1
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Salvadores M, Supek F. Cell cycle gene alterations associate with a redistribution of mutation risk across chromosomal domains in human cancers. NATURE CANCER 2024; 5:330-346. [PMID: 38200245 DOI: 10.1038/s43018-023-00707-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
Mutations in human cells exhibit increased burden in heterochromatic, late DNA replication time (RT) chromosomal domains, with variation in mutation rates between tissues mirroring variation in heterochromatin and RT. We observed that regional mutation risk further varies between individual tumors in a manner independent of cell type, identifying three signatures of domain-scale mutagenesis in >4,000 tumor genomes. The major signature reflects remodeling of heterochromatin and of the RT program domains seen across tumors, tissues and cultured cells, and is robustly linked with higher expression of cell proliferation genes. Regional mutagenesis is associated with loss of activity of the tumor-suppressor genes RB1 and TP53, consistent with their roles in cell cycle control, with distinct mutational patterns generated by the two genes. Loss of regional heterogeneity in mutagenesis is associated with deficiencies in various DNA repair pathways. These mutation risk redistribution processes modify the mutation supply towards important genes, diverting the course of somatic evolution.
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Affiliation(s)
- Marina Salvadores
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Fran Supek
- Genome Data Science, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
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2
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Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Rep 2024; 43:113664. [PMID: 38194345 DOI: 10.1016/j.celrep.2023.113664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/27/2023] [Accepted: 12/21/2023] [Indexed: 01/10/2024] Open
Abstract
Induced pluripotent stem cells (iPSCs) are the foundation of cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which could affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing, a process linked to both genome regulation and genome stability, is efficiently reprogrammed to the embryonic state. To answer this, we compare genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicate their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibits delayed replication at heterochromatic regions containing genes downregulated in iPSCs with incompletely reprogrammed DNA methylation. DNA replication delays are not the result of gene expression or DNA methylation aberrations and persist after cells differentiate to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and influence the quality of iPSCs.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Sakshi Bhatele
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA; Columbia University Stem Cell Initiative, New York, NY 10032, USA.
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA; Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.
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3
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Chanou A, Weiβ M, Holler K, Sajid A, Straub T, Krietsch J, Sanchi A, Ummethum H, Lee CSK, Kruse E, Trauner M, Werner M, Lalonde M, Lopes M, Scialdone A, Hamperl S. Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency. Nucleic Acids Res 2023; 51:12303-12324. [PMID: 37956271 PMCID: PMC10711542 DOI: 10.1093/nar/gkad1022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Stochastic origin activation gives rise to significant cell-to-cell variability in the pattern of genome replication. The molecular basis for heterogeneity in efficiency and timing of individual origins is a long-standing question. Here, we developed Methylation Accessibility of TArgeted Chromatin domain Sequencing (MATAC-Seq) to determine single-molecule chromatin accessibility of four specific genomic loci. MATAC-Seq relies on preferential modification of accessible DNA by methyltransferases combined with Nanopore-Sequencing for direct readout of methylated DNA-bases. Applying MATAC-Seq to selected early-efficient and late-inefficient yeast replication origins revealed large heterogeneity of chromatin states. Disruption of INO80 or ISW2 chromatin remodeling complexes leads to changes at individual nucleosomal positions that correlate with changes in their replication efficiency. We found a chromatin state with an accessible nucleosome-free region in combination with well-positioned +1 and +2 nucleosomes as a strong predictor for efficient origin activation. Thus, MATAC-Seq identifies the large spectrum of alternative chromatin states that co-exist on a given locus previously masked in population-based experiments and provides a mechanistic basis for origin activation heterogeneity during eukaryotic DNA replication. Consequently, our single-molecule chromatin accessibility assay will be ideal to define single-molecule heterogeneity across many fundamental biological processes such as transcription, replication, or DNA repair in vitro and ex vivo.
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Affiliation(s)
- Anna Chanou
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Karoline Holler
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Atiqa Sajid
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, Biomedical Center, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Andrea Sanchi
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Henning Ummethum
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Clare S K Lee
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Elisabeth Kruse
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Manuel Trauner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Marcel Werner
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Maxime Lalonde
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Antonio Scialdone
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
- Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Stephan Hamperl
- Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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4
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Lee CSK, Weiβ M, Hamperl S. Where and when to start: Regulating DNA replication origin activity in eukaryotic genomes. Nucleus 2023; 14:2229642. [PMID: 37469113 PMCID: PMC10361152 DOI: 10.1080/19491034.2023.2229642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/20/2023] [Accepted: 06/21/2023] [Indexed: 07/21/2023] Open
Abstract
In eukaryotic genomes, hundreds to thousands of potential start sites of DNA replication named origins are dispersed across each of the linear chromosomes. During S-phase, only a subset of origins is selected in a stochastic manner to assemble bidirectional replication forks and initiate DNA synthesis. Despite substantial progress in our understanding of this complex process, a comprehensive 'identity code' that defines origins based on specific nucleotide sequences, DNA structural features, the local chromatin environment, or 3D genome architecture is still missing. In this article, we review the genetic and epigenetic features of replication origins in yeast and metazoan chromosomes and highlight recent insights into how this flexibility in origin usage contributes to nuclear organization, cell growth, differentiation, and genome stability.
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Affiliation(s)
- Clare S K Lee
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Matthias Weiβ
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
| | - Stephan Hamperl
- Chromosome Dynamics and Genome Stability, Institute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany
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5
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Caballero M, Koren A. The landscape of somatic mutations in lymphoblastoid cell lines. CELL GENOMICS 2023; 3:100305. [PMID: 37388907 PMCID: PMC10300552 DOI: 10.1016/j.xgen.2023.100305] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/03/2023] [Accepted: 03/28/2023] [Indexed: 07/01/2023]
Abstract
Somatic mutations have important biological ramifications while exerting substantial rate, type, and genomic location heterogeneity. Yet, their sporadic occurrence makes them difficult to study at scale and across individuals. Lymphoblastoid cell lines (LCLs), a model system for human population and functional genomics, harbor large numbers of somatic mutations and have been extensively genotyped. By comparing 1,662 LCLs, we report that the mutational landscape of the genome varies across individuals in terms of the number of mutations, their genomic locations, and their spectra; this variation may itself be modulated by somatic trans-acting mutations. Mutations attributed to the translesion DNA polymerase η follow two different modes of formation, with one mode accounting for the hypermutability of the inactive X chromosome. Nonetheless, the distribution of mutations along the inactive X chromosome appears to follow an epigenetic memory of the active form.
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Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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6
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Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544654. [PMID: 37398435 PMCID: PMC10312660 DOI: 10.1101/2023.06.12.544654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Induced pluripotent stem cells (iPSC) are a widely used cell system and a foundation for cell therapy. Differences in gene expression, DNA methylation, and chromatin conformation, which have the potential to affect differentiation capacity, have been identified between iPSCs and embryonic stem cells (ESCs). Less is known about whether DNA replication timing - a process linked to both genome regulation and genome stability - is efficiently reprogrammed to the embryonic state. To answer this, we profiled and compared genome-wide replication timing between ESCs, iPSCs, and cells reprogrammed by somatic cell nuclear transfer (NT-ESCs). While NT-ESCs replicated their DNA in a manner indistinguishable from ESCs, a subset of iPSCs exhibit delayed replication at heterochromatic regions containing genes downregulated in iPSC with incompletely reprogrammed DNA methylation. DNA replication delays were not the result of gene expression and DNA methylation aberrations and persisted after differentiating cells to neuronal precursors. Thus, DNA replication timing can be resistant to reprogramming and lead to undesirable phenotypes in iPSCs, establishing it as an important genomic feature to consider when evaluating iPSC lines.
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Affiliation(s)
- Matthew M. Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Ning Wang
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Dashiell J. Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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7
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Weinstock JS, Laurie CA, Broome JG, Taylor KD, Guo X, Shuldiner AR, O’Connell JR, Lewis JP, Boerwinkle E, Barnes KC, Chami N, Kenny EE, Loos RJ, Fornage M, Redline S, Cade BE, Gilliland FD, Chen Z, Gauderman WJ, Kumar R, Grammer L, Schleimer RP, Psaty BM, Bis JC, Brody JA, Silverman EK, Yun JH, Qiao D, Weiss ST, Lasky-Su J, DeMeo DL, Palmer ND, Freedman BI, Bowden DW, Cho MH, Vasan RS, Johnson AD, Yanek LR, Becker LC, Kardia S, He J, Kaplan R, Heckbert SR, Smith NL, Wiggins KL, Arnett DK, Irvin MR, Tiwari H, Correa A, Raffield LM, Gao Y, de Andrade M, Rotter JI, Rich SS, Manichaikul AW, Konkle BA, Johnsen JM, Wheeler MM, Custer BS, Duggirala R, Curran JE, Blangero J, Gui H, Xiao S, Williams LK, Meyers DA, Li X, Ortega V, McGarvey S, Gu CC, Chen YDI, Lee WJ, Shoemaker MB, Darbar D, Roden D, Albert C, Kooperberg C, Desai P, Blackwell TW, Abecasis GR, Smith AV, Kang HM, Mathias R, Natarajan P, Jaiswal S, Reiner AP, Bick AG. The genetic determinants of recurrent somatic mutations in 43,693 blood genomes. SCIENCE ADVANCES 2023; 9:eabm4945. [PMID: 37126548 PMCID: PMC10132750 DOI: 10.1126/sciadv.abm4945] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.
