151
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TDP2 suppresses chromosomal translocations induced by DNA topoisomerase II during gene transcription. Nat Commun 2017; 8:233. [PMID: 28794467 PMCID: PMC5550487 DOI: 10.1038/s41467-017-00307-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
DNA double-strand breaks (DSBs) induced by abortive topoisomerase II (TOP2) activity are a potential source of genome instability and chromosome translocation. TOP2-induced DNA double-strand breaks are rejoined in part by tyrosyl-DNA phosphodiesterase 2 (TDP2)-dependent non-homologous end-joining (NHEJ), but whether this process suppresses or promotes TOP2-induced translocations is unclear. Here, we show that TDP2 rejoins DSBs induced during transcription-dependent TOP2 activity in breast cancer cells and at the translocation ‘hotspot’, MLL. Moreover, we find that TDP2 suppresses chromosome rearrangements induced by TOP2 and reduces TOP2-induced chromosome translocations that arise during gene transcription. Interestingly, however, we implicate TDP2-dependent NHEJ in the formation of a rare subclass of translocations associated previously with therapy-related leukemia and characterized by junction sequences with 4-bp of perfect homology. Collectively, these data highlight the threat posed by TOP2-induced DSBs during transcription and demonstrate the importance of TDP2-dependent non-homologous end-joining in protecting both gene transcription and genome stability. DNA double-strand breaks (DSBs) induced by topoisomerase II (TOP2) are rejoined by TDP2-dependent non-homologous end-joining (NHEJ) but whether this promotes or suppresses translocations is not clear. Here the authors show that TDP2 suppresses chromosome translocations from DSBs introduced during gene transcription.
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152
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Gangloff S, Arcangioli B. DNA repair and mutations during quiescence in yeast. FEMS Yeast Res 2017; 17:fox002. [PMID: 28087675 DOI: 10.1093/femsyr/fox002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2017] [Indexed: 12/20/2022] Open
Abstract
Life is maintained through alternating phases of cell division and quiescence. The causes and consequences of spontaneous mutations have been extensively explored in proliferating cells, and the major sources include errors of DNA replication and DNA repair. The foremost consequences are genetic variations within a cell population that can lead to heritable diseases and drive evolution. While most of our knowledge on DNA damage response and repair has been gained through cells actively dividing, it remains essential to also understand how DNA damage is metabolized in cells which are not dividing. In this review, we summarize the current knowledge concerning the type of lesions that arise in non-dividing budding and fission yeast cells, as well as the pathways used to repair them. We discuss the contribution of these models to our current understanding of age-related pathologies.
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153
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Michaelson JJ, Shin MK, Koh JY, Brueggeman L, Zhang A, Katzman A, McDaniel L, Fang M, Pufall M, Pieper AA. Neuronal PAS Domain Proteins 1 and 3 Are Master Regulators of Neuropsychiatric Risk Genes. Biol Psychiatry 2017; 82:213-223. [PMID: 28499489 PMCID: PMC6901278 DOI: 10.1016/j.biopsych.2017.03.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND NPAS3 has been established as a robust genetic risk factor in major mental illness. In mice, loss of neuronal PAS domain protein 3 (NPAS3) impairs postnatal hippocampal neurogenesis, while loss of the related protein NPAS1 promotes it. These and other findings suggest a critical role for NPAS proteins in neuropsychiatric functioning, prompting interest in the molecular pathways under their control. METHODS We used RNA sequencing coupled with chromatin immunoprecipitation sequencing to identify genes directly regulated by NPAS1 and NPAS3 in the hippocampus of wild-type, Npas1-/-, and Npas3-/- mice. Computational integration with human genetic and expression data revealed the disease relevance of NPAS-regulated genes and pathways. Specific findings were confirmed at the protein level by Western blot. RESULTS This is the first in vivo, transcriptome-scale investigation of genes regulated by NPAS1 and NPAS3. These transcription factors control an ensemble of genes that are themselves also major regulators of neuropsychiatric function. Specifically, Fmr1 (fragile X syndrome) and Ube3a (Angelman syndrome) are transcriptionally regulated by NPAS3, as is the neurogenesis regulator Notch. Dysregulation of these pathways was confirmed at the protein level. Furthermore, NPAS1/3 targets show increased human genetic burden for schizophrenia and intellectual disability. CONCLUSIONS Together, these data provide a clear, unbiased view of the full spectrum of genes regulated by NPAS1 and NPAS3 and show that these transcription factors are master regulators of neuropsychiatric function. These findings expose the molecular pathophysiology of NPAS1/3 mutations and provide a striking example of the shared, combinatorial nature of molecular pathways that underlie diagnostically distinct neuropsychiatric conditions.
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Affiliation(s)
- Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Biomedical Engineering, University of Iowa College of Engineering, University of Iowa, Iowa City, Iowa; Department of Communication Sciences and Disorders, University of Iowa College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa; Iowa Institute of Human Genetics, University of Iowa, Iowa City, Iowa; Genetics Cluster Initiative, University of Iowa, Iowa City, Iowa; The DeLTA Center, University of Iowa, Iowa City, Iowa; University of Iowa Informatics Initiative, University of Iowa, Iowa City, Iowa.
