1
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Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Catacchio CR, Porubsky D, Mao Y, Yoo D, Rautiainen M, Koren S, Nurk S, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Ventura M, Alexandrov IA, Eichler EE. The variation and evolution of complete human centromeres. Nature 2024; 629:136-145. [PMID: 38570684 PMCID: PMC11062924 DOI: 10.1038/s41586-024-07278-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Human centromeres have been traditionally very difficult to sequence and assemble owing to their repetitive nature and large size1. As a result, patterns of human centromeric variation and models for their evolution and function remain incomplete, despite centromeres being among the most rapidly mutating regions2,3. Here, using long-read sequencing, we completely sequenced and assembled all centromeres from a second human genome and compared it to the finished reference genome4,5. We find that the two sets of centromeres show at least a 4.1-fold increase in single-nucleotide variation when compared with their unique flanks and vary up to 3-fold in size. Moreover, we find that 45.8% of centromeric sequence cannot be reliably aligned using standard methods owing to the emergence of new α-satellite higher-order repeats (HORs). DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by >500 kb. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan and macaque genomes. Comparative analyses reveal a nearly complete turnover of α-satellite HORs, with characteristic idiosyncratic changes in α-satellite HORs for each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the short (p) and long (q) arms across centromeres and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
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Affiliation(s)
- Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Department of Genetics, Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Allison N Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Claudia R Catacchio
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - DongAhn Yoo
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies, Oxford, United Kingdom
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mario Ventura
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, Bari, Italy
| | - Ivan A Alexandrov
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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2
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Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Comparative genomics of macaques and integrated insights into genetic variation and population history. bioRxiv 2024:2024.04.07.588379. [PMID: 38645259 PMCID: PMC11030432 DOI: 10.1101/2024.04.07.588379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The crab-eating macaques ( Macaca fascicularis ) and rhesus macaques ( M. mulatta ) are widely studied nonhuman primates in biomedical and evolutionary research. Despite their significance, the current understanding of the complex genomic structure in macaques and the differences between species requires substantial improvement. Here, we present a complete genome assembly of a crab-eating macaque and 20 haplotype-resolved macaque assemblies to investigate the complex regions and major genomic differences between species. Segmental duplication in macaques is ∼42% lower, while centromeres are ∼3.7 times longer than those in humans. The characterization of ∼2 Mbp fixed genetic variants and ∼240 Mbp complex loci highlights potential associations with metabolic differences between the two macaque species (e.g., CYP2C76 and EHBP1L1 ). Additionally, hundreds of alternative splicing differences show post-transcriptional regulation divergence between these two species (e.g., PNPO ). We also characterize 91 large-scale genomic differences between macaques and humans at a single-base-pair resolution and highlight their impact on gene regulation in primate evolution (e.g., FOLH1 and PIEZO2 ). Finally, population genetics recapitulates macaque speciation and selective sweeps, highlighting potential genetic basis of reproduction and tail phenotype differences (e.g., STAB1 , SEMA3F , and HOXD13 ). In summary, the integrated analysis of genetic variation and population genetics in macaques greatly enhances our comprehension of lineage-specific phenotypes, adaptation, and primate evolution, thereby improving their biomedical applications in human diseases.
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3
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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.
