1
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Andrianova MA, Seplyarskiy VB, Terradas M, Sánchez-Heras AB, Mur P, Soto JL, Aiza G, Borràs E, Kondrashov FA, Kondrashov AS, Bazykin GA, Valle L. Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells. Eur J Hum Genet 2024:10.1038/s41431-024-01598-8. [PMID: 38658779 DOI: 10.1038/s41431-024-01598-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/16/2024] [Accepted: 03/18/2024] [Indexed: 04/26/2024] Open
Abstract
Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.
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Affiliation(s)
- Maria A Andrianova
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Vladimir B Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Mariona Terradas
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Ana Beatriz Sánchez-Heras
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Medical Oncology Department, Cancer Genetic Counseling Unit. Elche University Hospital, Elche, Spain
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain
| | - José Luis Soto
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO), Elche Health Department, Elche, Spain
- Molecular Genetics Unit, Elche University Hospital, Elche, Spain
| | - Gemma Aiza
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Emma Borràs
- Molecular Genetics Unit, Consorci Sanitari de Terrassa, Terrassa, Spain
| | - Fyodor A Kondrashov
- Institute of Science and Technology Austria, Klosterneuburg, Austria
- Evolutionary and Synthetic Biology Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Alexey S Kondrashov
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Georgii A Bazykin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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2
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Abstract
Despite years of active research into the role of DNA repair and replication in mutagenesis, surprisingly little is known about the origin of spontaneous human mutation in the germ line. With the advent of high-throughput sequencing, genome-scale data have revealed statistical properties of mutagenesis in humans. These properties include variation of the mutation rate and spectrum along the genome at different scales in relation to epigenomic features and dependency on parental age. Moreover, mutations originated in mothers are less frequent than mutations originated in fathers and have a distinct genomic distribution. Statistical analyses that interpret these patterns in the context of known biochemistry can provide mechanistic models of mutagenesis in humans.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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3
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Seplyarskiy VB, Soldatov RA, Koch E, McGinty RJ, Goldmann JM, Hernandez RD, Barnes K, Correa A, Burchard EG, Ellinor PT, McGarvey ST, Mitchell BD, Vasan RS, Redline S, Silverman E, Weiss ST, Arnett DK, Blangero J, Boerwinkle E, He J, Montgomery C, Rao DC, Rotter JI, Taylor KD, Brody JA, Chen YDI, de Las Fuentes L, Hwu CM, Rich SS, Manichaikul AW, Mychaleckyj JC, Palmer ND, Smith JA, Kardia SLR, Peyser PA, Bielak LF, O'Connor TD, Emery LS, Gilissen C, Wong WSW, Kharchenko PV, Sunyaev S. Population sequencing data reveal a compendium of mutational processes in the human germ line. Science 2021; 373:1030-1035. [PMID: 34385354 PMCID: PMC9217108 DOI: 10.1126/science.aba7408] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 07/14/2021] [Indexed: 12/16/2022]
Abstract
Biological mechanisms underlying human germline mutations remain largely unknown. We statistically decompose variation in the rate and spectra of mutations along the genome using volume-regularized nonnegative matrix factorization. The analysis of a sequencing dataset (TOPMed) reveals nine processes that explain the variation in mutation properties between loci. We provide a biological interpretation for seven of these processes. We associate one process with bulky DNA lesions that are resolved asymmetrically with respect to transcription and replication. Two processes track direction of replication fork and replication timing, respectively. We identify a mutagenic effect of active demethylation primarily acting in regulatory regions and a mutagenic effect of long interspersed nuclear elements. We localize a mutagenic process specific to oocytes from population sequencing data. This process appears transcriptionally asymmetric.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ruslan A Soldatov
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Evan Koch
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Ryan J McGinty
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Ryan D Hernandez
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
| | - Kathleen Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO 80045, USA
| | - Adolfo Correa
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Pediatrics, University of Mississippi Medical Center, Jackson, MS, USA
- Department of Population Health Science, University of Mississippi Medical Center, Jackson, MS, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA, USA
- Department of Medicine, University of California, San Francisco, CA, USA
| | - Patrick T Ellinor
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen T McGarvey
- International Health Institute, Brown University, Providence, RI, USA
- Department of Epidemiology, Brown University, Providence, RI, USA