| | - Min-Kyoo Shin
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Jin-Young Koh
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Angela Zhang
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Aaron Katzman
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Latisha McDaniel
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Mimi Fang
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Miles Pufall
- Department of Biochemistry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Andrew A Pieper
- Department of Psychiatry, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Neurology, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Free Radical and Radiation Biology Program, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Department of Veterans Affairs, University of Iowa Carver College of Medicine, University of Iowa, Iowa City, Iowa; Pappajohn Biomedical Institute, University of Iowa, Iowa City, Iowa; Weill Cornell Autism Research Program, Weill Cornell Medicine, Cornell University, New York, New York
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154
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Rasmussen KL, Tybjærg‐Hansen A, Nordestgaard BG, Frikke‐Schmidt R. Plasma apolipoprotein E levels and risk of dementia: A Mendelian randomization study of 106,562 individuals. Alzheimers Dement 2017; 14:71-80. [DOI: 10.1016/j.jalz.2017.05.006] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/22/2017] [Accepted: 05/25/2017] [Indexed: 10/19/2022]
Affiliation(s)
- Katrine L. Rasmussen
- Department of Clinical Biochemistry Rigshospitalet Copenhagen Denmark
- The Copenhagen General Population Study Herlev and Gentofte Hospital Herlev Denmark
- Copenhagen University Hospital Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Anne Tybjærg‐Hansen
- Department of Clinical Biochemistry Rigshospitalet Copenhagen Denmark
- The Copenhagen General Population Study Herlev and Gentofte Hospital Herlev Denmark
- Copenhagen University Hospital Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- The Copenhagen City Heart Study Frederiksberg Hospital Frederiksberg Denmark
| | - Børge G. Nordestgaard
- The Copenhagen General Population Study Herlev and Gentofte Hospital Herlev Denmark
- Copenhagen University Hospital Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
- The Copenhagen City Heart Study Frederiksberg Hospital Frederiksberg Denmark
- Department of Clinical Biochemistry Herlev and Gentofte Hospital Herlev Denmark
| | - Ruth Frikke‐Schmidt
- Department of Clinical Biochemistry Rigshospitalet Copenhagen Denmark
- The Copenhagen General Population Study Herlev and Gentofte Hospital Herlev Denmark
- Copenhagen University Hospital Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
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155
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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156
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Hull RM, Cruz C, Jack CV, Houseley J. Environmental change drives accelerated adaptation through stimulated copy number variation. PLoS Biol 2017; 15:e2001333. [PMID: 28654659 PMCID: PMC5486974 DOI: 10.1371/journal.pbio.2001333] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 05/23/2017] [Indexed: 01/01/2023] Open
Abstract
Copy number variation (CNV) is rife in eukaryotic genomes and has been implicated in many human disorders, particularly cancer, in which CNV promotes both tumorigenesis and chemotherapy resistance. CNVs are considered random mutations but often arise through replication defects; transcription can interfere with replication fork progression and stability, leading to increased mutation rates at highly transcribed loci. Here we investigate whether inducible promoters can stimulate CNV to yield reproducible, environment-specific genetic changes. We propose a general mechanism for environmentally-stimulated CNV and validate this mechanism for the emergence of copper resistance in budding yeast. By analysing a large cohort of individual cells, we directly demonstrate that CNV of the copper-resistance gene CUP1 is stimulated by environmental copper. CNV stimulation accelerates the formation of novel alleles conferring enhanced copper resistance, such that copper exposure actively drives adaptation to copper-rich environments. Furthermore, quantification of CNV in individual cells reveals remarkable allele selectivity in the rate at which specific environments stimulate CNV. We define the key mechanistic elements underlying this selectivity, demonstrating that CNV is regulated by both promoter activity and acetylation of histone H3 lysine 56 (H3K56ac) and that H3K56ac is required for CUP1 CNV and efficient copper adaptation. Stimulated CNV is not limited to high-copy CUP1 repeat arrays, as we find that H3K56ac also regulates CNV in 3 copy arrays of CUP1 or SFA1 genes. The impact of transcription on DNA damage is well understood, but our research reveals that this apparently problematic association forms a pathway by which mutations can be directed to particular loci in particular environments and furthermore that this mutagenic process can be regulated through histone acetylation. Stimulated CNV therefore represents an unanticipated and remarkably controllable pathway facilitating organismal adaptation to new environments. Evolutionary theory asserts that adaptive mutations, which improve cellular fitness in challenging environments, occur at random and cannot be controlled by the cell. The mutation mechanisms involved are of widespread importance, governing diverse processes from the acquisition of resistance during chemotherapy to the emergence of nonproductive clones during industrial fermentations. Here we ask whether eukaryotic cells are in fact capable of stimulating useful, adaptive mutations at environmentally relevant loci. We show that yeast cells exposed to copper stimulate copy number amplification of the copper resistance gene CUP1, leading to the rapid emergence of adapted clones, and that this stimulation depends on the highly regulated acetylation of histone H3 lysine 56. Stimulated copy number variation (CNV) operates at sites of preexisting copy number variation, which are common in eukaryotic genomes, and provides cells with a remarkable and unexpected ability to alter their own genome in response to the environment.
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Affiliation(s)
- Ryan M. Hull
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Cristina Cruz
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Carmen V. Jack
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, The Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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157
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Lim J, Giri PK, Kazadi D, Laffleur B, Zhang W, Grinstein V, Pefanis E, Brown LM, Ladewig E, Martin O, Chen Y, Rabadan R, Boyer F, Rothschild G, Cogné M, Pinaud E, Deng H, Basu U. Nuclear Proximity of Mtr4 to RNA Exosome Restricts DNA Mutational Asymmetry. Cell 2017; 169:523-537.e15. [PMID: 28431250 DOI: 10.1016/j.cell.2017.03.043] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 01/19/2017] [Accepted: 03/27/2017] [Indexed: 11/16/2022]
Abstract
The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus. Both the physical proximity and coupled activities of RNA helicase Mtr4 (and senataxin) with the noncoding RNA processing function of RNA exosome determine the strand-specific distribution of DNA mutations. Our study suggests that strand-specific DNA mutagenesis-associated mechanisms will play major roles in other undiscovered aspects of organismic development.
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Affiliation(s)
- Junghyun Lim
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Pankaj Kumar Giri
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - David Kazadi
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Veronika Grinstein
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Evangelos Pefanis
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lewis M Brown
- Department of Biological Sciences, Quantitative Proteomics Center, Columbia University, New York, NY 10027, USA
| | - Erik Ladewig
- Departments of Systems Biology and Biomedical Informatics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Ophélie Martin
- Université de Limoges, Centre National de la Recherche Scientifique, CHU Limoges, CRIBL, UMR 7276, 87000 Limoges, France
| | - Yuling Chen
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Raul Rabadan
- Departments of Systems Biology and Biomedical Informatics, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - François Boyer
- Université de Limoges, Centre National de la Recherche Scientifique, CHU Limoges, CRIBL, UMR 7276, 87000 Limoges, France
| | - Gerson Rothschild
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Michel Cogné
- Université de Limoges, Centre National de la Recherche Scientifique, CHU Limoges, CRIBL, UMR 7276, 87000 Limoges, France
| | - Eric Pinaud
- Université de Limoges, Centre National de la Recherche Scientifique, CHU Limoges, CRIBL, UMR 7276, 87000 Limoges, France
| | - Haiteng Deng
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Uttiya Basu
- Department of Microbiology and Immunology, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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158
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Abstract
Ataxia Telangiectasia Mutated (ATM) has been known for decades as the main kinase mediating the DNA Double-Strand Break Response (DDR). Extensive studies have revealed its dual role in locally promoting detection and repair of DSBs as well as in activating global DNA damage checkpoints. However, recent studies pinpoint additional unanticipated functions for ATM in modifying both the local chromatin landscape and the global chromosome organization, more particularly at persistent breaks. Given the emergence of a novel and unexpected class of DSBs prevalently arising in transcriptionally active genes and intrinsically difficult to repair, a specific role of ATM at refractory DSBs could be an important and so far overlooked feature of Ataxia Telangiectasia (A-T) a severe disorder associated with ATM mutations.
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Affiliation(s)
- Thomas Clouaire
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, France.
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159
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Physiological functions of programmed DNA breaks in signal-induced transcription. Nat Rev Mol Cell Biol 2017; 18:471-476. [PMID: 28537575 DOI: 10.1038/nrm.2017.43] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The idea that signal-dependent transcription might involve the generation of transient DNA nicks or even breaks in the regulatory regions of genes, accompanied by activation of DNA damage repair pathways, would seem to be counterintuitive, as DNA damage is usually considered harmful to cellular integrity. However, recent studies have generated a substantial body of evidence that now argues that programmed DNA single- or double-strand breaks can, at least in specific cases, have a role in transcription regulation. Here, we discuss the emerging functions of DNA breaks in the relief of DNA torsional stress and in promoter and enhancer activation.