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Affiliation(s)
- Joshua S. Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Cecelia A. Laurie
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Jai G. Broome
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Alan R. Shuldiner
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Jeffrey R. O’Connell
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Joshua P. Lewis
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
| | - Eric Boerwinkle
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kathleen C. Barnes
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Nathalie Chami
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eimear E. Kenny
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J. F. Loos
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
| | - Brian E. Cade
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Frank D. Gilliland
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhanghua Chen
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - W. James Gauderman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Rajesh Kumar
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Leslie Grammer
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Edwin K. Silverman
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jeong H. Yun
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dandi Qiao
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Scott T. Weiss
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Jessica Lasky-Su
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Dawn L. DeMeo
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Michael H. Cho
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Ramachandran S. Vasan
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lewis C. Becker
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Sharon Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Robert Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Susan R. Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
| | - Nicholas L. Smith
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
| | - Kerri L. Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Donna K. Arnett
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
| | | | - Hemant Tiwari
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Adolfo Correa
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yan Gao
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Mariza de Andrade
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S. Rich
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Ani W. Manichaikul
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
| | - Barbara A. Konkle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Jill M. Johnsen
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
| | | | | | - Ravindranath Duggirala
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Joanne E. Curran
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
| | - Hongsheng Gui
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Shujie Xiao
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - L. Keoki Williams
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
| | - Deborah A. Meyers
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Xingnan Li
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
| | - Victor Ortega
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
| | - Stephen McGarvey
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
| | - C. Charles Gu
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wen-Jane Lee
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
| | - M. Benjamin Shoemaker
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Dawood Darbar
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Dan Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Christine Albert
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Pinkal Desai
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
| | - Thomas W. Blackwell
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Goncalo R. Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
| | - Albert V. Smith
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Hyun M. Kang
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Rasika Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Alexander G. Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
| | - NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, University of Maryland, Baltimore, Baltimore, MD 21201, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- The Charles Bronfman Institute of Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Department of Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA
- Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Department of Internal Medicine, Section on Nephrology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
- Channing Division of Network Medicine and Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
- National Heart, Lung, and Blood Institute’s, Boston University’s Framingham Heart Study, Framingham, MA 01701, USA
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA 01701, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Kaiser Permanente Washington Health Research Institute, Kaiser Permanente Washington, Seattle, WA 98101, USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle, WA 98108, USA
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
- Dean’s Office, College of Public Health, University of Kentucky, Lexington, KY 40506, USA
- University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Department of Medicine, Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22903, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Research Institute, Bloodworks Northwest, Seattle, WA 98102, USA
- Genome Science, University of Washington, Seattle, WA 98195, USA
- Vitalant Research Institute, San Francisco, CA 94105, USA
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78520, USA
- Center for Individualized and Genomic Medicine Research (CIGMA), Henry Ford Health System, Detroit, MI 48202, USA
- Department of Medicine, Henry Ford Health System, Detroit, MI 48202, USA
- Division of Genetics, Genomics, and Precision Medicine, University of Arizona, Tucson, AZ 85721, USA
- Department of Medicine, University of Arizona, Tucson, AZ 85721, USA
- Wake Forest University School of Medicine, Winston-Salem, NC 27101, USA
- Department of Epidemiology and International Health Institute, Brown University School of Public Health, Providence, RI 02903, USA
- Division of Biostatistics, Washington University School of Medicine, Campus Box 8067, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
- Department of Medical Research, Taichung Veterans General Hospital, 1650, Sec. 4, Taiwan Boulevard, Taichung City, Taiwan
- Division of Cardiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Division of Cardiology, University of Illinois at Chicago, Chicago, IL 60607, USA
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Department of Cardiology, Cedars-Sinai, Los Angeles, CA 90048, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Division of Hematology and Oncology, Weill Cornell Medicine, New York, NY 10065, USA
- Englander Institute of Precision Medicine, Weill Cornell Medicine, New York 10065, NY, USA
- Regeneron Pharmaceuticals, Tarrytown, NY 10591, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University, Nashville, TN 37232, USA
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8
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Ilan Y. Constrained disorder principle-based variability is fundamental for biological processes: Beyond biological relativity and physiological regulatory networks. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:37-48. [PMID: 37068713 DOI: 10.1016/j.pbiomolbio.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/26/2023] [Accepted: 04/14/2023] [Indexed: 04/19/2023]
Abstract
The constrained disorder principle (CDP) defines systems based on their degree of disorder bounded by dynamic boundaries. The principle explains stochasticity in living and non-living systems. Denis Noble described the importance of stochasticity in biology, emphasizing stochastic processes at molecular, cellular, and higher levels in organisms as having a role beyond simple noise. The CDP and Noble's theories (NT) claim that biological systems use stochasticity. This paper presents the CDP and NT, discussing common notions and differences between the two theories. The paper presents the CDP-based concept of taking the disorder beyond its role in nature to correct malfunctions of systems and improve the efficiency of biological systems. The use of CDP-based algorithms embedded in second-generation artificial intelligence platforms is described. In summary, noise is inherent to complex systems and has a functional role. The CDP provides the option of using noise to improve functionality.
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Affiliation(s)
- Yaron Ilan
- Faculty of Medicine, Hebrew University, Department of Medicine, Hadassah Medical Center, Jerusalem, Israel.
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9
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Bracci AN, Dallmann A, Ding Q, Hubisz MJ, Caballero M, Koren A. The evolution of the human DNA replication timing program. Proc Natl Acad Sci U S A 2023; 120:e2213896120. [PMID: 36848554 PMCID: PMC10013799 DOI: 10.1073/pnas.2213896120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/23/2023] [Indexed: 03/01/2023] Open
Abstract
DNA is replicated according to a defined spatiotemporal program that is linked to both gene regulation and genome stability. The evolutionary forces that have shaped replication timing programs in eukaryotic species are largely unknown. Here, we studied the molecular causes and consequences of replication timing evolution across 94 humans, 95 chimpanzees, and 23 rhesus macaques. Replication timing differences recapitulated the species' phylogenetic tree, suggesting continuous evolution of the DNA replication timing program in primates. Hundreds of genomic regions had significant replication timing variation between humans and chimpanzees, of which 66 showed advances in replication origin firing in humans, while 57 were delayed. Genes overlapping these regions displayed correlated changes in expression levels and chromatin structure. Many human-chimpanzee variants also exhibited interindividual replication timing variation, pointing to ongoing evolution of replication timing at these loci. Association of replication timing variation with genetic variation revealed that DNA sequence evolution can explain replication timing variation between species. Taken together, DNA replication timing shows substantial and ongoing evolution in the human lineage that is driven by sequence alterations and could impact regulatory evolution at specific genomic sites.
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Affiliation(s)
- Alexa N. Bracci
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Anissa Dallmann
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Melissa J. Hubisz
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY14853
| | - Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY14853
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10
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Jaksik R, Wheeler DA, Kimmel M. Detection and characterization of constitutive replication origins defined by DNA polymerase epsilon. BMC Biol 2023; 21:41. [PMID: 36829160 PMCID: PMC9960419 DOI: 10.1186/s12915-023-01527-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 01/24/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Despite the process of DNA replication being mechanistically highly conserved, the location of origins of replication (ORI) may vary from one tissue to the next, or between rounds of replication in eukaryotes, suggesting flexibility in the choice of locations to initiate replication. Lists of human ORI therefore vary widely in number and location, and there are currently no methods available to compare them. Here, we propose a method of detection of ORI based on somatic mutation patterns generated by the mutator phenotype of damaged DNA polymerase epsilon (POLE). RESULTS We report the genome-wide localization of constitutive ORI in POLE-mutated human tumors using whole genome sequencing data. Mutations accumulated after many rounds of replication of unsynchronized dividing cell populations in tumors allow to identify constitutive origins, which we show are shared with high fidelity between individuals and tumor types. Using a Smith-Waterman-like dynamic programming approach, we compared replication origin positions obtained from multiple different methods. The comparison allowed us to define a consensus set of replication origins, identified consistently by multiple ORI detection methods. Many DNA features co-localized with the consensus set of ORI, including chromatin loop anchors, G-quadruplexes, S/MARs, and CpGs. Among all features, the H2A.Z histone exhibited the most significant association. CONCLUSIONS Our results show that mutation-based detection of replication origins is a viable approach to determining their location and associated sequence features.