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Affiliation(s)
| | - Brandon D. Pickett
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Monika Cechova
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Karol Pal
- Penn State University, University Park, PA, USA
| | - Sergey Nurk
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - DongAhn Yoo
- University of Washington School of Medicine, Seattle, WA, USA
| | - Qiuhui Li
- Johns Hopkins University, Baltimore, MD, USA
| | - Prajna Hebbar
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | | | | | - Erich Bomberg
- University of Münster, Münster, Germany
- MPI for Developmental Biology, Tübingen, Germany
| | - Gerard G. Bouffard
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shelise Y. Brooks
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lucia Carbone
- Oregon Health & Science University, Portland, OR, USA
- Oregon National Primate Research Center, Hillsboro, OR, USA
| | - Laura Carrel
- Penn State University School of Medicine, Hershey, PA, USA
| | | | | | - Chen-Shan Chin
- Foundation of Biological Data Sciences, Belmont, CA, USA
| | | | | | | | - Mark Diekhans
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - Amalia Dutra
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gage H. Garcia
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | - Diana Haddad
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Pille Hallast
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Glenn Hickey
- University of California Santa Cruz, Santa Cruz, CA, USA
| | - David A. Hillis
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | - Hyeonsoo Jeong
- University of Washington School of Medicine, Seattle, WA, USA
| | | | | | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Patrick Masterson
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Karen H. Miga
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Evgenia Pak
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Benedict Paten
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | - Arang Rhie
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | | | - Samuel Sacco
- University of California Santa Cruz, Santa Cruz, CA, USA
| | | | | | | | - Steven J. Solar
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Sweetalana
- Penn State University, University Park, PA, USA
| | - Alex Sweeten
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | | | - Alice C. Young
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Xinru Zhang
- Penn State University, University Park, PA, USA
| | | | | | | | - Soojin V. Yi
- University of California Santa Barbara, Santa Barbara, CA, USA
| | | | | | - Sergey Koren
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | | | - Evan Eichler
- University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam M. Phillippy
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
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4
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Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM. The complete sequence of a human Y chromosome. Nature 2023; 621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.
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Affiliation(s)
- Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Oxford Nanopore Technologies Inc., Oxford, UK
| | - Monika Cechova
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Savannah J Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A Alexandrov
- Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Jamie Allen
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Chen-Shan Chin
- GeneDX Holdings Corp, Stamford, CT, USA
- Foundation of Biological Data Science, Belmont, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | | | | | - Carlos Garcia Giron
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ariel Gershman
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer L Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical Center, Kansas City, MO, USA
| | - Patrick G S Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Andrea Guarracino
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
- Genomics Research Centre, Human Technopole, Milan, Italy
| | - Leanne Haggerty
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nancy F Hansen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Robert Harris
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jakob Heinz
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Stephen Hwang
- XDBio Program, Johns Hopkins University, Baltimore, MD, USA
| | - Miten Jain
- Department of Bioengineering, Department of Physics, Northeastern University, Boston, MA, USA
| | - Rupesh K Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Alexandra P Lewis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Christopher Markovic
- Genome Technology Access Center at the McDonnell Genome Institute, Washington University, St. Louis, MO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Ann M Mc Cartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Brandy M McNulty
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Paul Medvedev
- Department of Computer Science and Engineering, Pennsylvania State University, University Park, PA, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, USA
- Center for Computational Biology and Bioinformatics, Pennsylvania State University, University Park, PA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Saint Petersburg State University, St Petersburg, Russia
- UCL Queen Square Institute of Neurology, UCL, London, UK
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Hugh E Olsen
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Nathan D Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Luis F Paulin
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Steven L Salzberg
- Departments of Biomedical Engineering, Computer Science, and Biostatistics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
- Department of Computer Science, Rice University, Houston, TX, USA
| | | | | | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | | | - Likhitha Surapaneni
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Angela M Taravella Oill
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Marta Tomaszkiewicz
- Department of Biology, Pennsylvania State University, University Park, PA, USA
- Department of Biomedical Engineering, Pennsylvania State University, State College, PA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Allison C Watwood
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | | | | | - Melissa A Wilson
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Yiming Zhu
- Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA
| | - Justin M Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Investigator, Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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5
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Logsdon GA, Rozanski AN, Ryabov F, Potapova T, Shepelev VA, Mao Y, Rautiainen M, Koren S, Nurk S, Porubsky D, Lucas JK, Hoekzema K, Munson KM, Gerton JL, Phillippy AM, Alexandrov IA, Eichler EE. The variation and evolution of complete human centromeres. bioRxiv 2023:2023.05.30.542849. [PMID: 37398417 PMCID: PMC10312506 DOI: 10.1101/2023.05.30.542849] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
We completely sequenced and assembled all centromeres from a second human genome and used two reference sets to benchmark genetic, epigenetic, and evolutionary variation within centromeres from a diversity panel of humans and apes. We find that centromere single-nucleotide variation can increase by up to 4.1-fold relative to other genomic regions, with the caveat that up to 45.8% of centromeric sequence, on average, cannot be reliably aligned with current methods due to the emergence of new α-satellite higher-order repeat (HOR) structures and two to threefold differences in the length of the centromeres. The extent to which this occurs differs depending on the chromosome and haplotype. Comparing the two sets of complete human centromeres, we find that eight harbor distinctly different α-satellite HOR array structures and four contain novel α-satellite HOR variants in high abundance. DNA methylation and CENP-A chromatin immunoprecipitation experiments show that 26% of the centromeres differ in their kinetochore position by at least 500 kbp-a property not readily associated with novel α-satellite HORs. To understand evolutionary change, we selected six chromosomes and sequenced and assembled 31 orthologous centromeres from the common chimpanzee, orangutan, and macaque genomes. Comparative analyses reveal nearly complete turnover of α-satellite HORs, but with idiosyncratic changes in structure characteristic to each species. Phylogenetic reconstruction of human haplotypes supports limited to no recombination between the p- and q-arms of human chromosomes and reveals that novel α-satellite HORs share a monophyletic origin, providing a strategy to estimate the rate of saltatory amplification and mutation of human centromeric DNA.
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Affiliation(s)
- Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Allison N. Rozanski
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Fedor Ryabov
- Masters Program in National Research University Higher School of Economics, Moscow, Russia
| | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | | | - Yafei Mao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Julian K. Lucas
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Katherine M. Munson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | | | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ivan A. Alexandrov
- Department of Human Molecular Genetics and Biochemistry, Tel Aviv University, Tel Aviv, Israel
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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6
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Kumar S, Gahramanov V, Patel S, Yaglom J, Kaczmarczyk L, Alexandrov IA, Gerlitz G, Salmon-Divon M, Sherman MY. Evolution of Resistance to Irinotecan in Cancer Cells Involves Generation of Topoisomerase-Guided Mutations in Non-Coding Genome That Reduce the Chances of DNA Breaks. Int J Mol Sci 2023; 24:ijms24108717. [PMID: 37240063 DOI: 10.3390/ijms24108717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/01/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Resistance to chemotherapy is a leading cause of treatment failure. Drug resistance mechanisms involve mutations in specific proteins or changes in their expression levels. It is commonly understood that resistance mutations happen randomly prior to treatment and are selected during the treatment. However, the selection of drug-resistant mutants in culture could be achieved by multiple drug exposures of cloned genetically identical cells and thus cannot result from the selection of pre-existent mutations. Accordingly, adaptation must involve the generation of mutations de novo upon drug treatment. Here we explored the origin of resistance mutations to a widely used Top1 inhibitor, irinotecan, which triggers DNA breaks, causing cytotoxicity. The resistance mechanism involved the gradual accumulation of recurrent mutations in non-coding regions of DNA at Top1-cleavage sites. Surprisingly, cancer cells had a higher number of such sites than the reference genome, which may define their increased sensitivity to irinotecan. Homologous recombination repairs of DNA double-strand breaks at these sites following initial drug exposures gradually reverted cleavage-sensitive "cancer" sequences back to cleavage-resistant "normal" sequences. These mutations reduced the generation of DNA breaks upon subsequent exposures, thus gradually increasing drug resistance. Together, large target sizes for mutations and their Top1-guided generation lead to their gradual and rapid accumulation, synergistically accelerating the development of resistance.