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160
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Malaby AW, Martin SK, Wood RD, Doublié S. Expression and Structural Analyses of Human DNA Polymerase θ (POLQ). Methods Enzymol 2017; 592:103-121. [PMID: 28668117 PMCID: PMC5624038 DOI: 10.1016/bs.mie.2017.03.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA polymerase theta (pol θ) is an evolutionarily conserved protein encoded by the POLQ gene in mammalian genomes. Pol θ is the defining enzyme for a pathway of DSB repair termed "alternative end-joining" (altEJ) or "theta-mediated end-joining." This pathway contributes significantly to the radiation resistance of mammalian cells. It also modulates accuracy in repair of breaks that occur at stalled DNA replication forks, during diversification steps of the mammalian immune system, during repair of CRISPR-Cas9, and in many DNA integration events. Pol θ is a potentially important clinical target, particularly for cancers deficient in other break repair strategies. The enzyme is uniquely able to mediate joining of single-stranded 3' ends. Because of these unusual biochemical properties and its therapeutic importance, it is essential to study structures of pol θ bound to DNA. However, challenges for expression and purification are presented by the large size of pol θ (2590 residues in humans) and unusual juxtaposition of domains (a helicase-like domain and distinct DNA polymerase, separated by a region predicted to be largely disordered). Here we summarize work on the expression and purification of the full-length protein, and then focus on the design, expression, and purification of an active C-terminal polymerase fragment. The generation of this active construct was nontrivial and time consuming. Almost all published biochemical work to date has been performed with this domain fragment. Strategies to obtain and improve crystals of a ternary pol θ complex (enzyme:DNA:nucleotide) are also presented, along with key elements of the structure.
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Affiliation(s)
| | - Sara K Martin
- The University of Texas MD Anderson Cancer Center, Smithville, TX, United States; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Richard D Wood
- The University of Texas MD Anderson Cancer Center, Smithville, TX, United States; MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX, United States
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161
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Tubbs A, Nussenzweig A. Endogenous DNA Damage as a Source of Genomic Instability in Cancer. Cell 2017; 168:644-656. [PMID: 28187286 DOI: 10.1016/j.cell.2017.01.002] [Citation(s) in RCA: 850] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/22/2016] [Accepted: 01/04/2017] [Indexed: 12/19/2022]
Abstract
Genome instability, defined as higher than normal rates of mutation, is a double-edged sword. As a source of genetic diversity and natural selection, mutations are beneficial for evolution. On the other hand, genomic instability can have catastrophic consequences for age-related diseases such as cancer. Mutations arise either from inactivation of DNA repair pathways or in a repair-competent background due to genotoxic stress from celluar processes such as transcription and replication that overwhelm high-fidelity DNA repair. Here, we review recent studies that shed light on endogenous sources of mutation and epigenomic features that promote genomic instability during cancer evolution.
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Affiliation(s)
- Anthony Tubbs
- Laboratory of Genome Integrity, NIH, Bethesda, MD 20892, USA
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162
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Conflict Resolution in the Genome: How Transcription and Replication Make It Work. Cell 2017; 167:1455-1467. [PMID: 27912056 DOI: 10.1016/j.cell.2016.09.053] [Citation(s) in RCA: 177] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/20/2016] [Accepted: 09/27/2016] [Indexed: 01/12/2023]
Abstract
The complex machineries involved in replication and transcription translocate along the same DNA template, often in opposing directions and at different rates. These processes routinely interfere with each other in prokaryotes, and mounting evidence now suggests that RNA polymerase complexes also encounter replication forks in higher eukaryotes. Indeed, cells rely on numerous mechanisms to avoid, tolerate, and resolve such transcription-replication conflicts, and the absence of these mechanisms can lead to catastrophic effects on genome stability and cell viability. In this article, we review the cellular responses to transcription-replication conflicts and highlight how these inevitable encounters shape the genome and impact diverse cellular processes.
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163
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McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, Mills RE, Paquola ACM, Rodin RE, Rosenbluh C, Sestan N, Sherman MA, Shin JH, Song S, Straub RE, Thorpe J, Weinberger DR, Urban AE, Zhou B, Gage FH, Lehner T, Senthil G, Walsh CA, Chess A, Courchesne E, Gleeson JG, Kidd JM, Park PJ, Pevsner J, Vaccarino FM. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science 2017; 356:356/6336/eaal1641. [PMID: 28450582 DOI: 10.1126/science.aal1641] [Citation(s) in RCA: 172] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neuropsychiatric disorders have a complex genetic architecture. Human genetic population-based studies have identified numerous heritable sequence and structural genomic variants associated with susceptibility to neuropsychiatric disease. However, these germline variants do not fully account for disease risk. During brain development, progenitor cells undergo billions of cell divisions to generate the ~80 billion neurons in the brain. The failure to accurately repair DNA damage arising during replication, transcription, and cellular metabolism amid this dramatic cellular expansion can lead to somatic mutations. Somatic mutations that alter subsets of neuronal transcriptomes and proteomes can, in turn, affect cell proliferation and survival and lead to neurodevelopmental disorders. The long life span of individual neurons and the direct relationship between neural circuits and behavior suggest that somatic mutations in small populations of neurons can significantly affect individual neurodevelopment. The Brain Somatic Mosaicism Network has been founded to study somatic mosaicism both in neurotypical human brains and in the context of complex neuropsychiatric disorders.
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164
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Marnef A, Cohen S, Legube G. Transcription-Coupled DNA Double-Strand Break Repair: Active Genes Need Special Care. J Mol Biol 2017; 429:1277-1288. [PMID: 28363678 DOI: 10.1016/j.jmb.2017.03.024] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/22/2022]
Abstract
For decades, it has been speculated that specific loci on eukaryotic chromosomes are inherently susceptible to breakage. The advent of high-throughput genomic technologies has now paved the way to their identification. A wealth of data suggests that transcriptionally active loci are particularly fragile and that a specific DNA damage response is activated and dedicated to their repair. Here, we review current understanding of the crosstalk between transcription and double-strand break repair, from the reasons underlying the intrinsic fragility of genes to the mechanisms that restore the integrity of damaged transcription units.
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Affiliation(s)
- Aline Marnef
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Sarah Cohen
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France
| | - Gaëlle Legube
- LBCMCP, Centre de Biologie Intégrative (CBI), CNRS, Université de Toulouse, UT3, 118 Route de Narbonne, 31062 Toulouse, France.