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Affiliation(s)
- Roman Jaksik
- Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland.
| | - David A. Wheeler
- grid.39382.330000 0001 2160 926XHuman Genome Sequencing Centre, Baylor College of Medicine, Houston, TX USA ,grid.240871.80000 0001 0224 711XPresent Address: Clinical Genomics Group, Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, TN 38103 USA
| | - Marek Kimmel
- grid.6979.10000 0001 2335 3149Department of Systems Biology and Engineering and Biotechnology Centre, Silesian University of Technology, Gliwice, Poland ,grid.21940.3e0000 0004 1936 8278Department of Statistics, Rice University, Houston, TX USA ,grid.21940.3e0000 0004 1936 8278Department of Bioengineering, Rice University, Houston, TX USA
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11
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Genome-wide measurement of DNA replication fork directionality and quantification of DNA replication initiation and termination with Okazaki fragment sequencing. Nat Protoc 2023; 18:1260-1295. [PMID: 36653528 DOI: 10.1038/s41596-022-00793-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 11/09/2022] [Indexed: 01/19/2023]
Abstract
Studying the dynamics of genome replication in mammalian cells has been historically challenging. To reveal the location of replication initiation and termination in the human genome, we developed Okazaki fragment sequencing (OK-seq), a quantitative approach based on the isolation and strand-specific sequencing of Okazaki fragments, the lagging strand replication intermediates. OK-seq quantitates the proportion of leftward- and rightward-oriented forks at every genomic locus and reveals the location and efficiency of replication initiation and termination events. Here we provide the detailed experimental procedures for performing OK-seq in unperturbed cultured human cells and budding yeast and the bioinformatics pipelines for data processing and computation of replication fork directionality. Furthermore, we present the analytical approach based on a hidden Markov model, which allows automated detection of ascending, descending and flat replication fork directionality segments revealing the zones of replication initiation, termination and unidirectional fork movement across the entire genome. These tools are essential for the accurate interpretation of human and yeast replication programs. The experiments and the data processing can be accomplished within six days. Besides revealing the genome replication program in fine detail, OK-seq has been instrumental in numerous studies unravelling mechanisms of genome stability, epigenome maintenance and genome evolution.
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12
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Draetta EL, Lazarević D, Provero P, Cittaro D. The frequency of somatic mutations in cancer predicts the phenotypic relevance of germline mutations. Front Genet 2023; 13:1045301. [PMID: 36699457 PMCID: PMC9868957 DOI: 10.3389/fgene.2022.1045301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 12/28/2022] [Indexed: 01/12/2023] Open
Abstract
Genomic sequence mutations can be pathogenic in both germline and somatic cells. Several authors have observed that often the same genes are involved in cancer when mutated in somatic cells and in genetic diseases when mutated in the germline. Recent advances in high-throughput sequencing techniques have provided us with large databases of both types of mutations, allowing us to investigate this issue in a systematic way. Hence, we applied a machine learning based framework to this problem, comparing multiple models. The models achieved significant predictive power as shown by both cross-validation and their application to recently discovered gene/phenotype associations not used for training. We found that genes characterized by high frequency of somatic mutations in the most common cancers and ancient evolutionary age are most likely to be involved in abnormal phenotypes and diseases. These results suggest that the combination of tolerance for mutations at the cell viability level (measured by the frequency of somatic mutations in cancer) and functional relevance (demonstrated by evolutionary conservation) are the main predictors of disease genes. Our results thus confirm the deep relationship between pathogenic mutations in somatic and germline cells, provide new insight into the common origin of cancer and genetic diseases, and can be used to improve the identification of new disease genes.
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Affiliation(s)
- Edoardo Luigi Draetta
- University of Milan, Milan, Italy,Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dejan Lazarević
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Paolo Provero
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,Department of Neurosciences “Rita Levi Montalcini”, University of Turin, Turin, Italy
| | - Davide Cittaro
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy,*Correspondence: Davide Cittaro ,
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13
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Wang RJ, Al-Saffar SI, Rogers J, Hahn MW. Human generation times across the past 250,000 years. SCIENCE ADVANCES 2023; 9:eabm7047. [PMID: 36608127 PMCID: PMC9821931 DOI: 10.1126/sciadv.abm7047] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The generation times of our recent ancestors can tell us about both the biology and social organization of prehistoric humans, placing human evolution on an absolute time scale. We present a method for predicting historical male and female generation times based on changes in the mutation spectrum. Our analyses of whole-genome data reveal an average generation time of 26.9 years across the past 250,000 years, with fathers consistently older (30.7 years) than mothers (23.2 years). Shifts in sex-averaged generation times have been driven primarily by changes to the age of paternity, although we report a substantial increase in female generation times in the recent past. We also find a large difference in generation times among populations, reaching back to a time when all humans occupied Africa.
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Affiliation(s)
- Richard J. Wang
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
- Corresponding author.
| | - Samer I. Al-Saffar
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew W. Hahn
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Computer Science, Indiana University, Bloomington, IN 47405, USA
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14
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Rivera-Mulia JC, Trevilla-Garcia C, Martinez-Cifuentes S. Optimized Repli-seq: improved DNA replication timing analysis by next-generation sequencing. Chromosome Res 2022; 30:401-414. [PMID: 35781769 PMCID: PMC10124313 DOI: 10.1007/s10577-022-09703-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 06/15/2022] [Accepted: 06/15/2022] [Indexed: 01/25/2023]
Abstract
The human genome is divided into functional units that replicate at specific times during S-phase. This temporal program is known as replication timing (RT) and is coordinated with the spatial organization of the genome and transcriptional activity. RT is also cell type-specific, dynamically regulated during development, and alterations in RT are observed in multiple diseases. Thus, the precise measure of RT is critical to understand the role of RT in gene function regulation. Distinct methods for assaying the RT program exist; however, conventional methods require thousands of cells as input, prohibiting its applicability to samples with limited cell numbers such as those from disease patients or from early developing embryos. Although single-cell RT analyses have been developed, these methods are low throughput, require generation of numerous libraries, increased sequencing costs, and produce low resolution data. Here, we developed an improved method to measure RT genome-wide that enables high-resolution analysis of low input samples. This method incorporates direct cell sorting into lysis buffer, as well as DNA fragmentation and library preparation in a single tube, resulting in higher yields, increased quality, and reproducibility with decreased costs. We also performed a systematic data processing analysis to provide standardized parameters for RT measurement. This optimized method facilitates RT analysis and will enable its application to a broad range of studies investigating the role of RT in gene expression, nuclear architecture, and disease.
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Affiliation(s)
- Juan Carlos Rivera-Mulia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA.
- Stem Cell Institute, University of Minnesota Medical School, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota Medical School, Minneapolis, MN, USA.
| | - Claudia Trevilla-Garcia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Santiago Martinez-Cifuentes
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Medical School, Minneapolis, MN, USA
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15
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Exploration of Tools for the Interpretation of Human Non-Coding Variants. Int J Mol Sci 2022; 23:ijms232112977. [PMID: 36361767 PMCID: PMC9654743 DOI: 10.3390/ijms232112977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/17/2022] [Accepted: 10/23/2022] [Indexed: 02/01/2023] Open
Abstract
The advent of Whole Genome Sequencing (WGS) broadened the genetic variation detection range, revealing the presence of variants even in non-coding regions of the genome, which would have been missed using targeted approaches. One of the most challenging issues in WGS analysis regards the interpretation of annotated variants. This review focuses on tools suitable for the functional annotation of variants falling into non-coding regions. It couples the description of non-coding genomic areas with the results and performance of existing tools for a functional interpretation of the effect of variants in these regions. Tools were tested in a controlled genomic scenario, representing the ground-truth and allowing us to determine software performance.
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16
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Heskett MB, Vouzas AE, Smith LG, Yates PA, Boniface C, Bouhassira EE, Spellman PT, Gilbert DM, Thayer MJ. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability. Nat Commun 2022; 13:6301. [PMID: 36273230 PMCID: PMC9588035 DOI: 10.1038/s41467-022-34099-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/13/2022] [Indexed: 01/18/2023] Open
Abstract
ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain "Inactivation/Stability Centers" that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
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Affiliation(s)
- Michael B Heskett
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
| | - Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, FL, 32306, USA
| | - Leslie G Smith
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Phillip A Yates
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA
| | - Christopher Boniface
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - Eric E Bouhassira
- Department of Cell Biology and Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Paul T Spellman
- Department of Molecular and Medical Genetics Oregon Health & Science University, Portland, OR, 97239, USA
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute Oregon Health & Science University, Portland, OR, 97239, USA
| | - David M Gilbert
- San Diego Biomedical Research Institute, San Diego, CA, 92121, USA
| | - Mathew J Thayer
- Department of Chemical Physiology and Biochemistry Oregon Health & Science University, Portland, OR, 97239, USA.
