatin domain is reproduced following DNA replication and transmitted from one cell generation to the next. Here, we review the multiple mechanisms that potentially affect the inheritance of epigenetic information in somatic cells. We consider models of how histones might be recycled following replication, and discuss the importance of positive-feedback loops, long-range gene interactions and the complex network of trans-acting factors in the transmission of chromatin states.
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Affiliation(s)
- Raphaël Margueron
- Howard Hughes Medical Institute, Department of Biochemistry, New York University School of Medicine, 522 First Avenue, New York, New York 10016, USA
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21
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Li PC, Chretien L, Côté J, Kelly TJ, Forsburg SL. S. pombe replication protein Cdc18 (Cdc6) interacts with Swi6 (HP1) heterochromatin protein: region specific effects and replication timing in the centromere. Cell Cycle 2011; 10:323-36. [PMID: 21239883 DOI: 10.4161/cc.10.2.14552] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin in S. pombe is associated with gene silencing at telomeres, the mating locus and centromeres. The compact heterochromatin structure raises the question how it unpacks and reforms during DNA replication. We show that the essential DNA replication factor Cdc18 (CDC6) associates with heterochromatin protein 1 (Swi6) in vivo and in vitro. Biochemical mapping and mutational analysis of the association domains show that the N-terminus of Cdc18 interacts with the chromoshadow domain of Swi6. Mutations in Swi6 that disrupt this interaction disrupt silencing and delay replication in the centromere. A mutation cdc18-I43A that reduces Cdc18 association with Swi6 has no silencing defect at the centromere, but changes Swi6 distribution and accelerates the timing of centromere replication. We suggest that fine tuning of Swi6 association at replication origins is important for negative as well as positive control of replication initiation.
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Affiliation(s)
- Pao-Chen Li
- Program in Molecular and Computational Biology, University of Southern California, Los Angeles, CA, USA
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22
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Skinner MK, Manikkam M, Guerrero-Bosagna C. Epigenetic transgenerational actions of endocrine disruptors. Reprod Toxicol 2010; 31:337-43. [PMID: 21055462 DOI: 10.1016/j.reprotox.2010.10.012] [Citation(s) in RCA: 195] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2010] [Revised: 10/21/2010] [Accepted: 10/26/2010] [Indexed: 12/22/2022]
Abstract
Environmental factors have a significant impact on biology. Therefore, environmental toxicants through similar mechanisms can modulate biological systems to influence physiology and promote disease states. The majority of environmental toxicants do not have the capacity to modulate DNA sequence, but can alter the epigenome. In the event an environmental toxicant such as an endocrine disruptor modifies the epigenome of a somatic cell, this may promote disease in the individual exposed, but not be transmitted to the next generation. In the event a toxicant modifies the epigenome of the germ line permanently, then the disease promoted can become transgenerationaly transmitted to subsequent progeny. The current review focuses on the ability of environmental factors such as endocrine disruptors to promote transgenerational phenotypes.
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Affiliation(s)
- Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, United States.
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23
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Huang H, Yu Z, Zhang S, Liang X, Chen J, Li C, Ma J, Jiao R. Drosophila CAF-1 regulates HP1-mediated epigenetic silencing and pericentric heterochromatin stability. J Cell Sci 2010; 123:2853-61. [PMID: 20663913 DOI: 10.1242/jcs.063610] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Chromatin assembly factor 1 (CAF-1) was initially characterized as a histone deliver in the process of DNA-replication-coupled chromatin assembly in eukaryotic cells. Here, we report that CAF-1 p180, the largest subunit of Drosophila CAF-1, participates in the process of heterochromatin formation and functions to maintain pericentric heterochromatin stability. We provide evidence that Drosophila CAF-1 p180 plays a role in both classes of position effect variegation (PEV) and in the expression of heterochromatic genes. A decrease in the expression of Drosophila CAF-1 p180 leads to a decrease in both H3K9 methylation at pericentric heterochromatin regions and the recruitment of heterochromatin protein 1 (HP1) to the chromocenter of the polytene chromosomes. The artificial targeting of HP1 to a euchromatin location leads to the enrichment of Drosophila CAF-1 p180 at this ectopic heterochromatin, suggesting the mutual recruitment of HP1 and CAF-1 p180. We also show that the spreading of heterochromatin is compromised in flies that have reduced CAF-1 p180. Furthermore, reduced CAF-1 p180 causes a defect in the dynamics of heterochromatic markers in early Drosophila embryos. Together, these findings suggest that Drosophila CAF-1 p180 is an essential factor in the epigenetic control of heterochromatin formation and/or maintenance.