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165
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So A, Le Guen T, Lopez BS, Guirouilh-Barbat J. Genomic rearrangements induced by unscheduled DNA double strand breaks in somatic mammalian cells. FEBS J 2017; 284:2324-2344. [PMID: 28244221 DOI: 10.1111/febs.14053] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/02/2017] [Accepted: 02/24/2017] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can lead to profound genome rearrangements and/or cell death. They routinely occur in genomes due to endogenous or exogenous stresses. Efficient repair systems, canonical non-homologous end-joining and homologous recombination exist in the cell and not only ensure the maintenance of genome integrity but also, via specific programmed DNA double-strand breaks, permit its diversity and plasticity. However, these repair systems need to be tightly controlled because they can also generate genomic rearrangements. Thus, when DSB repair is not properly regulated, genome integrity is no longer guaranteed. In this review, we will focus on non-programmed genome rearrangements generated by DSB repair, in somatic cells. We first discuss genome rearrangements induced by homologous recombination and end-joining. We then discuss recently described rearrangement mechanisms, driven by microhomologies, that do not involve the joining of DNA ends but rather initiate DNA synthesis (microhomology-mediated break-induced replication, fork stalling and template switching and microhomology-mediated template switching). Finally, we discuss chromothripsis, which is the shattering of a localized region of the genome followed by erratic rejoining.
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Affiliation(s)
- Ayeong So
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Tangui Le Guen
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Bernard S Lopez
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Josée Guirouilh-Barbat
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
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166
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Genome-wide mapping of long-range contacts unveils clustering of DNA double-strand breaks at damaged active genes. Nat Struct Mol Biol 2017; 24:353-361. [PMID: 28263325 PMCID: PMC5385132 DOI: 10.1038/nsmb.3387] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 02/07/2017] [Indexed: 12/29/2022]
Abstract
The ability of DNA Double Strand Breaks (DSBs) to cluster in mammalian cells has been subjected to intense debate over the past few years. Here we used a high throughput chromosome conformation capture assay (Capture Hi-C) to investigate clustering of DSBs induced at defined loci in the human genome. We unambiguously found that DSBs do cluster but only when induced in transcriptionally active genes. Clustering of damaged genes mainly occurs during the G1 cell cycle phase and coincides with delayed repair. Moreover DSB clustering depends on the MRN complex, as well as the Formin 2 (FMN2) nuclear actin organizer and the LINC (LInker of Nuclear and Cytoplasmic skeleton) complex, suggesting that active mechanisms promote DSB clustering. This work reveals that when damaged, active genes exhibit a very peculiar behavior compared to the rest of the genome, being mostly left unrepaired and clustered in G1 while being repaired by homologous recombination in post-replicative cells.
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167
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry 2017; 22:430-440. [PMID: 27240532 DOI: 10.1038/mp.2016.88] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022]
Abstract
Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10-9, 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.
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Affiliation(s)
- I Kushima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Nakatochi
- Bioinformatics Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - J Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Maeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Noma
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Hamada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - A Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M-C Cheng
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Y-A Chuang
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - C-H Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - M Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - T Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - A Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - T Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - T Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - S Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ohmori
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - S Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - N Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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168
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Iida T, Iwanami A, Sanosaka T, Kohyama J, Miyoshi H, Nagoshi N, Kashiwagi R, Toyama Y, Matsumoto M, Nakamura M, Okano H. Whole-Genome DNA Methylation Analyses Revealed Epigenetic Instability in Tumorigenic Human iPS Cell-Derived Neural Stem/Progenitor Cells. Stem Cells 2017; 35:1316-1327. [PMID: 28142229 DOI: 10.1002/stem.2581] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 01/09/2017] [Indexed: 12/18/2022]
Abstract
Although human induced pluripotent stem cell (hiPSC) derivatives are considered promising cellular resources for regenerative medicine, their tumorigenicity potentially limits their clinical application in hiPSC technologies. We previously demonstrated that oncogenic hiPSC-derived neural stem/progenitor cells (hiPSC-NS/PCs) produced tumor-like tissues that were distinct from teratomas. To gain insight into the mechanisms underlying the regulation of tumorigenicity in hiPSC-NS/PCs, we performed an integrated analysis using the Infinium HumanMethylation450 BeadChip array and the HumanHT-12 v4.0 Expression BeadChip array to compare the comprehensive DNA methylation and gene expression profiles of tumorigenic hiPSC-NS/PCs (253G1-NS/PCs) and non-tumorigenic cells (201B7-NS/PCs). Although the DNA methylation profiles of 253G1-hiPSCs and 201B7-hiPSCs were similar regardless of passage number, the methylation status of the global DNA methylation profiles of 253G1-NS/PCs and 201B7-NS/PCs differed; the genomic regions surrounding the transcriptional start site of the CAT and PSMD5 genes were hypermethylated in 253G1-NS/PCs but not in 201B7-NS/PCs. Interestingly, the aberrant DNA methylation profile was more pronounced in 253G1-NS/PCs that had been passaged more than 15 times. In addition, we identified aberrations in DNA methylation at the RBP1 gene locus; the DNA methylation frequency in RBP1 changed as 253G1-NS/PCs were sequentially passaged. These results indicate that different NS/PC clones have different DNA methylomes and that DNA methylation patterns are unstable as cells are passaged. Therefore, DNA methylation profiles should be included in the criteria used to evaluate the tumorigenicity of hiPSC-NS/PCs in the clinical setting. Stem Cells 2017;35:1316-1327.
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Affiliation(s)
- Tsuyoshi Iida
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan.,Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Akio Iwanami
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Hiroyuki Miyoshi
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Narihito Nagoshi
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Rei Kashiwagi
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Yoshiaki Toyama
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Morio Matsumoto
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Masaya Nakamura
- Department of Orthopedic Surgery, Keio University School of Medicine, Shinjuku, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku, Tokyo, Japan
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169
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Affiliation(s)
- Andrew G Newman
- Institute for Cell and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Paraskevi Bessa
- Institute for Cell and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Tarabykin
- Institute for Cell and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Prim B Singh
- Institute for Cell and Neurobiology, Charité Universitätsmedizin Berlin, Berlin, Germany.,Department of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool, UK
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170
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Shining a light on early stress responses and late-onset disease vulnerability. Proc Natl Acad Sci U S A 2017; 114:2109-2111. [PMID: 28179564 DOI: 10.1073/pnas.1700323114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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171
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Sharma A, Ansari AH, Kumari R, Pandey R, Rehman R, Mehani B, Varma B, Desiraju BK, Mabalirajan U, Agrawal A, Mukhopadhyay A. Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res 2017; 5:2520. [PMID: 28149503 DOI: 10.12688/f1000research.9495.2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/08/2016] [Indexed: 12/11/2022] Open
Abstract
Somatic variation in DNA can cause cells to deviate from the preordained genomic path in both disease and healthy conditions. Here, using exome sequencing of paired tissue samples, we show that the normal human brain harbors somatic single base variations measuring up to 0.48% of the total variations. Interestingly, about 64% of these somatic variations in the brain are expected to lead to non-synonymous changes, and as much as 87% of these represent G:C>T:A transversion events. Further, the transversion events in the brain were mostly found in the frontal cortex, whereas the corpus callosum from the same individuals harbors the reference genotype. We found a significantly higher amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the corpus callosum of the same subjects (p<0.01), correlating with the higher G:C>T:A transversions in the cortex. We found significant enrichment for axon guidance and related pathways for genes harbouring somatic variations. This could represent either a directed selection of genetic variations in these pathways or increased susceptibility of some loci towards oxidative stress. This study highlights that oxidative stress possibly influence single nucleotide somatic variations in normal human brain.