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Affiliation(s)
- Santosh Kumar
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Valid Gahramanov
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Shivani Patel
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Julia Yaglom
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Lukasz Kaczmarczyk
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | - Ivan A Alexandrov
- Department of Anatomy and Anthropology & Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Gabi Gerlitz
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
| | | | - Michael Y Sherman
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel
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7
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Altemose N, Glennis A, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science 2022; 376:eabl4178. [PMID: 35357911 PMCID: PMC9233505 DOI: 10.1126/science.abl4178] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.
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Affiliation(s)
- Nicolas Altemose
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - A. Glennis
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Pragya Sidhwani
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Sasha A. Langley
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Lev Uralsky
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Colin J. Shew
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | | | | | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Olga Kunyavskaya
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mobin Asri
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Ryan Lorig-Roach
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | | | - Tamara Potapova
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | | | - Fedor Gusev
- Vavilov Institute of General Genetics, Moscow, Russia
| | - Kristof Tigyi
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Shelise Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Alice Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Sofie R. Salama
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology, Sochi, Russia
- Vavilov Institute of General Genetics, Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Gary H. Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Abby F. Dernburg
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | | | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT. USA
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research, Kansas City, MO, USA
- University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
| | - Rachel J. O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Charles H. Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Ivan A. Alexandrov
- Vavilov Institute of General Genetics, Moscow, Russia
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
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8
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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022; 376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 911] [Impact Index Per Article: 455.5] [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] [Indexed: 12/11/2022]
Abstract
Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.
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Affiliation(s)
- Sergey Nurk
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Mikko Rautiainen
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Andrey V. Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
| | - Alla Mikheenko
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
| | - Lev Uralsky
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
| | - Sergey Aganezov
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Savannah J. Hoyt
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Mark Diekhans
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Michael Alonge
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | | | | | - Gerard G. Bouffard
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Shelise Y. Brooks
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gina V. Caldas
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
| | - Nae-Chyun Chen
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Haoyu Cheng
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | | | | | | | - Philip C. Dishuck
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Richard Durbin
- Wellcome Sanger Institute; Cambridge, UK
- Department of Genetics, University of Cambridge; Cambridge, UK
| | - Tatiana Dvorkina
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
| | | | - Giulio Formenti
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Robert S. Fulton
- Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
| | | | - Erik Garrison
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- University of Tennessee Health Science Center; Memphis, TN, USA
| | - Patrick G.S. Grady
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | | | - Ira M. Hall
- Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
| | - Nancy F. Hansen
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Gabrielle A. Hartley
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Marina Haukness
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | | | - Chirag Jain
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
- Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Erich D. Jarvis
- Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Mikhail Kolmogorov
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | | | - Milinn Kremitzki
- McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA
- Department of Biomedical Informatics, Harvard Medical School; Boston, MA
| | - Valerie V. Maduro
- Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Tobias Marschall
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
| | - Ann M. McCartney
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | - Jennifer McDaniel
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Danny E. Miller
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
| | - James C. Mullikin
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
- Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Eugene W. Myers
- Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
| | - Nathan D. Olson
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | | | - Pavel A. Pevzner
- Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
| | - David Porubsky
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
| | - Tamara Potapova
- Stowers Institute for Medical Research; Kansas City, MO, USA
| | - Evgeny I. Rogaev
- Sirius University of Science and Technology; Sochi, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA
- Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
| | | | - Steven L. Salzberg
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Valerie A. Schneider
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
| | - Colin J. Shew