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Affiliation(s)
- Hai Huang
- State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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24
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Kirkland JG, Kamakaka RT. tRNA insulator function: insight into inheritance of transcription states? Epigenetics 2010; 5:96-9. [PMID: 20168086 DOI: 10.4161/epi.5.2.10775] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA in eukaryotes is invariably present as a complex with histone and non-histone proteins called chromatin. These proteins play an important role in the proper regulation of genes during development and differentiation. Transcription factors and the covalent modifications of DNA, histone and non-histone proteins establish an epigenetic state that is heritable and which does not involve a change in genotype. The heritability of transcription states through cell division brings up specific questions: How are epigenetic marks established and re-established in the daughter cells following DNA replication and mitosis? In this article we explore what is known of the cell cycle dependence of epigenetic inheritance with particular emphasis on yeast loci and discuss the role of specific proteins responsible for the establishment and maintenance of these states.
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Affiliation(s)
- Jacob G Kirkland
- Department of MCD Biology, Sinsheimer Labs, University of California, Santa Cruz, CA, USA
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25
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Histone modifications, DNA methylation, and schizophrenia. Neurosci Biobehav Rev 2009; 34:882-8. [PMID: 19879893 DOI: 10.1016/j.neubiorev.2009.10.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2009] [Revised: 09/22/2009] [Accepted: 10/21/2009] [Indexed: 02/08/2023]
Abstract
Studies have demonstrated that several schizophrenia candidate genes are especially susceptible to changes in transcriptional activity as a result of histone modifications and DNA methylation. Increased expression of epigenetic enzymes which generally reduce transcription have been reported in schizophrenia postmortem brain samples. An abnormal chromatin state leading to reduced candidate gene expression can be explained by aberrant coordination of epigenetic mechanisms in schizophrenia. Dynamic epigenetic processes are difficult to study using static measures such as postmortem brain samples. Therefore, we have developed a model using cultured peripheral blood mononuclear cells (PBMCs) capable of pharmacologically probing these processes in human subjects. This approach has revealed several promising findings indicating that schizophrenia subject PBMC chromatin may be less capable of responding to agents which normally 'open' chromatin. We suggest that the ability to appropriately modify chromatin structure may be a factor in treatment response. Several pharmacological approaches for targeting epigenetic processes are reviewed.
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26
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Guerrero-Bosagna CM, Skinner MK. Epigenetic transgenerational effects of endocrine disruptors on male reproduction. Semin Reprod Med 2009; 27:403-8. [PMID: 19711250 DOI: 10.1055/s-0029-1237428] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Endocrine-disrupting chemicals generally function as steroid receptor signaling antagonists or agonists that influence development to promote adult-onset disease. Exposure to the endocrine disruptors during the initiation of male reproductive tract development interferes with the normal hormonal signaling and formation of male reproductive organs. In particular, exposure to the endocrine disruptor vinclozolin promotes transgenerational transmission of adult-onset disease states such as male infertility, increased frequencies of tumors, prostate disease, kidney diseases, and immune abnormalities that develop as males age. An epigenetic change in the germ line would be involved in the transgenerational transmission of these induced phenotypes. Nevertheless, other studies have also reported transgenerational transmission of induced epigenetic changes, without altering the germ line. Here we propose a nomenclature to help clarify both cases of transgenerational epigenetic transmission. An intrinsic epigenetic transgenerational process would require a germ-line involvement, a permanent alteration in the germ cell epigenome, and only one exposure to the environmental factor. An extrinsic epigenetic transgenerational process would involve an epigenetic alteration in a somatic tissue and require exposure at each generation to maintain the transgenerational phenotype.