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Affiliation(s)
- Anchal Sharma
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Asgar Hussain Ansari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Renu Kumari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Rakhshinda Rehman
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bharati Mehani
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bapu K Desiraju
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Ulaganathan Mabalirajan
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Anurag Agrawal
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Arijit Mukhopadhyay
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; School of Environment and Life Sciences, University of Salford, Manchester, UK
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172
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Abstract
Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.
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Affiliation(s)
- Michalis Fragkos
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
| | - Valeria Naim
- a CNRS UMR8200 , University Paris-Saclay , Gustave Roussy, Villejuif , France
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173
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Pruitt SC, Qin M, Wang J, Kunnev D, Freeland A. A Signature of Genomic Instability Resulting from Deficient Replication Licensing. PLoS Genet 2017; 13:e1006547. [PMID: 28045896 PMCID: PMC5242545 DOI: 10.1371/journal.pgen.1006547] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 01/18/2017] [Accepted: 12/19/2016] [Indexed: 11/23/2022] Open
Abstract
Insufficient licensing of DNA replication origins has been shown to result in genome instability, stem cell deficiency, and cancers. However, it is unclear whether the DNA damage resulting from deficient replication licensing occurs generally or if specific sites are preferentially affected. To map locations of ongoing DNA damage in vivo, the DNAs present in red blood cell micronuclei were sequenced. Many micronuclei are the product of DNA breaks that leave acentromeric remnants that failed to segregate during mitosis and should reflect the locations of breaks. To validate the approach we show that micronuclear sequences identify known common fragile sites under conditions that induce breaks at these locations (hydroxyurea). In MCM2 deficient mice a different set of preferred breakage sites is identified that includes the tumor suppressor gene Tcf3, which is known to contribute to T-lymphocytic leukemias that arise in these mice, and the 45S rRNA gene repeats. Many RBC micronuclei result from double strand DNA breaks that give rise to acentromeric chromosomal fragments that fail to incorporate into nuclei during mitosis and consequently remain in the cell following enucleation. Here, RBC micronuclear DNA is sequenced (Mic-Seq) to define the locations of breaks genome-wide and this assay is used to study ongoing genome instability resulting from insufficient DNA replication origin licensing. Using a mouse model, we show that there is increased instability at discrete sites across the genome, which include genes that are recurrently deleted in the T-lymphocytic leukemias that eventually arise in these mice. Mic-Seq may provide an effective means of predicting locations that are susceptible to genetic damage and these predictions may have prognostic value.
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Affiliation(s)
- Steven C. Pruitt
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- * E-mail:
| | - Maochun Qin
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Dimiter Kunnev
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Amy Freeland
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, New York, United States of America
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174
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Abstract
DNA topological transitions occur when replication forks encounter other DNA transactions such as transcription. Failure in resolving such conflicts leads to generation of aberrant replication and transcription intermediates that might have adverse effects on genome stability. Cells have evolved numerous surveillance mechanisms to avoid, tolerate, and resolve such replication-transcription conflicts. Defects or non-coordination in such cellular mechanisms might have catastrophic effect on cell viability. In this chapter, we review consequences of replication encounters with transcription and its associated events, topological challenges, and how these inevitable conflicts alter the genome structure and functions.
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175
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Recurrently Breaking Genes in Neural Progenitors: Potential Roles of DNA Breaks in Neuronal Function, Degeneration and Cancer. RESEARCH AND PERSPECTIVES IN NEUROSCIENCES 2017. [DOI: 10.1007/978-3-319-60192-2_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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176
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Watson LA, Tsai LH. In the loop: how chromatin topology links genome structure to function in mechanisms underlying learning and memory. Curr Opin Neurobiol 2016; 43:48-55. [PMID: 28024185 DOI: 10.1016/j.conb.2016.12.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/01/2016] [Accepted: 12/05/2016] [Indexed: 12/18/2022]
Abstract
Different aspects of learning, memory, and cognition are regulated by epigenetic mechanisms such as covalent DNA modifications and histone post-translational modifications. More recently, the modulation of chromatin architecture and nuclear organization is emerging as a key factor in dynamic transcriptional regulation of the post-mitotic neuron. For instance, neuronal activity induces relocalization of gene loci to 'transcription factories', and specific enhancer-promoter looping contacts allow for precise transcriptional regulation. Moreover, neuronal activity-dependent DNA double-strand break formation in the promoter of immediate early genes appears to overcome topological constraints on transcription. Together, these findings point to a critical role for genome topology in integrating dynamic environmental signals to define precise spatiotemporal gene expression programs supporting cognitive processes.
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Affiliation(s)
| | - Li-Huei Tsai
- Picower Institute for Learning and Memory, USA; Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Building 46, Room 4235A, Cambridge, MA 02139, USA.
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177
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Hazan I, Hofmann TG, Aqeilan RI. Tumor Suppressor Genes within Common Fragile Sites Are Active Players in the DNA Damage Response. PLoS Genet 2016; 12:e1006436. [PMID: 27977694 PMCID: PMC5157955 DOI: 10.1371/journal.pgen.1006436] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The role of common fragile sites (CFSs) in cancer remains controversial. Two main views dominate the discussion: one suggests that CFS loci are hotspots of genomic instability leading to inactivation of genes encoded within them, while the other view proposes that CFSs are functional units and that loss of the encoded genes confers selective pressure, leading to cancer development. The latter view is supported by emerging evidence showing that expression of a given CFS is associated with genome integrity and that inactivation of CFS-resident tumor suppressor genes leads to dysregulation of the DNA damage response (DDR) and increased genomic instability. These two viewpoints of CFS function are not mutually exclusive but rather coexist; when breaks at CFSs are not repaired accurately, this can lead to deletions by which cells acquire growth advantage because of loss of tumor suppressor activities. Here, we review recent advances linking some CFS gene products with the DDR, genomic instability, and carcinogenesis and discuss how their inactivation might represent a selective advantage for cancer cells.