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17
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Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Hum Mol Genet 2022; 31:2899-2917. [PMID: 35394024 PMCID: PMC9433724 DOI: 10.1093/hmg/ddac082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/18/2022] [Accepted: 04/03/2022] [Indexed: 11/14/2022] Open
Abstract
Cellular proliferation depends on the accurate and timely replication of the genome. Several genetic diseases are caused by mutations in key DNA replication genes; however, it remains unclear whether these genes influence the normal program of DNA replication timing. Similarly, the factors that regulate DNA replication dynamics are poorly understood. To systematically identify trans-acting modulators of replication timing, we profiled replication in 184 cell lines from three cell types, encompassing 60 different gene knockouts or genetic diseases. Through a rigorous approach that considers the background variability of replication timing, we concluded that most samples displayed normal replication timing. However, mutations in two genes showed consistently abnormal replication timing. The first gene was RIF1, a known modulator of replication timing. The second was MCM10, a highly conserved member of the pre-replication complex. Cells from a single patient carrying MCM10 mutations demonstrated replication timing variability comprising 46% of the genome and at different locations than RIF1 knockouts. Replication timing alterations in the mutated MCM10 cells were predominantly comprised of replication delays and initiation site gains and losses. Taken together, this study demonstrates the remarkable robustness of the human replication timing program and reveals MCM10 as a novel candidate modulator of DNA replication timing.
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Affiliation(s)
- Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tiffany Ge
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Ana Rita Rebelo
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Sean Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Kayla Brooks
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Michael Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | | | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dongsung Kim
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, USA
| | - Marcus Smolka
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, NY 10032, USA
- Columbia University Stem Cell Initiative, New York, NY 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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18
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Multiple Stochastic Parameters Influence Genome Dynamics in a Heterozygous Diploid Eukaryotic Model. J Fungi (Basel) 2022; 8:jof8070650. [PMID: 35887406 PMCID: PMC9323731 DOI: 10.3390/jof8070650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 12/10/2022] Open
Abstract
The heterozygous diploid genome of Candida albicans displays frequent genomic rearrangements, in particular loss-of-heterozygosity (LOH) events, which can be seen on all eight chromosomes and affect both laboratory and clinical strains. LOHs, which are often the consequence of DNA damage repair, can be observed upon stresses reminiscent of the host environment, and result in homozygous regions of various sizes depending on the molecular mechanisms at their origins. Recent studies have shed light on the biological importance of these frequent and ubiquitous LOH events in C. albicans. In diploid Saccharomyces cerevisiae, LOH facilitates the passage of recessive beneficial mutations through Haldane’s sieve, allowing rapid evolutionary adaptation. This also appears to be true in C. albicans, where the full potential of an adaptive mutation is often only observed upon LOH, as illustrated in the case of antifungal resistance and niche adaptation. To understand the genome-wide dynamics of LOH events in C. albicans, we constructed a collection of 15 strains, each one carrying a LOH reporter system on a different chromosome arm. This system involves the insertion of two fluorescent marker genes in a neutral genomic region on both homologs, allowing spontaneous LOH events to be detected by monitoring the loss of one of the fluorescent markers using flow cytometry. Using this collection, we observed significant LOH frequency differences between genomic loci in standard laboratory growth conditions; however, we further demonstrated that comparable heterogeneity was also observed for a given genomic locus between independent strains. Additionally, upon exposure to stress, three outcomes could be observed in C. albicans, where individual strains displayed increases, decreases, or no effect of stress in terms of LOH frequency. Our results argue against a general stress response triggering overall genome instability. Indeed, we showed that the heterogeneity of LOH frequency in C. albicans is present at various levels, inter-strain, intra-strain, and inter-chromosomes, suggesting that LOH events may occur stochastically within a cell, though the genetic background potentially impacts genome stability in terms of LOH throughout the genome in both basal and stress conditions. This heterogeneity in terms of genome stability may serve as an important adaptive strategy for the predominantly clonal human opportunistic pathogen C. albicans, by quickly generating a wide spectrum of genetic variation combinations potentially permitting subsistence in a rapidly evolving environment.
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High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control. Nat Commun 2022; 13:2402. [PMID: 35504890 PMCID: PMC9065153 DOI: 10.1038/s41467-022-30212-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/21/2022] [Indexed: 12/28/2022] Open
Abstract
DNA replication initiates from replication origins firing throughout S phase. Debate remains about whether origins are a fixed set of loci, or a loose agglomeration of potential sites used stochastically in individual cells, and about how consistent their firing time is. We develop an approach to profile DNA replication from whole-genome sequencing of thousands of single cells, which includes in silico flow cytometry, a method for discriminating replicating and non-replicating cells. Using two microfluidic platforms, we analyze up to 2437 replicating cells from a single sample. The resolution and scale of the data allow focused analysis of replication initiation sites, demonstrating that most occur in confined genomic regions. While initiation order is remarkably similar across cells, we unexpectedly identify several subtypes of initiation regions in late-replicating regions. Taken together, high throughput, high resolution sequencing of individual cells reveals previously underappreciated variability in replication initiation and progression.
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20
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Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Res 2021; 31:2155-2169. [PMID: 34810218 PMCID: PMC8647822 DOI: 10.1101/gr.275953.121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Haploid human embryonic stem cells (ESCs) provide a powerful genetic system but diploidize at high rates. We hypothesized that diploidization results from aberrant DNA replication. To test this, we profiled DNA replication timing in isogenic haploid and diploid ESCs. The greatest difference was the earlier replication of the X Chromosome in haploids, consistent with the lack of X-Chromosome inactivation. We also identified 21 autosomal regions that had delayed replication in haploids, extending beyond the normal S phase and into G2/M. Haploid-delays comprised a unique set of quiescent genomic regions that are also underreplicated in polyploid placental cells. The same delays were observed in female ESCs with two active X Chromosomes, suggesting that increased X-Chromosome dosage may cause delayed autosomal replication. We propose that incomplete replication at the onset of mitosis could prevent cell division and result in re-entry into the cell cycle and whole genome duplication.
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Affiliation(s)
- Matthew M Edwards
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Michael V Zuccaro
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Ido Sagi
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | - Dan Vershkov
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nissim Benvenisty
- The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Dieter Egli
- Department of Pediatrics and Naomi Berrie Diabetes Center, Columbia University, New York, New York 10032, USA
- Columbia University Stem Cell Initiative, New York, New York 10032, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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21
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The genetic architecture of DNA replication timing in human pluripotent stem cells. Nat Commun 2021; 12:6746. [PMID: 34799581 PMCID: PMC8604924 DOI: 10.1038/s41467-021-27115-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/29/2021] [Indexed: 12/11/2022] Open
Abstract
DNA replication follows a strict spatiotemporal program that intersects with chromatin structure but has a poorly understood genetic basis. To systematically identify genetic regulators of replication timing, we exploited inter-individual variation in human pluripotent stem cells from 349 individuals. We show that the human genome's replication program is broadly encoded in DNA and identify 1,617 cis-acting replication timing quantitative trait loci (rtQTLs) - sequence determinants of replication initiation. rtQTLs function individually, or in combinations of proximal and distal regulators, and are enriched at sites of histone H3 trimethylation of lysines 4, 9, and 36 together with histone hyperacetylation. H3 trimethylation marks are individually repressive yet synergistically associate with early replication. We identify pluripotency-related transcription factors and boundary elements as positive and negative regulators of replication timing, respectively. Taken together, human replication timing is controlled by a multi-layered mechanism with dozens of effectors working combinatorially and following principles analogous to transcription regulation.
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22
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Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. Genetics 2021; 219:6369517. [PMID: 34740250 PMCID: PMC8570783 DOI: 10.1093/genetics/iyab147] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/01/2021] [Indexed: 11/23/2022] Open
Abstract
Regulation of DNA replication and copy number is necessary to promote genome stability and maintain cell and tissue function. DNA replication is regulated temporally in a process known as replication timing (RT). Rap1-interacting factor 1 (Rif1) is a key regulator of RT and has a critical function in copy number control in polyploid cells. Previously, we demonstrated that Rif1 functions with SUUR to inhibit replication fork progression and promote underreplication (UR) of specific genomic regions. How Rif1-dependent control of RT factors into its ability to promote UR is unknown. By applying a computational approach to measure RT in Drosophila polyploid cells, we show that SUUR and Rif1 have differential roles in controlling UR and RT. Our findings reveal that Rif1 acts to promote late replication, which is necessary for SUUR-dependent underreplication. Our work provides new insight into the process of UR and its links to RT.