- Department of Anthropology, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, MD, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Susan Redline
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Edwin Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Scott T Weiss
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Donna K Arnett
- Department of Epidemiology, University of Kentucky, Lexington, KY, USA
| | - John Blangero
- Department of Human Genetics, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
- South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX, USA
| | - Eric Boerwinkle
- University of Texas Health Science Center at Houston, Houston, TX, USA
- Baylor College of Medicine Human Genome Sequencing Center, Houston, TX, USA
| | - Jiang He
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
- Tulane University Translational Science Institute, Tulane University, New Orleans, LA , USA
| | - Courtney Montgomery
- Division of Genomics and Data Science, Department of Arthritis and Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - D C Rao
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, 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, 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, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Yii-Der Ida Chen
- Department of Pediatrics, The Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Lisa de Las Fuentes
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine, St. Louis, MO, USA
| | - Chii-Min Hwu
- National Yang-Ming University School of Medicine, Taipei, Taiwan
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ani W Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA
- Survey Research Center, Institute for Social Research, University of Michigan 426 Thompson St, Room Ann Arbor, MI 48104, USA
| | - Sharon L R Kardia
- Survey Research Center, Institute for Social Research, University of Michigan 426 Thompson St, Room Ann Arbor, MI 48104, USA
| | - Patricia A Peyser
- Survey Research Center, Institute for Social Research, University of Michigan 426 Thompson St, Room Ann Arbor, MI 48104, USA
| | - Lawrence F Bielak
- Survey Research Center, Institute for Social Research, University of Michigan 426 Thompson St, Room Ann Arbor, MI 48104, USA
| | - Timothy D O'Connor
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center, Baltimore, MD, USA
| | - Leslie S Emery
- University of Washington Department of Biostatistics, Seattle, WA 98195, USA
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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4
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Goldmann JM, Seplyarskiy VB, Wong WSW, Vilboux T, Neerincx PB, Bodian DL, Solomon BD, Veltman JA, Deeken JF, Gilissen C, Niederhuber JE. Publisher Correction: Germline de novo mutation clusters arise during oocyte aging in genomic regions with high double-strand-break incidence. Nat Genet 2021; 53:1270. [PMID: 34302146 DOI: 10.1038/s41588-021-00905-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jakob M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Vladimir B Seplyarskiy
- Division of Genetics, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, USA.,Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia
| | - Wendy S W Wong
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Thierry Vilboux
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Pieter B Neerincx
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.,Genomics Coordination Center, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dale L Bodian
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Benjamin D Solomon
- Department of Pediatrics, Inova Children's Hospital, Inova Health System, Falls Church, VA, USA.,Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Joris A Veltman
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK
| | - John F Deeken
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA
| | - Christian Gilissen
- Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Nijmegen, the Netherlands.
| | - John E Niederhuber
- Inova Translational Medicine Institute (ITMI), Inova Health Systems, Falls Church, VA, USA. .,Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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5
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Seplyarskiy VB, Akkuratov EE, Akkuratova N, Andrianova MA, Nikolaev SI, Bazykin GA, Adameyko I, Sunyaev SR. Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations. Nat Genet 2019; 51:36-41. [PMID: 30510240 PMCID: PMC6317876 DOI: 10.1038/s41588-018-0285-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
Abstract
Studies in experimental systems have identified a multitude of mutational mechanisms including DNA replication infidelity and DNA damage followed by inefficient repair or replicative bypass. However, the relative contributions of these mechanisms to human germline mutation remain unknown. Here, we show that error-prone damage bypass on the lagging strand plays a major role in human mutagenesis. Transcription-coupled DNA repair removes lesions on the transcribed strand; lesions on the non-transcribed strand are preferentially converted into mutations. In human polymorphism we detect a striking similarity between mutation types predominant on the non-transcribed strand and on the strand lagging during replication. Moreover, damage-induced mutations in cancers accumulate asymmetrically with respect to the direction of replication, suggesting that DNA lesions are resolved asymmetrically. We experimentally demonstrate that replication delay greatly attenuates the mutagenic effect of ultraviolet irradiation, confirming that replication converts DNA damage into mutations. We estimate that at least 10% of human mutations arise due to DNA damage.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Evgeny E Akkuratov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Natalia Akkuratova