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Affiliation(s)
- Idit Hazan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Thomas G. Hofmann
- Cellular Senescence Group, Department of Epigenetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rami I. Aqeilan
- Lautenberg Center for Immunology and Cancer Research, IMRIC, Hebrew University-Hadassah Medical School, Jerusalem, Israel
- Department of Cancer Biology and Genetics, The Ohio State University Wexner Medical Center, Columbus, Ohio, United States of America
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, Vermont, United States of America
- * E-mail:
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178
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Abstract
Post-zygotic variation refers to genetic changes that arise in the soma of an individual and that are not usually inherited by the next generation. Although there is a paucity of research on such variation, emerging studies show that it is common: individuals are complex mosaics of genetically distinct cells, to such an extent that no two somatic cells are likely to have the exact same genome. Although most types of mutation can be involved in post-zygotic variation, structural genetic variants are likely to leave the largest genomic footprint. Somatic variation has diverse physiological roles and pathological consequences, particularly when acquired variants influence the clonal trajectories of the affected cells. Post-zygotic variation is an important confounder in medical genetic testing and a promising avenue for research: future studies could involve analyses of sorted and single cells from multiple tissue types to fully explore its potential.
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179
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Poot M. Retrotransposing Gremlins May Disrupt Our Brain's Genomes. Mol Syndromol 2016; 8:55-57. [PMID: 28611545 DOI: 10.1159/000453247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2016] [Indexed: 11/19/2022] Open
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180
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Abstract
Somatic mosaicism refers to the fact that cells within an organism have different genomes. It is now clear that somatic mosaicism occurs in all brains and that somatic mutations in a subset of cells can cause various rare neurodevelopmental disorders. However, for most individuals, the extent and consequences of somatic mosaicism are largely unknown. The complexity and unique features of the brain suggest that somatic mosaicism can play an important role in behavior and cognition. Here we review recent manuscripts showing instances of somatic mosaicism in the brain and estimating its extent and possible biological consequences. The consequences of somatic mosaicism span vast dimensions -from a single-locus variant, to genes and gene networks, to cells, to the interactions of the mosaic cells via neural networks affecting behavior and cognition. We highlight how systems biology approaches are particularly well suited for the complex emerging field of brain somatic mosaicism.
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Affiliation(s)
| | | | - Fred H Gage
- Salk Institute for Biological Studies, La Jolla, CA, USA
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181
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Stanley CE, Kulathinal RJ. Neurogenomics and the role of a large mutational target on rapid behavioral change. Biol Direct 2016; 11:60. [PMID: 27825385 PMCID: PMC5101817 DOI: 10.1186/s13062-016-0162-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/24/2016] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage. However, unlike other rapidly evolving functional systems such as sperm-egg interactions and immune defense, the genetic basis of rapid behavioral change remains elusive. PRESENTATION OF THE HYPOTHESIS Here we propose that the rapid divergence and widespread novelty of innate and adaptive behavior is primarily a function of its genomic architecture. Specifically, we hypothesize that the broad diversity of behavioral phenotypes present at micro- and macroevolutionary scales is promoted by a disproportionately large mutational target of neurogenic genes. We present evidence that these large neuro-behavioral targets are significant and ubiquitous in animal genomes and suggest that behavior's novelty and rapid emergence are driven by a number of factors including more selection on a larger pool of variants, a greater role of phenotypic plasticity, and/or unique molecular features present in large genes. We briefly discuss the origins of these large neurogenic genes, as they relate to the remarkable diversity of metazoan behaviors, and highlight key consequences on both behavioral traits and neurogenic disease across, respectively, evolutionary and ontogenetic time scales. TESTING THE HYPOTHESIS Current approaches to studying the genetic mechanisms underlying rapid phenotypic change primarily focus on identifying signatures of Darwinian selection in protein-coding regions. In contrast, the large mutational target hypothesis places genomic architecture and a larger allelic pool at the forefront of rapid evolutionary change, particularly in genetic systems that are polygenic and regulatory in nature. Genomic data from brain and neural tissues in mammals as well as a preliminary survey of neurogenic genes from comparative genomic data support this hypothesis while rejecting both positive and relaxed selection on proteins or higher mutation rates. In mammals and invertebrates, neurogenic genes harbor larger protein-coding regions and possess a richer regulatory repertoire of miRNA targets and transcription factor binding sites. Overall, neurogenic genes cover a disproportionately large genomic fraction, providing a sizeable substrate for evolutionary, genetic, and molecular mechanisms to act upon. Readily available comparative and functional genomic data provide unexplored opportunities to test whether a distinct neurogenomic architecture can promote rapid behavioral change via several mechanisms unique to large genes, and which components of this large footprint are uniquely metazoan. IMPLICATIONS OF THE HYPOTHESIS The large mutational target hypothesis highlights the eminent roles of mutation and functional genomic architecture in generating rapid developmental and evolutionary change. It has broad implications on our understanding of the genetics of complex adaptive traits such as behavior by focusing on the importance of mutational input, from SNPs to alternative transcripts to transposable elements, on driving evolutionary rates of functional systems. Such functional divergence has important implications in promoting behavioral isolation across short- and long-term timescales. Due to genome-scaled polygenic adaptation, the large target effect also contributes to our inability to identify adapted behavioral candidate genes. The presence of large neurogenic genes, particularly in the mammalian brain and other neural tissues, further offers emerging insight into the etiology of neurodevelopmental and neurodegenerative diseases. The well-known correlation between neurological spectrum disorders in children and paternal age may simply be a direct result of aging fathers accumulating mutations across these large neurodevelopmental genes. The large mutational target hypothesis can also explain the rapid evolution of other functional systems covering a large genomic fraction such as male fertility and its preferential association with hybrid male sterility among closely related taxa. Overall, a focus on mutational potential may increase our power in understanding the genetic basis of complex phenotypes such as behavior while filling a general gap in understanding their evolution.
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Affiliation(s)
- Craig E. Stanley
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
- Institute of Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122 USA
| | - Rob J. Kulathinal
- Department of Biology, Temple University, Philadelphia, PA 19122 USA
- Institute of Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA 19122 USA
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182
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Oestergaard VH, Lisby M. Transcription-replication conflicts at chromosomal fragile sites-consequences in M phase and beyond. Chromosoma 2016; 126:213-222. [PMID: 27796495 DOI: 10.1007/s00412-016-0617-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 12/29/2022]
Abstract
Collision between the molecular machineries responsible for transcription and replication is an important source of genome instability. Certain transcribed regions known as chromosomal fragile sites are particularly prone to recombine and mutate in a manner that correlates with specific transcription and replication patterns. At the same time, these chromosomal fragile sites engage in aberrant DNA structures in mitosis. Here, we discuss the mechanistic details of transcription-replication conflicts including putative scenarios for R-loop-induced replication inhibition to understand how transcription-replication conflicts transition from S phase into various aberrant DNA structures in mitosis.
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Affiliation(s)
- Vibe H Oestergaard
- Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200, Copenhagen N, Denmark.
| | - Michael Lisby
- Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200, Copenhagen N, Denmark.