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Ying Sims
- Wellcome Sanger Institute; Cambridge, UK
| | | | - Daniela C. Soto
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan Sović
- Pacific Biosciences; Menlo Park, CA, USA
- Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
| | | | - Aaron Streets
- Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
- Chan Zuckerberg Biohub; San Francisco, CA, USA
| | - Beth A. Sullivan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
| | - Françoise Thibaud-Nissen
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | | | - Justin Wagner
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Brian P. Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
| | | | | | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
| | - Stephanie M. Yan
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Alice C. Young
- NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
| | - Rajiv C. McCoy
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Megan Y. Dennis
- Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
| | - Ivan A. Alexandrov
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
- Vavilov Institute of General Genetics; Moscow, Russia
- Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
| | - Jennifer L. Gerton
- Stowers Institute for Medical Research; Kansas City, MO, USA
- Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
| | - Rachel J. O’Neill
- Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
| | - Justin M. Zook
- Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
| | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
- Department of Biology, Johns Hopkins University; Baltimore, MD, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
- Howard Hughes Medical Institute; Chevy Chase, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
- Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
| | - Adam M. Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
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9
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Abstract
We are entering a new era in genomics where entire centromeric regions are accurately represented in human reference assemblies. Access to these high-resolution maps will enable new surveys of sequence and epigenetic variation in the population and offer new insight into satellite array genomics and centromere function. Here, we focus on the sequence organization and evolution of alpha satellites, which are credited as the genetic and genomic definition of human centromeres due to their interaction with inner kinetochore proteins and their importance in the development of human artificial chromosome assays. We provide an overview of alpha satellite repeat structure and array organization in the context of these high-quality reference data sets; discuss the emergence of variation-based surveys; and provide perspective on the role of this new source of genetic and epigenetic variation in the context of chromosome biology, genome instability, and human disease.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; .,Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ivan A Alexandrov
- Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia; .,Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg 199004, Russia.,Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia
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10
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Shepelev VA, Uralsky LI, Alexandrov AA, Yurov YB, Rogaev EI, Alexandrov IA. Annotation of suprachromosomal families reveals uncommon types of alpha satellite organization in pericentromeric regions of hg38 human genome assembly. Genom Data 2015; 5:139-146. [PMID: 26167452 PMCID: PMC4496801 DOI: 10.1016/j.gdata.2015.05.035] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- V A Shepelev
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia ; Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - L I Uralsky
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - A A Alexandrov
- Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov sq. 2, Moscow 123182, Russia
| | - Y B Yurov
- Research Center of Mental Health, Russian Academy of Medical Sciences, Zagorodnoe sh. 2, Moscow 113152, Russia
| | - E I Rogaev
- Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow 119991, Russia ; Center for Brain Neurobiology and Neurogenetics, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; Department of Psychiatry, Brudnick Neuropsychiatric Research Institute, University of Massachusetts Medical School, Worcester, MA 01604, USA ; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119234, Russia
| | - I A Alexandrov
- Research Center of Mental Health, Russian Academy of Medical Sciences, Zagorodnoe sh. 2, Moscow 113152, Russia
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11
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Shepelev VA, Alexandrov AA, Yurov YB, Alexandrov IA. The evolutionary origin of man can be traced in the layers of defunct ancestral alpha satellites flanking the active centromeres of human chromosomes. PLoS Genet 2009; 5:e1000641. [PMID: 19749981 PMCID: PMC2729386 DOI: 10.1371/journal.pgen.1000641] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2009] [Accepted: 08/11/2009] [Indexed: 02/01/2023] Open
Abstract
Alpha satellite domains that currently function as centromeres of human chromosomes are flanked by layers of older alpha satellite, thought to contain dead centromeres of primate progenitors, which lost their function and the ability to homogenize satellite repeats, upon appearance of a new centromere. Using cladistic analysis of alpha satellite monomers, we elucidated complete layer patterns on chromosomes 8, 17, and X and related them to each other and to primate alpha satellites. We show that discrete and chronologically ordered alpha satellite layers are partially symmetrical around an active centromere and their succession is partially shared in non-homologous chromosomes. The layer structure forms a visual representation of the human evolutionary lineage with layers corresponding to ancestors of living primates and to entirely fossil taxa. Surprisingly, phylogenetic comparisons suggest that alpha satellite arrays went through periods of unusual hypermutability after they became "dead" centromeres. The layer structure supports a model of centromere evolution where new variants of a satellite repeat expanded periodically in the genome by rounds of inter-chromosomal transfer/amplification. Each wave of expansion covered all or many chromosomes and corresponded to a new primate taxon. Complete elucidation of the alpha satellite phylogenetic record would give a unique opportunity to number and locate the positions of major extinct taxa in relation to human ancestors shared with extant primates. If applicable to other satellites in non-primate taxa, analysis of centromeric layers could become an invaluable tool for phylogenetic studies.