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Affiliation(s)
- Souradip Das
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Madison Caballero
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Tatyana Kolesnikova
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Igor Zhimulev
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia.,Laboratory of Structural, Functional and Comparative Genomics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Jared Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
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23
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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24
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Meiotic recombination mirrors patterns of germline replication in mice and humans. Cell 2021; 184:4251-4267.e20. [PMID: 34260899 DOI: 10.1016/j.cell.2021.06.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/02/2021] [Accepted: 06/21/2021] [Indexed: 12/29/2022]
Abstract
Genetic recombination generates novel trait combinations, and understanding how recombination is distributed across the genome is key to modern genetics. The PRDM9 protein defines recombination hotspots; however, megabase-scale recombination patterning is independent of PRDM9. The single round of DNA replication, which precedes recombination in meiosis, may establish these patterns; therefore, we devised an approach to study meiotic replication that includes robust and sensitive mapping of replication origins. We find that meiotic DNA replication is distinct; reduced origin firing slows replication in meiosis, and a distinctive replication pattern in human males underlies the subtelomeric increase in recombination. We detected a robust correlation between replication and both contemporary and historical recombination and found that replication origin density coupled with chromosome size determines the recombination potential of individual chromosomes. Our findings and methods have implications for understanding the mechanisms underlying DNA replication, genetic recombination, and the landscape of mammalian germline variation.
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25
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Abstract
Immediately following the discovery of the structure of DNA and the semi-conservative replication of the parental DNA sequence into two new DNA strands, it became apparent that DNA replication is organized in a temporal and spatial fashion during the S phase of the cell cycle, correlated with the large-scale organization of chromatin in the nucleus. After many decades of limited progress, technological advances in genomics, genome engineering, and imaging have finally positioned the field to tackle mechanisms underpinning the temporal and spatial regulation of DNA replication and the causal relationships between DNA replication and other features of large-scale chromosome structure and function. In this review, we discuss these major recent discoveries as well as expectations for the coming decade.
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Affiliation(s)
- Athanasios E Vouzas
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
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26
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Abstract
Safeguards against excess DNA replication are often dysregulated in cancer, and driving cancer cells towards over-replication is a promising therapeutic strategy. We determined DNA synthesis patterns in cancer cells undergoing partial genome re-replication due to perturbed regulatory interactions (re-replicating cells). These cells exhibited slow replication, increased frequency of replication initiation events, and a skewed initiation pattern that preferentially reactivated early-replicating origins. Unlike in cells exposed to replication stress, which activated a novel group of hitherto unutilized (dormant) replication origins, the preferred re-replicating origins arose from the same pool of potential origins as those activated during normal growth. Mechanistically, the skewed initiation pattern reflected a disproportionate distribution of pre-replication complexes on distinct regions of licensed chromatin prior to replication. This distinct pattern suggests that circumventing the strong inhibitory interactions that normally prevent excess DNA synthesis can occur via at least two pathways, each activating a distinct set of replication origins.
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27
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Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell 2021; 183:197-210.e32. [PMID: 33007263 DOI: 10.1016/j.cell.2020.08.006] [Citation(s) in RCA: 115] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/08/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.
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Affiliation(s)
- Kevin Hadi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Xiaotong Yao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julie M Behr
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Aditya Deshpande
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Huasong Tian
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joel Rosiene
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Madison Darmofal
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | | | - Emily M Adney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Alon Shaiber
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zoran Gajic
- New York Genome Center, New York, NY 10013, USA
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kenneth Eng
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremiah A Wala
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Minita Shah
- New York Genome Center, New York, NY 10013, USA
| | | | | | - Mayu O Frank
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Franklin Huang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sally Dewhurst
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - John Maciejowski
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge S Reis-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David A Knowles
- New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bud Mishra
- Departments of Computer Science, Mathematics and Cell Biology, Courant Institute and NYU School of Medicine, New York University, New York, NY 10012, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Kenji M Oman
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Carissa A Sanchez
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lucian P Smith
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Patricia C Galipeau
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Thomas G Paulson
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaohong Li
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Wilkes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
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28
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Koren A, Massey DJ, Bracci AN. TIGER: inferring DNA replication timing from whole-genome sequence data. Bioinformatics 2021; 37:4001-4005. [PMID: 33704387 PMCID: PMC8913259 DOI: 10.1093/bioinformatics/btab166] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/19/2021] [Accepted: 03/08/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. RESULTS We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. AVAILABILITY AND IMPLEMENTATION TIGER is available at https://github.com/TheKorenLab/TIGER. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
| | - Alexa N Bracci
- Department of Molecular Biology and Genetics, Cornell University, Ithaca NY 14850 USA
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29
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Abstract
A common assumption in dating patrilineal events using Y-chromosome sequencing data is that the Y-chromosome mutation rate is invariant across haplogroups. Previous studies revealed interhaplogroup heterogeneity in phylogenetic branch length. Whether this heterogeneity is caused by interhaplogroup mutation rate variation or nongenetic confounders remains unknown. Here, we analyzed whole-genome sequences from cultured cells derived from >1,700 males. We confirmed the presence of branch length heterogeneity. We demonstrate that sex-chromosome mutations that appear within cell lines, which likely occurred somatically or in vitro (and are thus not influenced by nongenetic confounders) are informative for germline mutational processes. Using within-cell-line mutations, we computed a relative Y-chromosome somatic mutation rate, and uncovered substantial variation (up to 83.3%) in this proxy for germline mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Ya Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- New York Genome Center, New York, NY
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- Department of Computational Biology, Cornell University, Ithaca, NY
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30
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Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV. Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. Mol Cell 2021; 81:426-441.e8. [PMID: 33545059 DOI: 10.1016/j.molcel.2021.01.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 09/25/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022]
Abstract
Eukaryotic genomes replicate via spatially and temporally regulated origin firing. Cyclin-dependent kinase (CDK) and Dbf4-dependent kinase (DDK) promote origin firing, whereas the S phase checkpoint limits firing to prevent nucleotide and RPA exhaustion. We used chemical genetics to interrogate human DDK with maximum precision, dissect its relationship with the S phase checkpoint, and identify DDK substrates. We show that DDK inhibition (DDKi) leads to graded suppression of origin firing and fork arrest. S phase checkpoint inhibition rescued origin firing in DDKi cells and DDK-depleted Xenopus egg extracts. DDKi also impairs RPA loading, nascent-strand protection, and fork restart. Via quantitative phosphoproteomics, we identify the BRCA1-associated (BRCA1-A) complex subunit MERIT40 and the cohesin accessory subunit PDS5B as DDK effectors in fork protection and restart. Phosphorylation neutralizes autoinhibition mediated by intrinsically disordered regions in both substrates. Our results reveal mechanisms through which DDK controls the duplication of large vertebrate genomes.
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Affiliation(s)
- Mathew J K Jones
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD 4102, Australia.
| | - Camille Gelot
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Stephanie Munk
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | - Amnon Koren
- Cornell University, Department of Molecular Biology and Genetics, Ithaca, NY 14853, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Yoshitaka Kawasoe
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kelly A George
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ruth E Santos
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Jesper V Olsen
- University of Copenhagen and Novo Nordisk Foundation Center for Protein Research, Copenhagen 2200, Denmark
| | | | - Mark G Frattini
- Division of Hematology/Oncology, Columbia University Medical Center, New York, NY 10032, USA
| | - Tatsuro S Takahashi
- Graduate School of Science, Kyushu University, Nishi-ku, Fukuoka 819-0395, Japan
| | - Prasad V Jallepalli
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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31
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Chromosomal coordination and differential structure of asynchronous replicating regions. Nat Commun 2021; 12:1035. [PMID: 33589603 PMCID: PMC7884787 DOI: 10.1038/s41467-021-21348-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/18/2021] [Indexed: 02/05/2023] Open
Abstract
Stochastic asynchronous replication timing (AS-RT) is a phenomenon in which the time of replication of each allele is different, and the identity of the early allele varies between cells. By taking advantage of stable clonal pre-B cell populations derived from C57BL6/Castaneous mice, we have mapped the genome-wide AS-RT loci, independently of genetic differences. These regions are characterized by differential chromatin accessibility, mono-allelic expression and include new gene families involved in specifying cell identity. By combining population level mapping with single cell FISH, our data reveal the existence of a novel regulatory program that coordinates a fixed relationship between AS-RT regions on any given chromosome, with some loci set to replicate in a parallel and others set in the anti-parallel orientation. Our results show that AS-RT is a highly regulated epigenetic mark established during early embryogenesis that may be used for facilitating the programming of mono-allelic choice throughout development. Most regions of the mammalian genome replicate both alleles in a synchronous manner, but some loci have been found to replicate asynchronously and the time of replication of each allele is different. Here the authors, by employing clonal mouse cells from a hybrid strain chart replication timing over the entire genome, using polymorphisms to distinguish between the paternal and maternal alleles.