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | | | - Sergey I Nikolaev
- Inserm U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Department of Dermatology and Venereology, Université Paris 7, St. Louis Hospital, Paris, France
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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6
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Andrianova MA, Chetan GK, Sibin MK, Mckee T, Merkler D, Narasinga RK, Ribaux P, Blouin JL, Makrythanasis P, Seplyarskiy VB, Antonarakis SE, Nikolaev SI. Germline PMS2 and somatic POLE exonuclease mutations cause hypermutability of the leading DNA strand in biallelic mismatch repair deficiency syndrome brain tumours. J Pathol 2017; 243:331-341. [PMID: 28805995 DOI: 10.1002/path.4957] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Revised: 08/02/2017] [Accepted: 08/09/2017] [Indexed: 12/18/2022]
Abstract
Biallelic mismatch repair deficiency (bMMRD) in tumours is frequently associated with somatic mutations in the exonuclease domains of DNA polymerases POLE or POLD1, and results in a characteristic mutational profile. In this article, we describe the genetic basis of ultramutated high-grade brain tumours in the context of bMMRD. We performed exome sequencing of two second-cousin patients from a large consanguineous family of Indian origin with early onset of high-grade glioblastoma and astrocytoma. We identified a germline homozygous nonsense variant, p.R802*, in the PMS2 gene. Additionally, by genome sequencing of these tumours, we found extremely high somatic mutation rates (237/Mb and 123/Mb), as well as somatic mutations in the proofreading domain of POLE polymerase (p.P436H and p.L424V), which replicates the leading DNA strand. Most interestingly, we found, in both cancers, that the vast majority of mutations were consistent with the signature of POLE exo- , i.e. an abundance of C>A and C>T mutations, particularly in special contexts, on the leading strand. We showed that the fraction of mutations under positive selection among mutations in tumour suppressor genes is more than two-fold lower in ultramutated tumours than in other glioblastomas. Genetic analyses enabled the diagnosis of the two consanguineous childhood brain tumours as being due to a combination of PMS2 germline and POLE somatic variants, and confirmed them as bMMRD/POLE exo- disorders. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Ghati Kasturirangan Chetan
- Department of Human Genetics, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Madathan Kandi Sibin
- Department of Human Genetics, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Thomas Mckee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Doron Merkler
- Department of Pathology and Immunology, Université de Genève (UNIGE), Geneva, Switzerland
| | - Rao Kvl Narasinga
- Department of Neuro-surgery, National Institute of Mental Health & Neurosciences (NIMHANS), Bangalore, India
| | - Pascale Ribaux
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Blouin
- Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Periklis Makrythanasis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Moscow, Russia.,Moscow State University, Moscow, Russia.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva, Geneva, Switzerland.,Service of Genetic Medicine, Geneva University Hospitals (HUG), Geneva, Switzerland
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7
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Andrianova MA, Bazykin GA, Nikolaev SI, Seplyarskiy VB. Human mismatch repair system balances mutation rates between strands by removing more mismatches from the lagging strand. Genome Res 2017; 27:1336-1343. [PMID: 28512192 PMCID: PMC5538550 DOI: 10.1101/gr.219915.116] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/09/2017] [Indexed: 12/13/2022]
Abstract
Mismatch repair (MMR) is one of the main systems maintaining fidelity of replication. Differences in correction of errors produced during replication of the leading and the lagging DNA strands were reported in yeast and in human cancers, but the causes of these differences remain unclear. Here, we analyze data on human cancers with somatic mutations in two of the major DNA polymerases, delta and epsilon, that replicate the genome. We show that these cancers demonstrate a substantial asymmetry of the mutations between the leading and the lagging strands. The direction of this asymmetry is the opposite between cancers with mutated polymerases delta and epsilon, consistent with the role of these polymerases in replication of the lagging and the leading strands in human cells, respectively. Moreover, the direction of strand asymmetry observed in cancers with mutated polymerase delta is similar to that observed in MMR-deficient cancers. Together, these data indicate that polymerase delta (possibly together with polymerase alpha) contributes more mismatches during replication than its leading-strand counterpart, polymerase epsilon; that most of these mismatches are repaired by the MMR system; and that MMR repairs about three times more mismatches produced in cells during lagging strand replication compared with the leading strand.