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183
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ZIKA virus elicits P53 activation and genotoxic stress in human neural progenitors similar to mutations involved in severe forms of genetic microcephaly. Cell Death Dis 2016; 7:e2440. [PMID: 27787521 PMCID: PMC5133962 DOI: 10.1038/cddis.2016.266] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/20/2016] [Accepted: 07/26/2016] [Indexed: 12/30/2022]
Abstract
Epidemiological evidence from the current outbreak of Zika virus (ZIKV) and recent studies in animal models indicate a strong causal link between ZIKV and microcephaly. ZIKV infection induces cell-cycle arrest and apoptosis in proliferating neural progenitors. However, the mechanisms leading to these phenotypes are still largely obscure. In this report, we explored the possible similarities between transcriptional responses induced by ZIKV in human neural progenitors and those elicited by three different genetic mutations leading to severe forms of microcephaly in mice. We found that the strongest similarity between all these conditions is the activation of common P53 downstream genes. In agreement with these observations, we report that ZIKV infection increases total P53 levels and nuclear accumulation, as well as P53 Ser15 phosphorylation, correlated with genotoxic stress and apoptosis induction. Interestingly, increased P53 activation and apoptosis are induced not only in cells expressing high levels of viral antigens but also in cells showing low or undetectable levels of the same proteins. These results indicate that P53 activation is an early and specific event in ZIKV-infected cells, which could result from cell-autonomous and/or non-cell-autonomous mechanisms. Moreover, we highlight a small group of P53 effector proteins that could act as critical mediators, not only in ZIKV-induced microcephaly but also in many genetic microcephaly syndromes.
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184
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Weiss KM. The cat in between: Nature, nurture, . . . neither! Evol Anthropol 2016; 25:222-227. [PMID: 27753215 DOI: 10.1002/evan.21489] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Indexed: 12/22/2022]
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185
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Sharma A, Ansari AH, Kumari R, Pandey R, Rehman R, Mehani B, Varma B, Desiraju BK, Mabalirajan U, Agrawal A, Mukhopadhyay A. Human brain harbors single nucleotide somatic variations in functionally relevant genes possibly mediated by oxidative stress. F1000Res 2016; 5:2520. [PMID: 28149503 PMCID: PMC5265704 DOI: 10.12688/f1000research.9495.3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/11/2017] [Indexed: 12/14/2022] Open
Abstract
Somatic variation in DNA can cause cells to deviate from the preordained genomic
path in both disease and healthy conditions. Here, using exome sequencing of
paired tissue samples, we show that the normal human brain harbors somatic
single base variations measuring up to 0.48% of the total variations.
Interestingly, about 64% of these somatic variations in the brain are expected
to lead to non-synonymous changes, and as much as 87% of these represent
G:C>T:A transversion events. Further, the transversion events in the brain
were mostly found in the frontal cortex, whereas the corpus callosum from the
same individuals harbors the reference genotype. We found a significantly higher
amount of 8-OHdG (oxidative stress marker) in the frontal cortex compared to the
corpus callosum of the same subjects (p<0.01), correlating with the higher
G:C>T:A transversions in the cortex. We found significant enrichment for axon
guidance and related pathways for genes harbouring somatic variations. This
could represent either a directed selection of genetic variations in these
pathways or increased susceptibility of some loci towards oxidative stress. This
study highlights that oxidative stress possibly influence single nucleotide
somatic variations in normal human brain.
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Affiliation(s)
- Anchal Sharma
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Asgar Hussain Ansari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Renu Kumari
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Rakhshinda Rehman
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bharati Mehani
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India
| | - Binuja Varma
- CSIR Ayurgenomics Unit- TRISUTRA, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Bapu K Desiraju
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Ulaganathan Mabalirajan
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Anurag Agrawal
- Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; Molecular Immunogenetics Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India
| | - Arijit Mukhopadhyay
- Genomics & Molceular Medicine Unit, CSIR-Institute of Genomics & Integrative Biology, Delhi, 110020, India; Academy of Scientific and Innovative Research, CSIR-Institute of Genomics & Integrative Biology (AcSIR-IGIB), Delhi, 110020, India; School of Environment and Life Sciences, University of Salford, Manchester, UK
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186
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Moore DL, Jessberger S. Creating Age Asymmetry: Consequences of Inheriting Damaged Goods in Mammalian Cells. Trends Cell Biol 2016; 27:82-92. [PMID: 27717533 DOI: 10.1016/j.tcb.2016.09.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 12/15/2022]
Abstract
Accumulating evidence suggests that mammalian cells asymmetrically segregate cellular components ranging from genomic DNA to organelles and damaged proteins during cell division. Asymmetric inheritance upon mammalian cell division may be specifically important to ensure cellular fitness and propagate cellular potency to individual progeny, for example in the context of somatic stem cell division. We review here recent advances in the field and discuss potential effects and underlying mechanisms that mediate asymmetric segregation of cellular components during mammalian cell division.
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Affiliation(s)
- Darcie L Moore
- Department of Neuroscience, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA.
| | - Sebastian Jessberger
- Brain Research Institute, Faculty of Medicine and Science, University of Zurich, 8057 Zurich, Switzerland.
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187
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PAXX and XLF DNA repair factors are functionally redundant in joining DNA breaks in a G1-arrested progenitor B-cell line. Proc Natl Acad Sci U S A 2016; 113:10619-24. [PMID: 27601633 DOI: 10.1073/pnas.1611882113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Classical nonhomologous end joining (C-NHEJ) is a major mammalian DNA double-strand break (DSB) repair pathway. Core C-NHEJ factors, such as XRCC4, are required for joining DSB intermediates of the G1 phase-specific V(D)J recombination reaction in progenitor lymphocytes. Core factors also contribute to joining DSBs in cycling mature B-lineage cells, including DSBs generated during antibody class switch recombination (CSR) and DSBs generated by ionizing radiation. The XRCC4-like-factor (XLF) C-NHEJ protein is dispensable for V(D)J recombination in normal cells, but because of functional redundancy, it is absolutely required for this process in cells deficient for the ataxia telangiectasia-mutated (ATM) DSB response factor. The recently identified paralogue of XRCC4 and XLF (PAXX) factor has homology to these two proteins and variably contributes to ionizing radiation-induced DSB repair in human and chicken cells. We now report that PAXX is dispensable for joining V(D)J recombination DSBs in G1-arrested mouse pro-B-cell lines, dispensable for joining CSR-associated DSBs in a cycling mouse B-cell line, and dispensable for normal ionizing radiation resistance in both G1-arrested and cycling pro-B lines. However, we find that combined deficiency for PAXX and XLF in G1-arrested pro-B lines abrogates DSB joining during V(D)J recombination and sensitizes the cells to ionizing radiation exposure. Thus, PAXX provides core C-NHEJ factor-associated functions in the absence of XLF and vice versa in G1-arrested pro-B-cell lines. Finally, we also find that PAXX deficiency has no impact on V(D)J recombination DSB joining in ATM-deficient pro-B lines. We discuss implications of these findings with respect to potential PAXX and XLF functions in C-NHEJ.