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Affiliation(s)
- Valery A. Shepelev
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | - Yuri B. Yurov
- Mental Health Research Centre, Russian Academy of Medical Sciences, Moscow, Russia
| | - Ivan A. Alexandrov
- Mental Health Research Centre, Russian Academy of Medical Sciences, Moscow, Russia
- * E-mail:
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12
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Rakhimov RR, Prokof’ev AI, Bah R, Pegram SA, Hwang JS, Khodak AA, Alexandrov IA, Aleksandrov AI. Dechlorination of diphenyl chlorophosphate with tin and sodium 3,6-di-tert-butyl-ortho-semiquinones. Inorganica Chim Acta 2007. [DOI: 10.1016/j.ica.2007.02.036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Kazakov AE, Shepelev VA, Tumeneva IG, Alexandrov AA, Yurov YB, Alexandrov IA. Interspersed repeats are found predominantly in the “old” α satellite families. Genomics 2003; 82:619-27. [PMID: 14611803 DOI: 10.1016/s0888-7543(03)00182-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The biased distribution of dispersed repeat insertions in various types of primate specific alpha satellites (AS) is being discussed in the literature in relation to the modes of AS evolution and their possible roles in maintenance and disruption of functional centromeres. However, such a bias has not been properly documented on a genome-wide scale so far. In this work, using a representative sample of about 100 insertions we show that the "old" AS contains at least 10 times more dispersed repeats than the "new" one. In the new arrays insertions accumulate mostly in poorly homogenized areas, presumably in the edges, and in the old AS, throughout the whole array length. Dating of L1 insertions in the old AS revealed that their massive accumulation started at or after the time when the new AS emerged and expanded in the genome and the centromere function had shifted to the new AS arrays.
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Affiliation(s)
- Alexei E Kazakov
- Mental Health Research Center, Russian Academy of Medical Sciences, Zagorodnoe sh.2, Moscow 113152, Russia
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14
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Romanova LY, Alexandrov IA, Blagosklonny MV, Nordan RP, Garfield S, Acs P, Nguyen P, Trepel J, Blumberg PM, Mushinski JF. Regulation of actin cytoskeleton in lymphocytes: PKC-delta disrupts IL-3-induced membrane ruffles downstream of Rac1. J Cell Physiol 1999; 179:157-69. [PMID: 10199555 DOI: 10.1002/(sici)1097-4652(199905)179:2<157::aid-jcp6>3.0.co;2-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In the murine pre-B lymphoid cell line Baf3, the presence of IL-3 is required for the formation of membrane ruffles that intensely stain for actin and are responsible for the elongated cell phenotype. Withdrawal of IL-3 dissolves ruffled protrusions and converts the cell phenotype to round. Flow cytometric analysis of the cell shape showed that an inactive analog of Rac1 but not inactive RhoA or inactive cdc42 rounds the cells in the presence of IL-3. Constitutively activated Rac1 restores the elongated cell phenotype to IL-3-starved cells. We conclude that the activity of Rac1 is necessary and sufficient for the IL-3-induced assembly of membrane ruffles. Similar to the IL-3 withdrawal, phorbol 12-myristate 13-acetate (PMA) dissolves actin-formed membrane ruffles and rounds the cells in the presence of IL-3. Flow cytometric analysis of the cell shape demonstrated that in the presence of IL-3 the PMA-induced cell rounding cannot be abolished by constitutively active Rac1 but can be imitated by inactive Rac1. These data indicate that PMA disrupts the IL-3 pathway downstream of Rac1. Cells rounded by PMA return to the elongated phenotype concomitantly with PKC depletion. PMA-induced cell rounding can be reversed by the PKC-specific inhibitor GF109203X. Experiments with overexpression in Baf3 of individual PKC isoforms and a dominant negative PKC-delta indicate that activation of PKC-delta but not other PKC isoforms is responsible for disruption of membrane ruffles.