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Affiliation(s)
- Carlos M Guerrero-Bosagna
- Center for Reproductive Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4231, USA
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27
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Di Tomaso MV, Martínez-López W, Folle GA, Palitti F. Modulation of chromosome damage localization by DNA replication timing. Int J Radiat Biol 2009; 82:877-86. [PMID: 17178628 DOI: 10.1080/09553000600973335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE Non-random occurrence of induced chromosome breakpoints (BP) has been repeatedly reported. DNA synthesis and chromatin remodeling may influence chromosome BP localization. The CHO9 X chromosome exhibits an early replicating short euchromatic arm (Xpe) and a late replicating long heterochromatic arm (Xqh). We investigated the role played by DNA replication and related chromatin remodeling processes on BP distribution in eu/heterochromatin using the CHO9 X chromosome as a model. MATERIALS AND METHODS BP induced by etoposide, a topoisomerase II inhibitor, as well as by the S-dependent clastogens ultraviolet-C light (UV-C) and methyl methanesulfonate (MMS) were mapped to CHO9 X chromosome arms. The base analogue 5-bromo-2'-deoxyuridine (BrdUrd) was pulse-added immediately after UV-C irradiation or during etoposide and MMS treatments (40 min) to identify cells in early S-phase (Xpe labeled) or late S-phase (Xqh labeled) after indirect BrdUrd immunodetection in metaphase spreads using primary anti-BrdUrd and secondary fluorochrome-tagged antibodies. RESULTS During early S-phase, BP induced by etoposide and MMS mapped preferentially to Xpe while BP produced by UV-C localized randomly. BP induced by all agents during late S-phase clustered in Xqh. CONCLUSIONS Results obtained suggest that replication time of eu/heterochromatin as well as chromatin remodeling may determine BP localization on the CHO9 X chromosome.
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Affiliation(s)
- M V Di Tomaso
- Department of Genetic Toxicology and Chromosome Pathology, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay.
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28
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Yehezkel S, Segev Y, Viegas-Péquignot E, Skorecki K, Selig S. Hypomethylation of subtelomeric regions in ICF syndrome is associated with abnormally short telomeres and enhanced transcription from telomeric regions. Hum Mol Genet 2008; 17:2776-89. [PMID: 18558631 DOI: 10.1093/hmg/ddn177] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Telomeres and adjacent subtelomeric regions are packaged as heterochromatin in many organisms. The heterochromatic features include DNA methylation, histones H3-Lys9 (Lysine 9) and H4-Lys20 (Lysine 20) methylation and heterochromatin protein1 alpha binding. Subtelomeric DNA is hypomethylated in human sperm and ova, and these regions are subjected to de novo methylation during development. In mice this activity is carried out by DNA methyltransferase 3b (Dnmt3b). Mutations in DNMT3B in humans lead to the autosomal-recessive ICF (immunodeficiency, centromeric region instability, facial anomalies) syndrome. Here we show that, in addition to several satellite and non-satellite repeats, the subtelomeric regions in lymphoblastoid and fibroblast cells of ICF patients are also hypomethylated to similar levels as in sperm. Furthermore, the telomeres are abnormally short in both the telomerase-positive and -negative cells, and many chromosome ends lack detectable telomere fluorescence in situ hybridization signals from either one or both sister-chromatids. In contrast to Dnmt3a/b(-/-) mouse embryonic stem cells, increased telomere sister-chromatid exchange was not observed in ICF cells. Hypomethylation of subtelomeric regions was associated in the ICF cells with advanced telomere replication timing and elevated levels of transcripts emanating from telomeric regions, known as TERRA (telomeric-repeat-containing RNA) or TelRNA. The current findings provide a mechanistic explanation for the abnormal telomeric phenotype observed in ICF syndrome and highlights the link between TERRA/TelRNA and structural telomeric integrity.
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Affiliation(s)
- Shiran Yehezkel
- Department of Nephrology and Laboratory of Molecular Medicine, Rambam Medical Center and Rappaport Faculty of Medicine and Research Institute, Technion, Haifa 31096, Israel
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29
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Dohke K, Miyazaki S, Tanaka K, Urano T, Grewal SIS, Murakami Y. Fission yeast chromatin assembly factor 1 assists in the replication-coupled maintenance of heterochromatin. Genes Cells 2008; 13:1027-43. [PMID: 18761674 DOI: 10.1111/j.1365-2443.2008.01225.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chromatin assembly factor-1 (CAF1) is a well-conserved histone chaperone that loads the histone H3-H4 complex onto newly synthesized DNA in vitro through interaction with the replication factor PCNA. CAF1 is considered to be involved in heterochromatin maintenance in several organisms, but the evidence is circumstantial and functional details have not been established. We identified fission yeast CAF-1 (spCAF1), which interacts with PCNA in S phase. Depletion of spCAF1 caused defects in silencing at centromeric and mating locus heterochromatin, accompanied with a decrease in Swi6, the fission yeast HP1 homologue. Loss of spCAF1 destabilized both the silent and active states of chromatin at the meta-stable heterochromatic region, with a more pronounced effect on the silent state, indicating that spCAF1 is involved in the maintenance of heterochromatin. Swi6 dissociated from heterochromatin during G1/S phase appears to associate with spCAF1. In early S phase, spCAF1 localized to replicating heterochromatin as well as euchromatin and remained associated with Swi6, and Swi6 then bound to heterochromatin. Taken together, we propose that spCAF1 functions in heterochromatin maintenance by recruiting dislocated Swi6 during replication to replicated heterochromatin at the replication fork.