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188
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Abstract
DNA polymerase theta (pol θ) is encoded in the genomes of many eukaryotes, though not in fungi. Pol θ is encoded by the POLQ gene in mammalian cells. The C-terminal third of the protein is a family A DNA polymerase with additional insertion elements relative to prokaryotic homologs. The N-terminal third is a helicase-like domain with DNA-dependent ATPase activity. Pol θ is important in the repair of genomic double-strand breaks (DSBs) from many sources. These include breaks formed by ionizing radiation and topoisomerase inhibitors, breaks arising at stalled DNA replication forks, breaks introduced during diversification steps of the mammalian immune system, and DSB induced by CRISPR-Cas9. Pol θ participates in a route of DSB repair termed "alternative end-joining" (altEJ). AltEJ is independent of the DNA binding Ku protein complex and requires DNA end resection. Pol θ is able to mediate joining of two resected 3' ends harboring DNA sequence microhomology. "Signatures" of Pol θ action during altEJ are the frequent utilization of longer microhomologies, and the insertion of additional sequences at joining sites. The mechanism of end-joining employs the ability of Pol θ to tightly grasp a 3' terminus through unique contacts in the active site, allowing extension from minimally paired primers. Pol θ is involved in controlling the frequency of chromosome translocations and preserves genome integrity by limiting large deletions. It may also play a backup role in DNA base excision repair. POLQ is a member of a cluster of similarly upregulated genes that are strongly correlated with poor clinical outcome for breast cancer, ovarian cancer and other cancer types. Inhibition of pol θ is a compelling approach for combination therapy of radiosensitization.
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Affiliation(s)
- Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, P.O. Box 389, Smithville, TX 78957, USA; Graduate School of Biomedical Sciences at Houston, USA.
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405, USA.
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189
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Highly sensitive and unbiased approach for elucidating antibody repertoires. Proc Natl Acad Sci U S A 2016; 113:7846-51. [PMID: 27354528 DOI: 10.1073/pnas.1608649113] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Developing B lymphocytes undergo V(D)J recombination to assemble germ-line V, D, and J gene segments into exons that encode the antigen-binding variable region of Ig heavy (H) and light (L) chains. IgH and IgL chains associate to form the B-cell receptor (BCR), which, upon antigen binding, activates B cells to secrete BCR as an antibody. Each of the huge number of clonally independent B cells expresses a unique set of IgH and IgL variable regions. The ability of V(D)J recombination to generate vast primary B-cell repertoires results from a combinatorial assortment of large numbers of different V, D, and J segments, coupled with diversification of the junctions between them to generate the complementary determining region 3 (CDR3) for antigen contact. Approaches to evaluate in depth the content of primary antibody repertoires and, ultimately, to study how they are further molded by secondary mutation and affinity maturation processes are of great importance to the B-cell development, vaccine, and antibody fields. We now describe an unbiased, sensitive, and readily accessible assay, referred to as high-throughput genome-wide translocation sequencing-adapted repertoire sequencing (HTGTS-Rep-seq), to quantify antibody repertoires. HTGTS-Rep-seq quantitatively identifies the vast majority of IgH and IgL V(D)J exons, including their unique CDR3 sequences, from progenitor and mature mouse B lineage cells via the use of specific J primers. HTGTS-Rep-seq also accurately quantifies DJH intermediates and V(D)J exons in either productive or nonproductive configurations. HTGTS-Rep-seq should be useful for studies of human samples, including clonal B-cell expansions, and also for following antibody affinity maturation processes.
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190
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Detecting DNA double-stranded breaks in mammalian genomes by linear amplification-mediated high-throughput genome-wide translocation sequencing. Nat Protoc 2016; 11:853-71. [PMID: 27031497 DOI: 10.1038/nprot.2016.043] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Unbiased, high-throughput assays for detecting and quantifying DNA double-stranded breaks (DSBs) across the genome in mammalian cells will facilitate basic studies of the mechanisms that generate and repair endogenous DSBs. They will also enable more applied studies, such as those to evaluate the on- and off-target activities of engineered nucleases. Here we describe a linear amplification-mediated high-throughput genome-wide sequencing (LAM-HTGTS) method for the detection of genome-wide 'prey' DSBs via their translocation in cultured mammalian cells to a fixed 'bait' DSB. Bait-prey junctions are cloned directly from isolated genomic DNA using LAM-PCR and unidirectionally ligated to bridge adapters; subsequent PCR steps amplify the single-stranded DNA junction library in preparation for Illumina Miseq paired-end sequencing. A custom bioinformatics pipeline identifies prey sequences that contribute to junctions and maps them across the genome. LAM-HTGTS differs from related approaches because it detects a wide range of broken end structures with nucleotide-level resolution. Familiarity with nucleic acid methods and next-generation sequencing analysis is necessary for library generation and data interpretation. LAM-HTGTS assays are sensitive, reproducible, relatively inexpensive, scalable and straightforward to implement with a turnaround time of <1 week.
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191
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Affiliation(s)
- Thomas W Glover
- Departments of Human Genetics and Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Departments of Human Genetics and Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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192
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Schwer B, Wei PC, Chang AN, Kao J, Du Z, Meyers RM, Alt FW. Transcription-associated processes cause DNA double-strand breaks and translocations in neural stem/progenitor cells. Proc Natl Acad Sci U S A 2016; 113:2258-63. [PMID: 26873106 PMCID: PMC4776469 DOI: 10.1073/pnas.1525564113] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
High-throughput, genome-wide translocation sequencing (HTGTS) studies of activated B cells have revealed that DNA double-strand breaks (DSBs) capable of translocating to defined bait DSBs are enriched around the transcription start sites (TSSs) of active genes. We used the HTGTS approach to investigate whether a similar phenomenon occurs in primary neural stem/progenitor cells (NSPCs). We report that breakpoint junctions indeed are enriched around TSSs that were determined to be active by global run-on sequencing analyses of NSPCs. Comparative analyses of transcription profiles in NSPCs and B cells revealed that the great majority of TSS-proximal junctions occurred in genes commonly expressed in both cell types, possibly because this common set has higher transcription levels on average than genes transcribed in only one or the other cell type. In the latter context, among all actively transcribed genes containing translocation junctions in NSPCs, those with junctions located within 2 kb of the TSS show a significantly higher transcription rate on average than genes with junctions in the gene body located at distances greater than 2 kb from the TSS. Finally, analysis of repair junction signatures of TSS-associated translocations in wild-type versus classical nonhomologous end-joining (C-NHEJ)-deficient NSPCs reveals that both C-NHEJ and alternative end-joining pathways can generate translocations by joining TSS-proximal DSBs to DSBs on other chromosomes. Our studies show that the generation of transcription-associated DSBs is conserved across divergent cell types.
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Affiliation(s)
- Bjoern Schwer
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Pei-Chi Wei
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Amelia N Chang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Jennifer Kao
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Zhou Du
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Robin M Meyers
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115; Department of Genetics, Harvard Medical School, Boston, MA 02115; Department of Pediatrics, Harvard Medical School, Boston, MA 02115
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193
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