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32
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Pentzold C, Kokal M, Pentzold S, Weise A. Sites of chromosomal instability in the context of nuclear architecture and function. Cell Mol Life Sci 2020; 78:2095-2103. [PMID: 33219838 PMCID: PMC7966619 DOI: 10.1007/s00018-020-03698-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 10/02/2020] [Accepted: 10/31/2020] [Indexed: 12/13/2022]
Abstract
Chromosomal fragile sites are described as areas within the tightly packed mitotic chromatin that appear as breaks or gaps mostly tracing back to a loosened structure and not a real nicked break within the DNA molecule. Most facts about fragile sites result from studies in mitotic cells, mainly during metaphase and mainly in lymphocytes. Here, we synthesize facts about the genomic regions that are prone to form gaps and breaks on metaphase chromosomes in the context of interphase. We conclude that nuclear architecture shapes the activity profile of the cell, i.e. replication timing and transcriptional activity, thereby influencing genomic integrity during interphase with the potential to cause fragility in mitosis. We further propose fragile sites as examples of regions specifically positioned in the interphase nucleus with putative anchoring points at the nuclear lamina to enable a tightly regulated replication–transcription profile and diverse signalling functions in the cell. Consequently, fragility starts before the actual display as chromosomal breakage in metaphase to balance the initial contradiction of cellular overgrowth or malfunctioning and maintaining diversity in molecular evolution.
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Affiliation(s)
- Constanze Pentzold
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany.
| | - Miriam Kokal
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
| | - Stefan Pentzold
- Research Center Lobeda, Jena University Hospital, 07747, Jena, Germany
| | - Anja Weise
- Institute of Human Genetics, University Hospital, Friedrich Schiller University Jena, 07747, Jena, Germany
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Abstract
Mutation of the human genome results in three classes of genomic variation: single nucleotide variants; short insertions or deletions; and large structural variants (SVs). Some mutations occur during normal processes, such as meiotic recombination or B cell development, and others result from DNA replication or aberrant repair of breaks in sequence-specific contexts. Regardless of mechanism, mutations are subject to selection, and some hotspots can manifest in disease. Here, we discuss genomic regions prone to mutation, mechanisms contributing to mutation susceptibility, and the processes leading to their accumulation in normal and somatic genomes. With further, more accurate human genome sequencing, additional mutation hotspots, mechanistic details of their formation, and the relevance of hotspots to evolution and disease are likely to be discovered.
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34
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Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends Genet 2020; 36:868-879. [PMID: 32739030 PMCID: PMC7572746 DOI: 10.1016/j.tig.2020.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
Genomic DNA is replicated every cell cycle by the programmed activation of replication origins at specific times and chromosomal locations. The factors that define the locations of replication origins and their typical activation times in eukaryotic cells are poorly understood. Previous studies highlighted the role of activating factors and epigenetic modifications in regulating replication initiation. Here, we review the role that repressive pathways - and their alleviation - play in establishing the genomic landscape of replication initiation. Several factors mediate this repression, in particular, factors associated with inactive chromatin. Repression can support organized, yet stochastic, replication initiation, and its absence could explain instances of rapid and random replication or re-replication.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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35
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Georgieva D, Liu Q, Wang K, Egli D. Detection of base analogs incorporated during DNA replication by nanopore sequencing. Nucleic Acids Res 2020; 48:e88. [PMID: 32710620 PMCID: PMC7470954 DOI: 10.1093/nar/gkaa517] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 05/28/2020] [Accepted: 06/05/2020] [Indexed: 01/23/2023] Open
Abstract
DNA synthesis is a fundamental requirement for cell proliferation and DNA repair, but no single method can identify the location, direction and speed of replication forks with high resolution. Mammalian cells have the ability to incorporate thymidine analogs along with the natural A, T, G and C bases during DNA synthesis, which allows for labeling of replicating or repaired DNA. Here, we demonstrate the use of the Oxford Nanopore Technologies MinION to detect 11 different thymidine analogs including CldU, BrdU, IdU as well as EdU alone or coupled to Biotin and other bulky adducts in synthetic DNA templates. We also show that the large adduct Biotin can be distinguished from the smaller analog IdU, which opens the possibility of using analog combinations to identify the location and direction of DNA synthesis. Furthermore, we detect IdU label on single DNA molecules in the genome of mouse pluripotent stem cells and using CRISPR/Cas9-mediated enrichment, determine replication rates using newly synthesized DNA strands in human mitochondrial DNA. We conclude that this novel method, termed Replipore sequencing, has the potential for on target examination of DNA replication in a wide range of biological contexts.
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Affiliation(s)
- Daniela Georgieva
- Integrated Program in Cellular, Molecular, and Biomedical Studies, Columbia University, New York, NY 10032, USA.,Naomi Berrie Diabetes Center, Columbia University, New York NY 10032, USA.,Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA
| | - Qian Liu
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dieter Egli
- Naomi Berrie Diabetes Center, Columbia University, New York NY 10032, USA.,Columbia Stem Cell Initiative, Columbia University, New York, NY 10032, USA.,Department of Pediatrics and Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
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36
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Replication timing alterations in leukemia affect clinically relevant chromosome domains. Blood Adv 2020; 3:3201-3213. [PMID: 31698451 DOI: 10.1182/bloodadvances.2019000641] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 08/18/2019] [Indexed: 12/29/2022] Open
Abstract
Human B-cell precursor acute lymphoid leukemias (BCP-ALLs) comprise a group of genetically and clinically distinct disease entities with features of differentiation arrest at known stages of normal B-lineage differentiation. We previously showed that BCP-ALL cells display unique and clonally heritable, stable DNA replication timing (RT) programs (ie, programs describing the variable order of replication and subnuclear 3D architecture of megabase-scale chromosomal units of DNA in different cell types). To determine the extent to which BCP-ALL RT programs mirror or deviate from specific stages of normal human B-cell differentiation, we transplanted immunodeficient mice with quiescent normal human CD34+ cord blood cells and obtained RT signatures of the regenerating B-lineage populations. We then compared these with RT signatures for leukemic cells from a large cohort of BCP-ALL patients with varied genetic subtypes and outcomes. The results identify BCP-ALL subtype-specific features that resemble specific stages of B-cell differentiation and features that seem to be associated with relapse. These results suggest that the genesis of BCP-ALL involves alterations in RT that reflect biologically significant and potentially clinically relevant leukemia-specific epigenetic changes.
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37
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Singh VK, Rastogi A, Hu X, Wang Y, De S. Mutational signature SBS8 predominantly arises due to late replication errors in cancer. Commun Biol 2020; 3:421. [PMID: 32747711 PMCID: PMC7400754 DOI: 10.1038/s42003-020-01119-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 07/02/2020] [Indexed: 02/08/2023] Open
Abstract
Although a majority of somatic mutations in cancer are passengers, their mutational signatures provide mechanistic insights into mutagenesis and DNA repair processes. Mutational signature SBS8 is common in most cancers, but its etiology is debated. Incorporating genomic, epigenomic, and cellular process features for multiple cell-types we develop genome-wide composite epigenomic context-maps relevant for mutagenesis and DNA repair. Analyzing somatic mutation data from multiple cancer types in their epigenomic contexts, we show that SBS8 preferentially occurs in gene-poor, lamina-proximal, late replicating heterochromatin domains. While SBS8 is uncommon among mutations in non-malignant tissues, in tumor genomes its proportions increase with replication timing and speed, and checkpoint defects further promote this signature - suggesting that SBS8 probably arises due to uncorrected late replication errors during cancer progression. Our observations offer a potential reconciliation among different perspectives in the debate about the etiology of SBS8 and its relationship with other mutational signatures.
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Affiliation(s)
- Vinod Kumar Singh
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Arnav Rastogi
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Xiaoju Hu
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Yaqun Wang
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Subhajyoti De
- Rutgers Cancer Institute, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA.
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38
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Loh PR, Genovese G, McCarroll SA. Monogenic and polygenic inheritance become instruments for clonal selection. Nature 2020; 584:136-141. [PMID: 32581363 PMCID: PMC7415571 DOI: 10.1038/s41586-020-2430-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/23/2020] [Indexed: 12/30/2022]
Abstract
Clonally expanded blood cells that contain somatic mutations (clonal haematopoiesis) are commonly acquired with age and increase the risk of blood cancer1-9. The blood clones identified so far contain diverse large-scale mosaic chromosomal alterations (deletions, duplications and copy-neutral loss of heterozygosity (CN-LOH)) on all chromosomes1,2,5,6,9, but the sources of selective advantage that drive the expansion of most clones remain unknown. Here, to identify genes, mutations and biological processes that give selective advantage to mutant clones, we analysed genotyping data from the blood-derived DNA of 482,789 participants from the UK Biobank10. We identified 19,632 autosomal mosaic chromosomal alterations and analysed these for relationships to inherited genetic variation. We found 52 inherited, rare, large-effect coding or splice variants in 7 genes that were associated with greatly increased vulnerability to clonal haematopoiesis with specific acquired CN-LOH mutations. Acquired mutations systematically replaced the inherited risk alleles (at MPL) or duplicated them to the homologous chromosome (at FH, NBN, MRE11, ATM, SH2B3 and TM2D3). Three of the genes (MRE11, NBN and ATM) encode components of the MRN-ATM pathway, which limits cell division after DNA damage and telomere attrition11-13; another two (MPL and SH2B3) encode proteins that regulate the self-renewal of stem cells14-16. In addition, we found that CN-LOH mutations across the genome tended to cause chromosomal segments with alleles that promote the expansion of haematopoietic cells to replace their homologous (allelic) counterparts, increasing polygenic drive for blood-cell proliferation traits. Readily acquired mutations that replace chromosomal segments with their homologous counterparts seem to interact with pervasive inherited variation to create a challenge for lifelong cytopoiesis.