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Affiliation(s)
- Kohei Dohke
- Department of Cell Biology, Institute for Virus Research, Kyoto University, Sakyo-ku, Kyoto 606-8507 Japan
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30
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Andreyeva EN, Kolesnikova TD, Belyaeva ES, Glaser RL, Zhimulev IF. Local DNA underreplication correlates with accumulation of phosphorylated H2Av in the Drosophila melanogaster polytene chromosomes. Chromosome Res 2008; 16:851-62. [PMID: 18704724 DOI: 10.1007/s10577-008-1244-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2008] [Revised: 06/05/2008] [Accepted: 06/05/2008] [Indexed: 12/29/2022]
Abstract
DNA in Drosophila melanogaster polytene chromosomes is known to be locally underreplicated in both pericentric and intercalary heterochromatin. When the SuUR gene is mutant, complete and partial suppression of underreplication are observed in intercalary and pericentric heterochromatin, respectively; in contrast, overexpression of SuUR results in stronger underreplication. Using antibodies against phosphorylated histone H2Av and flies with different levels of SuUR expression, we demonstrated a clear correlation between the extent of underreplication in specific chromosome regions and the accumulation of H2Av phosphorylated at S137 (gamma-H2AX) at the same sites. Phosphorylated H2Av is a well-established marker of DNA double-stranded breaks (DSB). Our data thus argue that DNA underreplication leads to DSBs and that DSBs accumulate as salivary gland cells progress throughout repeated endocycles. We speculate that ligation of free double-stranded DNA termini causes the formation of ectopic contacts between the underreplicated regions in heterochromatin.
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Affiliation(s)
- E N Andreyeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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31
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The chromatin remodelling factor dATRX is involved in heterochromatin formation. PLoS One 2008; 3:e2099. [PMID: 18461125 PMCID: PMC2324200 DOI: 10.1371/journal.pone.0002099] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 03/27/2008] [Indexed: 01/25/2023] Open
Abstract
Despite extensive study of heterochromatin, relatively little is known about the mechanisms by which such a structure forms. We show that the Drosophila homologue of the human α-thalassemia and mental retardation X-linked protein (dATRX), is important in the formation or maintenance of heterochromatin through modification of position effect variegation. We further show that there are two isoforms of the dATRX protein, the longer of which interacts directly with heterochromatin protein 1 (dHP-1) through a CxVxL motif both in vitro and in vivo. These two proteins co-localise at heterochromatin in a manner dependent on this motif. Consistent with this observation, the long isoform of the dATRX protein localises primarily to the heterochromatin at the chromocentre on salivary gland polytene chromosomes, whereas the short isoform binds to many sites along the chromosome arms. We suggest that the establishment of a regular nucleosomal organisation may be common to heterochromatin and transcriptionally repressed chromatin in other locations, and may require the action of ATP dependent chromatin remodelling factors.
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32
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Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat Struct Mol Biol 2008; 15:381-8. [DOI: 10.1038/nsmb.1406] [Citation(s) in RCA: 289] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/22/2008] [Indexed: 11/09/2022]
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33
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Drosophila sticky/citron kinase is a regulator of cell-cycle progression, genetically interacts with Argonaute 1 and modulates epigenetic gene silencing. Genetics 2008; 178:1311-25. [PMID: 18245345 DOI: 10.1534/genetics.107.082511] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The sticky/citron kinase protein is a conserved regulator of cell-cycle progression from invertebrates to humans. While this kinase is essential for completion of cytokinesis, sticky/citron kinase phenotypes disrupting neurogenesis and cell differentiation suggest additional non-cell-cycle functions. However, it is not known whether these phenotypes are an indirect consequence of sticky mutant cell-cycle defects or whether they define a novel function for this kinase. We have isolated a temperature-sensitive allele of the Drosophila sticky gene and we show that sticky/citron kinase is required for histone H3-K9 methylation, HP1 localization, and heterochromatin-mediated gene silencing. sticky genetically interacts with Argonaute 1 and sticky mutants exhibit context-dependent Su(var) and E(var) activity. These observations indicate that sticky/citron kinase functions to regulate both actin-myosin-mediated cytokinesis and epigenetic gene silencing, possibly linking cell-cycle progression to heterochromatin assembly and inheritance of gene expression states.