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Affiliation(s)
- Maria A Andrianova
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Lomonosov Moscow State University, Moscow 119234, Russia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland.,Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Vladimir B Seplyarskiy
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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8
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Abstract
Mutation rate varies along the human genome, and part of this variation is explainable by measurable local properties of the DNA molecule. Moreover, mutation rates differ between orthologous genomic regions of different species, but the drivers of this change are unclear. Here, we use data on human divergence from chimpanzee, human rare polymorphism, and human de novo mutations to predict the substitution rate at orthologous regions of non-human mammals. We show that the local mutation rates are very similar between human and apes, implying that their variation has a strong underlying cryptic component not explainable by the known genomic features. Mutation rates become progressively less similar in more distant species, and these changes are partially explainable by changes in the local genomic features of orthologous regions, most importantly, in the recombination rate. However, they are much more rapid, implying that the cryptic component underlying the mutation rate is more ephemeral than the known genomic features. These findings shed light on the determinants of mutation rate evolution. Key words local mutation rate, molecular evolution, recombination rate.
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Affiliation(s)
- Nadezhda V. Terekhanova
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir B. Seplyarskiy
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
| | - Ruslan A. Soldatov
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A. Bazykin
- Sector for Molecular Evolution, Institute for Information Transmission Problems of the RAS (Kharkevich Institute), Moscow, Russia
- M. V. Lomonosov Moscow State University, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
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9
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Seplyarskiy VB, Andrianova MA, Bazykin GA. APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context. Genome Res 2016; 27:175-184. [PMID: 27940951 PMCID: PMC5287224 DOI: 10.1101/gr.210336.116] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/01/2016] [Indexed: 12/18/2022]
Abstract
APOBEC3A/B cytidine deaminase is responsible for the majority of cancerous mutations in a large fraction of cancer samples. However, its role in heritable mutagenesis remains very poorly understood. Recent studies have demonstrated that both in yeast and in human cancerous cells, most APOBEC3A/B-induced mutations occur on the lagging strand during replication and on the nontemplate strand of transcribed regions. Here, we use data on rare human polymorphisms, interspecies divergence, and de novo mutations to study germline mutagenesis and to analyze mutations at nucleotide contexts prone to attack by APOBEC3A/B. We show that such mutations occur preferentially on the lagging strand and on nontemplate strands of transcribed regions. Moreover, we demonstrate that APOBEC3A/B-like mutations tend to produce strand-coordinated clusters, which are also biased toward the lagging strand. Finally, we show that the mutation rate is increased 3' of C→G mutations to a greater extent than 3' of C→T mutations, suggesting pervasive trans-lesion bypass of the APOBEC3A/B-induced damage. Our study demonstrates that 20% of C→T and C→G mutations in the TpCpW context-where W denotes A or T, segregating as polymorphisms in human population-or 1.4% of all heritable mutations are attributable to APOBEC3A/B activity.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Maria A Andrianova
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Lomonosov Moscow State University, Moscow 119234, Russia
| | - Georgii A Bazykin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow 127994, Russia.,Pirogov Russian National Research Medical University, Moscow 117997, Russia.,Lomonosov Moscow State University, Moscow 119234, Russia.,Skolkovo Institute of Science and Technology, Skolkovo 143026, Russia
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10
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Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau A, Ribaux PG, Popadin K, Basset-Seguin N, Ben Chaabene R, Santoni FA, Andrianova MA, Guipponi M, Garieri M, Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE, Nikolaev SI. Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma. Nat Genet 2016; 48:398-406. [PMID: 26950094 DOI: 10.1038/ng.3525] [Citation(s) in RCA: 308] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 02/11/2016] [Indexed: 12/13/2022]
Abstract
Basal cell carcinoma (BCC) of the skin is the most common malignant neoplasm in humans. BCC is primarily driven by the Sonic Hedgehog (Hh) pathway. However, its phenotypic variation remains unexplained. Our genetic profiling of 293 BCCs found the highest mutation rate in cancer (65 mutations/Mb). Eighty-five percent of the BCCs harbored mutations in Hh pathway genes (PTCH1, 73% or SMO, 20% (P = 6.6 × 10(-8)) and SUFU, 8%) and in TP53 (61%). However, 85% of the BCCs also harbored additional driver mutations in other cancer-related genes. We observed recurrent mutations in MYCN (30%), PPP6C (15%), STK19 (10%), LATS1 (8%), ERBB2 (4%), PIK3CA (2%), and NRAS, KRAS or HRAS (2%), and loss-of-function and deleterious missense mutations were present in PTPN14 (23%), RB1 (8%) and FBXW7 (5%). Consistent with the mutational profiles, N-Myc and Hippo-YAP pathway target genes were upregulated. Functional analysis of the mutations in MYCN, PTPN14 and LATS1 suggested their potential relevance in BCC tumorigenesis.