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Affiliation(s)
- Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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39
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Chintalapati M, Moorjani P. Evolution of the mutation rate across primates. Curr Opin Genet Dev 2020; 62:58-64. [PMID: 32634682 DOI: 10.1016/j.gde.2020.05.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 05/10/2020] [Accepted: 05/22/2020] [Indexed: 12/31/2022]
Abstract
Germline mutations are the source of all heritable variation. In the past few years, whole genome sequencing has allowed direct and comprehensive surveys of mutation patterns in humans and other species. These studies have documented substantial variation in both mutation rates and spectra across primates, the causes of which remain unclear. Here, we review what is currently known about mutation rates in primates, highlight the factors proposed to explain the variation across species, and discuss some implications of these findings on our understanding of the chronology of primate evolution and the process of mutagenesis.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States; Center for Computational Biology, University of California, Berkeley, CA, United States.
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40
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Bellanné-Chantelot C, Rabadan Moraes G, Schmaltz-Panneau B, Marty C, Vainchenker W, Plo I. Germline genetic factors in the pathogenesis of myeloproliferative neoplasms. Blood Rev 2020; 42:100710. [PMID: 32532454 DOI: 10.1016/j.blre.2020.100710] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 04/08/2020] [Accepted: 05/05/2020] [Indexed: 02/06/2023]
Abstract
Myeloproliferative neoplasms (MPN) are clonal hematological malignancies that lead to overproduction of mature myeloid cells. They are due to acquired mutations in genes encoding for AK2, MPL and CALR that result in the activation of the cytokine receptor/JAK2 signaling pathway. In addition, it exists germline variants that can favor the initiation of the disease or may affect its phenotype. First, they can be common risk alleles, which correspond to frequent single nucleotide variants present in control population and that contribute to the development of either sporadic or familial MPN. Second, some variants predispose to the onset of MPN with a higher penetrance and lead to familial clustering of MPN. Finally, some extremely rare genetic variants can induce MPN-like hereditary disease. We will review these different subtypes of germline genetic variants and discuss how they impact the initiation and/or development of the MPN disease.
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Affiliation(s)
- Christine Bellanné-Chantelot
- Department of Genetics, Assistance Publique-Hôpitaux de Paris (APHP), Hôpitaux Universitaires Pitié Salpêtrière-Charles Foix, Sorbonne Université, Paris, France; INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France
| | - Graciela Rabadan Moraes
- INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France; Université Paris Diderot (Paris 7), UMR1287, Gustave Roussy, Villejuif, France; Gustave Roussy, Villejuif, France
| | - Barbara Schmaltz-Panneau
- INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France; Gustave Roussy, Villejuif, France; Université Paris XI, UMR1287, Gustave Roussy, Villejuif, France
| | - Caroline Marty
- INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France; Gustave Roussy, Villejuif, France; Université Paris XI, UMR1287, Gustave Roussy, Villejuif, France
| | - William Vainchenker
- INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France; Gustave Roussy, Villejuif, France; Université Paris XI, UMR1287, Gustave Roussy, Villejuif, France
| | - Isabelle Plo
- INSERM, UMR1287, Laboratory of Excellence GR-Ex, Villejuif, France; Gustave Roussy, Villejuif, France; Université Paris XI, UMR1287, Gustave Roussy, Villejuif, France.
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41
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Pongor LS, Gross JM, Vera Alvarez R, Murai J, Jang SM, Zhang H, Redon C, Fu H, Huang SY, Thakur B, Baris A, Marino-Ramirez L, Landsman D, Aladjem MI, Pommier Y. BAMscale: quantification of next-generation sequencing peaks and generation of scaled coverage tracks. Epigenetics Chromatin 2020; 13:21. [PMID: 32321568 PMCID: PMC7175505 DOI: 10.1186/s13072-020-00343-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/11/2020] [Indexed: 12/12/2022] Open
Abstract
Background Next-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches. Results We have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (assay for transposase-accessible chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~ 100 Gb size) in minutes, outperforming currently available tools. Conclusions BAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice-aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).
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Affiliation(s)
- Lorinc S Pongor
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
| | - Jacob M Gross
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Roberto Vera Alvarez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Junko Murai
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Sang-Min Jang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Hongliang Zhang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Christophe Redon
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Haiqing Fu
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Shar-Yin Huang
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Bhushan Thakur
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Adrian Baris
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA
| | - Leonardo Marino-Ramirez
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - David Landsman
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, NIH, 8600 Rockville Pike, Bethesda, MD, 20892, USA
| | - Mirit I Aladjem
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, NIH, 37 Convent Dr, Bethesda, MD, 20892, USA.
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42
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Zhao PA, Sasaki T, Gilbert DM. High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells. Genome Biol 2020; 21:76. [PMID: 32209126 PMCID: PMC7092589 DOI: 10.1186/s13059-020-01983-8] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/04/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. RESULTS Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. CONCLUSIONS Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.
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Affiliation(s)
- Peiyao A Zhao
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, 319 Stadium Drive, Tallahassee, FL, 32306, USA.
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Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Res 2020; 28:49-67. [PMID: 31848781 PMCID: PMC7131883 DOI: 10.1007/s10577-019-09624-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 12/27/2022]
Abstract
Genomic DNA replicates according to a defined temporal program in which early-replicating loci are associated with open chromatin, higher gene density, and increased gene expression levels, while late-replicating loci tend to be heterochromatic and show higher rates of genomic instability. The ability to measure DNA replication dynamics at genome scale has proven crucial for understanding the mechanisms and cellular consequences of DNA replication timing. Several methods, such as quantification of nucleotide analog incorporation and DNA copy number analyses, can accurately reconstruct the genomic replication timing profiles of various species and cell types. More recent developments have expanded the DNA replication genomic toolkit to assays that directly measure the activity of replication origins, while single-cell replication timing assays are beginning to reveal a new level of replication timing regulation. The combination of these methods, applied on a genomic scale and in multiple biological systems, promises to resolve many open questions and lead to a holistic understanding of how eukaryotic cells replicate their genomes accurately and efficiently.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Dashiell J Massey
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA.
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44
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DNA copy-number measurement of genome replication dynamics by high-throughput sequencing: the sort-seq, sync-seq and MFA-seq family. Nat Protoc 2020; 15:1255-1284. [PMID: 32051615 DOI: 10.1038/s41596-019-0287-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/16/2019] [Indexed: 12/20/2022]
Abstract
Genome replication follows a defined temporal programme that can change during cellular differentiation and disease onset. DNA replication results in an increase in DNA copy number that can be measured by high-throughput sequencing. Here we present a protocol to determine genome replication dynamics using DNA copy-number measurements. Cell populations can be obtained in three variants of the method. First, sort-seq reveals the average replication dynamics across S phase in an unperturbed cell population; FACS is used to isolate replicating and non-replicating subpopulations from asynchronous cells. Second, sync-seq measures absolute replication time at specific points during S phase using a synchronized cell population. Third, marker frequency analysis can be used to reveal the average replication dynamics using copy-number analysis in any proliferating asynchronous cell culture. These approaches have been used to reveal genome replication dynamics in prokaryotes, archaea and a wide range of eukaryotes, including yeasts and mammalian cells. We have found this approach straightforward to apply to other organisms and highlight example studies from across the three domains of life. Here we present a Saccharomyces cerevisiae version of the protocol that can be performed in 7-10 d. It requires basic molecular and cellular biology skills, as well as a basic understanding of Unix and R.
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Kessler MD, Loesch DP, Perry JA, Heard-Costa NL, Taliun D, Cade BE, Wang H, Daya M, Ziniti J, Datta S, Celedón JC, Soto-Quiros ME, Avila L, Weiss ST, Barnes K, Redline SS, Vasan RS, Johnson AD, Mathias RA, Hernandez R, Wilson JG, Nickerson DA, Abecasis G, Browning SR, Zöllner S, O'Connell JR, Mitchell BD, O'Connor TD. De novo mutations across 1,465 diverse genomes reveal mutational insights and reductions in the Amish founder population. Proc Natl Acad Sci U S A 2020; 117:2560-2569. [PMID: 31964835 PMCID: PMC7007577 DOI: 10.1073/pnas.1902766117] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
De novo mutations (DNMs), or mutations that appear in an individual despite not being seen in their parents, are an important source of genetic variation whose impact is relevant to studies of human evolution, genetics, and disease. Utilizing high-coverage whole-genome sequencing data as part of the Trans-Omics for Precision Medicine (TOPMed) Program, we called 93,325 single-nucleotide DNMs across 1,465 trios from an array of diverse human populations, and used them to directly estimate and analyze DNM counts, rates, and spectra. We find a significant positive correlation between local recombination rate and local DNM rate, and that DNM rate explains a substantial portion (8.98 to 34.92%, depending on the model) of the genome-wide variation in population-level genetic variation from 41K unrelated TOPMed samples. Genome-wide heterozygosity does correlate with DNM rate, but only explains <1% of variation. While we are underpowered to see small differences, we do not find significant differences in DNM rate between individuals of European, African, and Latino ancestry, nor across ancestrally distinct segments within admixed individuals. However, we did find significantly fewer DNMs in Amish individuals, even when compared with other Europeans, and even after accounting for parental age and sequencing center. Specifically, we found significant reductions in the number of C→A and T→C mutations in the Amish, which seem to underpin their overall reduction in DNMs. Finally, we calculated near-zero estimates of narrow sense heritability (h2), which suggest that variation in DNM rate is significantly shaped by nonadditive genetic effects and the environment.