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34
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Arnold DR, Françon P, Zhang J, Martin K, Clarke HJ. Stem-loop binding protein expressed in growing oocytes is required for accumulation of mRNAs encoding histones H3 and H4 and for early embryonic development in the mouse. Dev Biol 2007; 313:347-58. [PMID: 18036581 DOI: 10.1016/j.ydbio.2007.10.032] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Revised: 10/18/2007] [Accepted: 10/22/2007] [Indexed: 11/29/2022]
Abstract
Growing oocytes accumulate mRNAs and proteins that support early embryogenesis. Among the most abundant of these maternal factors are the histones. Histone mRNA accumulation and translation are mainly restricted to S-phase in somatic cells, and the mechanism by which oocytes produce histones is unknown. In somatic cells, replication-dependent histone synthesis requires the stem-loop binding protein (SLBP). SLBP is expressed during S-phase, binds to the 3'-untranslated region of non-polyadenylated transcripts encoding the histones, and is required for their stabilization and translation. SLBP is expressed in oocytes of several species, suggesting a role in histone synthesis. To test this, we generated transgenic mice whose oocytes lack SLBP. mRNAs encoding histones H3 and H4 failed to accumulate in these oocytes. Unexpectedly, mRNAs encoding H2A and H2B were little affected. Embryos derived from SLBP-depleted oocytes reached the 2-cell stage, but most then became arrested. Histones H3 and H4, but not H2A or H2B, were substantially reduced in these embryos. The embryos also expressed high levels of gamma H2A.X. Injection of histones into SLBP-depleted embryos rescued them from developmental arrest. Thus, SLBP is an essential component of the mechanism by which growing oocytes of the mouse accumulate the histones that support early embryonic development.
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Affiliation(s)
- Daniel R Arnold
- Department of Obstetrics and Gynecology, McGill University, Montreal, Canada
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35
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Drosophila follicle cell amplicons as models for metazoan DNA replication: a cyclinE mutant exhibits increased replication fork elongation. Proc Natl Acad Sci U S A 2007; 104:16739-46. [PMID: 17940024 DOI: 10.1073/pnas.0707804104] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Gene clusters amplified in the ovarian follicle cells of Drosophila serve as powerful models for metazoan DNA replication. In response to developmental signals, specific genomic regions undergo amplification by repeated firing of replication origins and bidirectional movement of replication forks for approximately 50 kb in each direction. Previous work focused on initiation of amplification, defining replication origins, establishing the role of the prereplication complex and origin recognition complex (ORC), and uncovering regulatory functions for the Myb, E2F1, and Rb transcription factors. Here, we exploit follicle cell amplification to investigate the control of DNA replication fork progression and termination, poorly understood processes in metazoans. We identified a mutant in which, during gene amplification, the replication forks move twice as far from the origin compared with wild type. This phenotype is the result of an amino acid substitution mutation in the cyclinE gene, cyclinE(1f36). The rate of oogenesis is normal in cyclinE(1f36)/cyclinE(Pz8) mutant ovaries, indicating that increased replication fork progression is due to increased replication fork speed, possibly from increased processivity. The increased amplification domains observed in the mutant imply that there are not replication fork barriers preventing replication forks from progressing beyond the normal 100-kb amplified region. These results reveal a previously unrecognized role for CyclinE in controlling replication fork movement.
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Abstract
T lymphocyte development is directed by a gene-expression program that occurs in the complex nucleoprotein environment of chromatin. This review examines basic principles of chromatin regulation and evaluates ongoing progress toward understanding how the chromatin template is manipulated to control gene expression and gene recombination in developing thymocytes. Special attention is devoted to the loci encoding T cell receptors alpha and beta, T cell coreceptors CD4 and CD8, and the enzyme terminal deoxynucleotidyl transferase. The properties of SATB1, a notable organizer of thymocyte chromatin, are also addressed.
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Affiliation(s)
- Michael S Krangel
- Department of Immunology, Duke University Medical Center, Durham, North Carolina 27710 USA.