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Affiliation(s)
- Ximena Bonilla
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | | | - Bryan King
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Fedor Bezrukov
- Department of Physics, University of Connecticut, Storrs, Connecticut, USA
- RIKEN BNL Research Center, Brookhaven National Laboratory, Upton, New York, USA
| | - Gürkan Kaya
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Vincent Zoete
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Hayley J Sharpe
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Thomas McKee
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Audrey Letourneau
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Pascale G Ribaux
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Konstantin Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Nicole Basset-Seguin
- Department of Dermatology, Saint Louis Hospital, Paris 7 University, Paris, France
| | - Rouaa Ben Chaabene
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Federico A Santoni
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Maria A Andrianova
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
- Pirogov Russian National Research Medical University, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Michel Guipponi
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
| | - Marco Garieri
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Carole Verdan
- Service of Clinical Pathology, University Hospitals of Geneva, Geneva, Switzerland
| | - Kerstin Grosdemange
- Department of Dermatology, University Hospitals of Geneva, Geneva, Switzerland
| | - Olga Sumara
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, University of Würzburg, Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Iannis Aifantis
- Department of Pathology, New York University School of Medicine, New York, New York, USA
| | - Olivier Michielin
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland
| | - Frederic J de Sauvage
- Department of Molecular Oncology, Genentech, Inc., South San Francisco, California, USA
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
- Institute of Genetics and Genomics of Geneva (iGE3), Geneva, Switzerland
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
- Service of Genetic Medicine, University Hospitals of Geneva, Geneva, Switzerland
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11
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Seplyarskiy VB, Soldatov RA, Popadin KY, Antonarakis SE, Bazykin GA, Nikolaev SI. APOBEC-induced mutations in human cancers are strongly enriched on the lagging DNA strand during replication. Genome Res 2016; 26:174-82. [PMID: 26755635 PMCID: PMC4728370 DOI: 10.1101/gr.197046.115] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 12/10/2015] [Indexed: 12/31/2022]
Abstract
APOBEC3A and APOBEC3B, cytidine deaminases of the APOBEC family, are among the main factors causing mutations in human cancers. APOBEC deaminates cytosines in single-stranded DNA (ssDNA). A fraction of the APOBEC-induced mutations occur as clusters ("kataegis") in single-stranded DNA produced during repair of double-stranded breaks (DSBs). However, the properties of the remaining 87% of nonclustered APOBEC-induced mutations, the source and the genomic distribution of the ssDNA where they occur, are largely unknown. By analyzing genomic and exomic cancer databases, we show that >33% of dispersed APOBEC-induced mutations occur on the lagging strand during DNA replication, thus unraveling the major source of ssDNA targeted by APOBEC in cancer. Although methylated cytosine is generally more mutation-prone than nonmethylated cytosine, we report that methylation reduces the rate of APOBEC-induced mutations by a factor of roughly two. Finally, we show that in cancers with extensive APOBEC-induced mutagenesis, there is almost no increase in mutation rates in late replicating regions (contrary to other cancers). Because late-replicating regions are depleted in exons, this results in a 1.3-fold higher fraction of mutations residing within exons in such cancers. This study provides novel insight into the APOBEC-induced mutagenesis and describes the peculiarity of the mutational processes in cancers with the signature of APOBEC-induced mutations.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Konstantin Y Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Stylianos E Antonarakis
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland
| | - Georgii A Bazykin
- Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia, 127051; Lomonosov Moscow State University, Moscow, Russia, 119991; Pirogov Russian National Research Medical University, Moscow, Russia, 117997
| | - Sergey I Nikolaev
- Department of Genetic Medicine and Development, University of Geneva Medical School, 1211 Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, 1211 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1211 Geneva, Switzerland
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12
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Seplyarskiy VB, Bazykin GA, Soldatov RA. Polymerase ζ Activity Is Linked to Replication Timing in Humans: Evidence from Mutational Signatures. Mol Biol Evol 2015; 32:3158-72. [PMID: 26376651 DOI: 10.1093/molbev/msv184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Replication timing is an important determinant of germline mutation patterns, with a higher rate of point mutations in late replicating regions. Mechanisms underlying this association remain elusive. One of the suggested explanations is the activity of error-prone DNA polymerases in late-replicating regions. Polymerase zeta (pol ζ), an essential error-prone polymerase biased toward transversions, also has a tendency to produce dinucleotide mutations (DNMs), complex mutational events that simultaneously affect two adjacent nucleotides. Experimental studies have shown that pol ζ is strongly biased toward GC→AA/TT DNMs. Using primate