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Affiliation(s)
- Michael D Kessler
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Douglas P Loesch
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - James A Perry
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Nancy L Heard-Costa
- Department of Neurology, Boston University School of Medicine, Boston, MA 02118
- Framingham Heart Study, Framingham, MA 01702
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan School of Public Health, Ann Arbor, MI 48109
| | - Brian E Cade
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Heming Wang
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142
| | - Michelle Daya
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045
| | - John Ziniti
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Soma Datta
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
| | - Juan C Celedón
- Division of Pediatric Pulmonary Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Manuel E Soto-Quiros
- Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica
| | - Lydiana Avila
- Department of Pediatrics, Hospital Nacional de Niños, 10103 San José, Costa Rica
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115
- Department of Medicine, Harvard Medical School, Boston, MA 02115
| | - Kathleen Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045
| | - Susan S Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA 02115
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02215
| | | | - Andrew D Johnson
- Framingham Heart Study, Framingham, MA 01702
- Population Sciences Branch, Division of Intramural Research, National Heart, Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, The Johns Hopkins School of Medicine, Baltimore, MD 21224
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD 21218
| | - Ryan Hernandez
- Quantitative Life Sciences, McGill University, Montreal, QC H3A OG4, Canada
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216
| | | | - Goncalo Abecasis
- School of Public Health, University of Michigan, Ann Arbor, MI 48109
| | - Sharon R Browning
- Department of Biostatistics, University of Washington, Seattle, WA 98195
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD 21201
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201;
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
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Lynch KL, Alvino GM, Kwan EX, Brewer BJ, Raghuraman MK. The effects of manipulating levels of replication initiation factors on origin firing efficiency in yeast. PLoS Genet 2019; 15:e1008430. [PMID: 31584938 PMCID: PMC6795477 DOI: 10.1371/journal.pgen.1008430] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 10/16/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Chromosome replication in Saccharomyces cerevisiae is initiated from ~300 origins that are regulated by DNA sequence and by the limited abundance of six trans-acting initiation proteins (Sld2, Sld3, Dpb11, Dbf4, Sld7 and Cdc45). We set out to determine how the levels of individual factors contribute to time of origin activation and/or origin efficiency using induced depletion of single factors and overexpression of sets of multiple factors. Depletion of Sld2 or Sld3 slows growth and S phase progression, decreases origin efficiency across the genome and impairs viability as a result of incomplete replication of the rDNA. We find that the most efficient early origins are relatively unaffected by depletion of either Sld2 or Sld3. However, Sld3 levels, and to a lesser extent Sld2 levels, are critical for firing of the less efficient early origins. Overexpression of Sld3 simultaneously with Sld2, Dpb11 and Dbf4 preserves the relative efficiency of origins. Only when Cdc45 and Sld7 are also overexpressed is origin efficiency equalized between early- and late-firing origins. Our data support a model in which Sld3 together with Cdc45 (and/or Sld7) is responsible for the differential efficiencies of origins across the yeast genome. Eukaryotic chromosome duplication begins at sites called origins of replication along the chromosomal DNA. A conserved property of eukaryotic origins is that they vary in efficiency—the proportion of cells in a population in which they “fire”—and in the average time of activation within S phase, but the molecular details underlying this variation are not well understood. Previous work has shown that limiting concentrations of a set of conserved replication initiation proteins referred to as “SSDDCS” (Sld2, Sld3, Dbf4, Dpb11, Cdc45, and Sld7) are rate limiting for origin activation in budding yeast and other eukaryotes; combined overexpression of these proteins increases and/or advances origin firing. However, it remained possible that different factors affect different aspects of origin activation (e.g., timing vs. efficiency). Here, by depleting individual factors or by overexpressing sets of factors in budding yeast, we demonstrate that it is levels of Sld3, Cdc45 and/or Sld7 levels are primarily responsible for modulating the differences in relative origin efficiency and timing. This work gives further insights into what shapes the landscape of genome duplication.
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Affiliation(s)
- Kelsey L. Lynch
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Gina M. Alvino
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Elizabeth X. Kwan
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bonita J. Brewer
- Molecular and Cellular Biology Program, University of Washington, Seattle, Washington, United States of America
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - M. K. Raghuraman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- * E-mail:
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47
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Control of DNA replication timing in the 3D genome. Nat Rev Mol Cell Biol 2019; 20:721-737. [DOI: 10.1038/s41580-019-0162-y] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2019] [Indexed: 12/27/2022]
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Amos W. Flanking heterozygosity influences the relative probability of different base substitutions in humans. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191018. [PMID: 31598319 PMCID: PMC6774961 DOI: 10.1098/rsos.191018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Understanding when, where and which mutations are mostly likely to occur impacts many areas of evolutionary biology, from genetic diseases to phylogenetic reconstruction. Africans and non-African humans differ in the mutability of different triplet base combinations. Africans and non-Africans also differ in mutation rate, possibly because heterozygosity is mutagenic, such that diversity lost when humans expanded out of Africa also lowered the mutation rate. I show that these phenomena are linked: as flanking heterozygosity increases, some triplets become progressively more mutable while others become less so. Africans and non-African show near-identical patterns of dependence on heterozygosity. Thus, the striking differences in triplet mutation frequency between Africans and non-Africans, at least in part, seem to be an emergent property, driven by the way changes in heterozygosity 'out of Africa' have differentially impacted the mutability of different triplets. As heterozygosity decreased, the mutation spectrum outside Africa became enriched for triplet mutations that are favoured by low heterozygosity while those favoured by high heterozygosity became relatively rarer.
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Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes. Proc Natl Acad Sci U S A 2019; 116:17916-17924. [PMID: 31427530 PMCID: PMC6731651 DOI: 10.1073/pnas.1900714116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The sources of human germline mutations are poorly understood. Part of the difficulty is that mutations occur very rarely, and so direct pedigree-based approaches remain limited in the numbers that they can examine. To address this problem, we consider the spectrum of low-frequency variants in a dataset (Genome Aggregation Database, gnomAD) of 13,860 human X chromosomes and autosomes. X-autosome differences are reflective of germline sex differences and have been used extensively to learn about male versus female mutational processes; what is less appreciated is that they also reflect chromosome-level biochemical features that differ between the X and autosomes. We tease these components apart by comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes. In so doing, we are able to ascribe specific mutation patterns to replication timing and recombination and to identify differences in the types of mutations that accrue in males and females. In particular, we identify C > G as a mutagenic signature of male meiotic double-strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes.
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50
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Rees M, Ellner SP. Why So Variable: Can Genetic Variance in Flowering Thresholds Be Maintained by Fluctuating Selection? Am Nat 2019; 194:E13-E29. [PMID: 31251648 DOI: 10.1086/703436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We use integral projection models (IPMs) and individual-based simulations to study the evolution of genetic variance in two monocarpic plant systems. Previous approaches combining IPMs with an adaptive dynamics-style invasion analysis predicted that genetic variability in the size threshold for flowering will not be maintained, which conflicts with empirical evidence. We ask whether this discrepancy can be resolved by making more realistic assumptions about the underlying genetic architecture, assuming a multilocus quantitative trait in an outcrossing diploid species. To do this, we embed the infinitesimal model of quantitative genetics into an IPM for a size-structured cosexual plant species. The resulting IPM describes the joint dynamics of individual size and breeding value of the evolving trait. We apply this general framework to the monocarpic perennials Oenothera glazioviana and Carlina vulgaris. The evolution of heritable variation in threshold size is explored in both individual-based models (IBMs) and IPMs, using a mutation rate modifier approach. In the Oenothera model, where the environment is constant, there is selection against producing genetically variable offspring. In the Carlina model, where the environment varies between years, genetically variable offspring provide a selective advantage, allowing the maintenance of genetic variability. The contrasting predictions of adaptive dynamics and quantitative genetics models for the same system suggest that fluctuating selection may be more effective at maintaining genetic variation than previously thought.
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