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Shelling AN, Ferguson LR. Genetic variation in human disease and a new role for copy number variants. Mutat Res 2007; 622:33-41. [PMID: 17555771 DOI: 10.1016/j.mrfmmm.2007.04.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Accepted: 04/29/2007] [Indexed: 05/15/2023]
Abstract
While complex diseases, such as inflammatory bowel disease, do not follow distinctive Mendelian inheritance patterns, there is now considerable evidence from twin and pedigree studies to show that there are significant genetic influences in the development of many such diseases. In times past, this type of information was considered to be interesting, and was used mainly to alert other members of the families that they may also be at increased risk of developing the disease. However, with the ability to evaluate the genetic basis of common disease, this information will have important consequences for the diagnosis, prevention and treatment of the disorder. The genetic basis for common disease is likely to be more complicated than we had previously anticipated, since we now recognise epigenetic causes of disease, and other subtle gene regulatory mechanisms. Copy number variants have been highlighted in this review, as being a phenomenon that we have known about for a long time, but that has not previously been clearly associated with human disease. As complex disease is related to changes in gene expression, any variation in the human genome that alters gene expression is now a candidate for being involved in the disease process.
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Affiliation(s)
- Andrew N Shelling
- Department of Obstetrics and Gynaecology, The University of Auckland, New Zealand; Nutrigenomics New Zealand, New Zealand.
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Smallwood A, Estève PO, Pradhan S, Carey M. Functional cooperation between HP1 and DNMT1 mediates gene silencing. Genes Dev 2007; 21:1169-78. [PMID: 17470536 PMCID: PMC1865489 DOI: 10.1101/gad.1536807] [Citation(s) in RCA: 247] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Mammalian euchromatic gene silencing results from the combined repressive effects of histone and DNA methyltransferases. Little is known of the mechanism by which these enzymes cooperate to induce silencing. Here we show that mammalian HP1 family members mediate communication between histone and DNA methyltransferases. In vitro, methylation of histone 3 Lys 9 by G9a creates a binding platform for HP1alpha, beta, and gamma. DNMT1 interacts with HP1 resulting in increased DNA methylation on DNA and chromatin templates in vitro. The functional and physical interaction can be recapitulated in vivo. Binding of GAL4-HP1 to a reporter construct is sufficient to induce repression and DNA methylation in DNMT1 wild-type but not DNMT1-null cells. Additionally, silencing of the Survivin gene coincides with recruitment of G9a and HP1 in DNMT1 wild-type but not null cells. We conclude that direct interactions between HP1 and DNMT1 mediate silencing of euchromatic genes.
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Affiliation(s)
- Andrea Smallwood
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
| | | | | | - Michael Carey
- Department of Biological Chemistry, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, California 90095, USA
- Corresponding author.E-MAIL ; FAX (310) 206-9598
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39
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Abstract
Inheritance and maintenance of the DNA sequence and its organization into chromatin are central for eukaryotic life. To orchestrate DNA-replication and -repair processes in the context of chromatin is a challenge, both in terms of accessibility and maintenance of chromatin organization. To meet the challenge of maintenance, cells have evolved efficient nucleosome-assembly pathways and chromatin-maturation mechanisms that reproduce chromatin organization in the wake of DNA replication and repair. The aim of this Review is to describe how these pathways operate and to highlight how the epigenetic landscape may be stably maintained even in the face of dramatic changes in chromatin structure.
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Affiliation(s)
- Anja Groth
- Laboratory of Nuclear Dynamics and Genome Plasticity, UMR 218 CNRS/Institut Curie, 26 rue d'Ulm, 75248 Paris, Cedex 5, France
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40
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Gvozdev VA, Abramov YA, Kogan GL, Lavrov SA. Distorted heterochromatin replication in Drosophila melanogaster polytene chromosomes as a result of euchromatin-heterochromatin rearrangements. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407010024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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41
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Estève PO, Chin HG, Smallwood A, Feehery GR, Gangisetty O, Karpf AR, Carey MF, Pradhan S. Direct interaction between DNMT1 and G9a coordinates DNA and histone methylation during replication. Genes Dev 2006; 20:3089-103. [PMID: 17085482 PMCID: PMC1635145 DOI: 10.1101/gad.1463706] [Citation(s) in RCA: 412] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Chromatin methylation is necessary for stable repression of gene expression during mammalian development. During cell division, DNMT1 maintains the DNA methylation pattern of the newly synthesized daughter strand, while G9a methylates H3K9. Here, DNMT1 is shown to directly bind G9a both in vivo and in vitro and to colocalize in the nucleus during DNA replication. The complex of DNMT1 and G9a colocalizes with dimethylated H3K9 (H3K9me2) at replication foci. Similarly, another H3K9 histone methyltransferase, SUV39H1, colocalizes with DNMT1 on heterochromatic regions of the nucleoli exclusively before cell division. Both DNMT1 and G9a are loaded onto the chromatin simultaneously in a ternary complex with loading factor PCNA during chromatin replication. Small interfering RNA (siRNA) knockdown of DNMT1 impairs DNA methylation, G9a loading, and H3K9 methylation on chromatin and rDNA repeats, confirming DNMT1 as the primary loading factor. Additionally, the complex of DNMT1 and G9a led to enhanced DNA and histone methylation of in vitro assembled chromatin substrates. Thus, direct cooperation between DNMT1 and G9a provides a mechanism of coordinated DNA and H3K9 methylation during cell division.