divergence data, we show that the GC→AA/TT pol ζ mutational signature is the most frequent among DNMs, and its rate exceeds the mean rate of other DNM types by a factor of approximately 10. Unlike the overall rate of DNMs, the pol ζ signature drastically increases with the replication time in the human genome. Finally, the pol ζ signature is enriched in transcribed regions, and there is a strong prevalence of GC→TT over GC→AA DNMs on the nontemplate strand, indicating association with transcription. A recurrently occurring GC→TT DNM in HRAS and SOD1 genes causes the Costello syndrome and amyotrophic lateral sclerosis correspondently; we observe an approximately 1 kb long mutation hotspot enriched by transversions near these DNMs in both cases, suggesting a link between these diseases and pol ζ activity. This study uncovers the genomic preferences of pol ζ, shedding light on a novel cause of mutational heterogeneity along the genome.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Georgii A Bazykin
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ruslan A Soldatov
- Institute of Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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13
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Baranova MA, Logacheva MD, Penin AA, Seplyarskiy VB, Safonova YY, Naumenko SA, Klepikova AV, Gerasimov ES, Bazykin GA, James TY, Kondrashov AS. Extraordinary Genetic Diversity in a Wood Decay Mushroom. Mol Biol Evol 2015; 32:2775-83. [PMID: 26163667 PMCID: PMC4576712 DOI: 10.1093/molbev/msv153] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Populations of different species vary in the amounts of genetic diversity they possess. Nucleotide diversity π, the fraction of nucleotides that are different between two randomly chosen genotypes, has been known to range in eukaryotes between 0.0001 in Lynx lynx and 0.16 in Caenorhabditis brenneri. Here, we report the results of a comparative analysis of 24 haploid genotypes (12 from the United States and 12 from European Russia) of a split-gill fungus Schizophyllum commune. The diversity at synonymous sites is 0.20 in the American population of S. commune and 0.13 in the Russian population. This exceptionally high level of nucleotide diversity also leads to extreme amino acid diversity of protein-coding genes. Using whole-genome resequencing of 2 parental and 17 offspring haploid genotypes, we estimate that the mutation rate in S. commune is high, at 2.0 × 10−8 (95% CI: 1.1 × 10−8 to 4.1 × 10−8) per nucleotide per generation. Therefore, the high diversity of S. commune is primarily determined by its elevated mutation rate, although high effective population size likely also plays a role. Small genome size, ease of cultivation and completion of the life cycle in the laboratory, free-living haploid life stages and exceptionally high variability of S. commune make it a promising model organism for population, quantitative, and evolutionary genetics.
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Affiliation(s)
- Maria A Baranova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Maria D Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aleksey A Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir B Seplyarskiy
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia
| | - Yana Y Safonova
- Algorithmic Biology Lab, St. Petersburg Academic University of the Russian Academy of Sciences, St Petersburg, Russia
| | - Sergey A Naumenko
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Anna V Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Evgeny S Gerasimov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Georgii A Bazykin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Moscow, Russia Pirogov Russian National Research Medical University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan
| | - Alexey S Kondrashov
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan
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14
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Seplyarskiy VB, Logacheva MD, Penin AA, Baranova MA, Leushkin EV, Demidenko NV, Klepikova AV, Kondrashov FA, Kondrashov AS, James TY. Crossing-over in a hypervariable species preferentially occurs in regions of high local similarity. Mol Biol Evol 2014; 31:3016-25. [PMID: 25135947 PMCID: PMC4209137 DOI: 10.1093/molbev/msu242] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Recombination between double-stranded DNA molecules is a key genetic process which occurs in a wide variety of organisms. Usually, crossing-over (CO) occurs during meiosis between genotypes with 98.0–99.9% sequence identity, because within-population nucleotide diversity only rarely exceeds 2%. However, some species are hypervariable and it is unclear how CO can occur between genotypes with less than 90% sequence identity. Here, we study CO in Schizophyllum commune, a hypervariable cosmopolitan basidiomycete mushroom, a frequently encountered decayer of woody substrates. We crossed two haploid individuals, from the United States and from Russia, and obtained genome sequences for their 17 offspring. The average genetic distance between the parents was 14%, making it possible to study CO at very high resolution. We found reduced levels of linkage disequilibrium between loci flanking the CO sites indicating that they are mostly confined to hotspots of recombination. Furthermore, CO events preferentially occurred in regions under stronger negative selection, in particular within exons that showed reduced levels of nucleotide diversity. Apparently, in hypervariable species CO must avoid regions of higher divergence between the recombining genomes due to limitations imposed by the mismatch repair system, with regions under strong negative selection providing the opportunity for recombination. These patterns are opposite to those observed in a number of less variable species indicating that population genomics of hypervariable species may reveal novel biological phenomena.
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Affiliation(s)
- Vladimir B Seplyarskiy
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Maria D Logacheva
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Aleksey A Penin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Maria A Baranova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Evgeny V Leushkin
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Institute of Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Natalia V Demidenko
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Anna V Klepikova
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Moscow, Moscow, Russia
| | - Fyodor A Kondrashov
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) Barcelona, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), 23 Pg. Lluís Companys, Barcelona, Spain
| | - Alexey S Kondrashov
- School of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Timothy Y James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
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Terekhanova NV, Bazykin GA, Neverov A, Kondrashov AS, Seplyarskiy VB. Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Mol Biol Evol 2013; 30:1315-25. [PMID: 23447710 PMCID: PMC3649671 DOI: 10.1093/molbev/mst036] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Evolution of sequences mostly involves independent changes at different sites. However, substitutions at neighboring sites may co-occur as multinucleotide replacement events (MNRs). Here, we compare noncoding sequences of several species of primates, and of three species of Drosophila fruit flies, in a phylogenetic analysis of the replacements that occurred between species at nearby nucleotide sites. Both in primates and in Drosophila, the frequency of single-nucleotide replacements is substantially elevated within 10 nucleotides from other replacements that occurred on the same lineage but not on another lineage. The data imply that dinucleotide replacements (DNRs) affecting sites at distances of up to 10 nucleotides from each other are responsible for 2.3% of single-nucleotide replacements in primate genomes and for 5.6% in Drosophila genomes. Among these DNRs, 26% and 69%, respectively, are in fact parts of replacements of three or more trinucleotide replacements (TNRs). The plurality of MNRs affect nearby nucleotides, so that at least six times as many DNRs affect two adjacent nucleotide sites than sites 10 nucleotides apart. Still, approximately 60% of DNRs, and approximately 90% of TNRs, span distances more than two (or three) nucleotides. MNRs make a major contribution to the observed clustering of substitutions: In the human–chimpanzee comparison, DNRs are responsible for 50% of cases when two nearby replacements are observed on the human lineage, and TNRs are responsible for 83% of cases when three replacements at three immediately adjacent sites are observed on the human lineage. The prevalence of MNRs matches that is observed in data on de novo mutations and is also observed in the regions with the lowest sequence conservation, suggesting that MNRs mainly have mutational origin; however, epistatic selection and/or gene conversion may also play a role.
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Affiliation(s)
- Nadezhda V Terekhanova
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
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16
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Seplyarskiy VB, Kharchenko P, Kondrashov AS, Bazykin GA. Heterogeneity of the transition/transversion ratio in Drosophila and Hominidae genomes. Mol Biol Evol 2012; 29:1943-55. [PMID: 22337862 DOI: 10.1093/molbev/mss071] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Mutation rate varies between sites in the genome. Part of this variation can be explained by well-recognized short nucleotide contexts, but a large component of this variation remains cryptic. We used data on interspecies divergence and intraspecies polymorphism in Drosophila and Hominidae to analyze variation of the average rate of the 12 possible kinds of single-nucleotide mutations and in the transition/transversion ratio κ at single-nucleotide resolution. Both the average mutation rate and κ vary by a factor of ~3 between nucleotide sites. The characteristic scale of variation in κ is up to at least ~30 nucleotides in Drosophila and ~5 nucleotides in Hominidae. Genome segments with locally elevated mutation rates possess lower values of κ; however, a substantial fraction of variation in κ cannot be directly explained by the local mutation rates.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Department of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
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