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Kolesnikova TD, Andreeva EN, Pindyurin AV, Ananko NG, Belyakin SN, Shloma VV, Yurlova AA, Makunin IV, Pokholkova GV, Volkova EI, Zarutskaya EA, Kokoza EB, Semeshin VF, Belyaeva ES, Zhimulev IF. Contribution of the SuUR gene to the organization of epigenetically repressed regions of Drosophila melanogaster chromosomes. RUSS J GENET+ 2006. [DOI: 10.1134/s1022795406080011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Belyaeva ES, Demakov SA, Pokholkova GV, Alekseyenko AA, Kolesnikova TD, Zhimulev IF. DNA underreplication in intercalary heterochromatin regions in polytene chromosomes of Drosophila melanogaster correlates with the formation of partial chromosomal aberrations and ectopic pairing. Chromosoma 2006; 115:355-66. [PMID: 16583218 DOI: 10.1007/s00412-006-0063-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Revised: 02/26/2006] [Accepted: 03/06/2006] [Indexed: 11/25/2022]
Abstract
We studied the influence of the Suppressor of Underreplication (SuUR) gene expression on the intercalary heterochromatin (IH) regions of Drosophila melanogaster polytene chromosomes. We observed a strong positive correlation between increased SuUR expression, underreplication extent, amount of DNA truncation, and formation of ectopic contacts in IH regions. SuUR overexpression from heat shock-driven transgene results in the formation of partial chromosomal aberrations whose breakpoints map exclusively to the regions of intercalary and pericentric heterochromatin. It is important to note that all these effects are seen only if SuUR overexpression is induced during early stages of chromosome polytenization. Therefore, we developed the idea that ectopic pairing results from the joining of free DNA ends, which are formed as a consequence of underreplication.
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Affiliation(s)
- Elena S Belyaeva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia
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Abstract
There has been remarkable progress in the last 20 years in defining the molecular mechanisms that regulate initiation of DNA synthesis in eukaryotic cells. Replication origins in the DNA nucleate the ordered assembly of protein factors to form a prereplication complex (preRC) that is poised for DNA synthesis. Transition of the preRC to an active initiation complex is regulated by cyclin-dependent kinases and other signaling molecules, which promote further protein assembly and activate the mini chromosome maintenance helicase. We will review these mechanisms and describe the state of knowledge about the proteins involved. However, we will also consider an additional layer of complexity. The DNA in the cell is packaged with histone proteins into chromatin. Chromatin structure provides an additional layer of heritable information with associated epigenetic modifications. Thus, we will begin by describing chromatin structure, and how the cell generally controls access to the DNA. Access to the DNA requires active chromatin remodeling, specific histone modifications, and regulated histone deposition. Studies in transcription have revealed a variety of mechanisms that regulate DNA access, and some of these are likely to be shared with DNA replication. We will briefly describe heterochromatin as a model for an epigenetically inherited chromatin state. Next, we will describe the mechanisms of replication initiation and how these are affected by constraints of chromatin. Finally, chromatin must be reassembled with appropriate modifications following passage of the replication fork, and our third major topic will be the reassembly of chromatin and its associated epigenetic marks. Thus, in this chapter, we seek to bring together the studies of replication initiation and the studies of chromatin into a single holistic narrative.
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Affiliation(s)
- Angel P Tabancay
- Molecular and Computational Biology Section University of Southern California Los Angeles, California 90089, USA
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