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Affiliation(s)
- L Y Romanova
- Laboratory of Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA.
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15
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Romanova LY, Alexandrov IA, Nordan RP, Blagosklonny MV, Mushinski JF. Cross-talk between protein kinase C-alpha (PKC-alpha) and -delta (PKC-delta): PKC-alpha elevates the PKC-delta protein level, altering its mRNA transcription and degradation. Biochemistry 1998; 37:5558-65. [PMID: 9548940 DOI: 10.1021/bi9731807] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Studies utilizing the overexpression of individual isoforms indicated that both PKC-alpha and -delta promote a number of biological effects, including inhibition of DNA synthesis associated with rearrangements of the actin cytoskeleton in the murine B-cell lymphoma (Baf3), differentiation of the murine promyelocyte line 32D, and activation of MAP kinase in CHO fibroblasts. We postulated that these results reflect some form of cross-regulation between PKC-alpha and -delta rather than their functional redundancy. In this report, we show that overexpression of PKC-alpha in Baf3 and 32D leads to an elevation of the endogenous PKC-delta mRNA and protein levels. The elevated steady-state PKC-delta mRNA level results from a combination of increased PKC-delta transcription and mRNA stability. Upregulation of PKC-delta mRNA by PKC-alpha occurs even after a selective depletion of the PKC-delta protein. In addition, phorbol ester-induced elevation of PKC-delta mRNA and protein levels can be prevented by the PKC inhibitor GF109203X, an indication of the requirement for PKC kinase activity. Inhibition of new protein synthesis by cycloheximide showed that upregulation of PKC-delta mRNA, as opposed to delayed downregulation of the PKC-delta protein, is primarily responsible for the accumulation of this isoform by PKC-alpha. In parental Baf3 and 32D cells and PKC-alpha overexpressers, PKC-alpha and PKC-delta are uniquely involved in cross-regulation, while PKC-epsilon, PKC-eta, and PKC-mu are not.
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Affiliation(s)
- L Y Romanova
- Laboratory of Genetics and Medicine Branch, National Cancer Institute, Bethesda, Maryland 20892, USA
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16
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Romanova LY, Deriagin GV, Mashkova TD, Tumeneva IG, Mushegian AR, Kisselev LL, Alexandrov IA. Evidence for selection in evolution of alpha satellite DNA: the central role of CENP-B/pJ alpha binding region. J Mol Biol 1996; 261:334-40. [PMID: 8780776 DOI: 10.1006/jmbi.1996.0466] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Conservation of DNA segments performing sequence-related functions is a landmark of selection and functional significance. Phylogenetic variability of alpha satellite and apparent absence of conserved regions calls its functional significance into question, even though sequence-specific alpha satellite-binding proteins pJ alpha and CENP-B have been discovered. Moreover, the function of pJ alpha is obscure and CENP-B binding satellite DNA, which is thought to participate in centromere formation, is found only in few species and not necessarily in all chromosomes. Analysis of alpha satellite evolution allows us to recognize the order in this variability. Here we report a new alpha satellite suprachromosomal family, which together with the four defined earlier, covers all known alpha satellite sequences. Although each family has its characteristic types of monomers, they all descend from two prototypes, A and B. We show that most differences between prototypes are concentrated in a short region (positions 35 to 51), which exists in two alternative states: it matches a binding site for pJ alpha in type A and the one for CENP-B in type B. Lower primates have only type A monomers whereas great apes have both A and B. The new family is formed by monomeric types almost identical to A and B prototypes, thus representing a living relic of alpha satellite. Analysis of these data shows that selection-driven evolution, rather than random fixation of mutations, formed the distinction between A and B types. To our knowledge, this is the first evidence for selection in any of the known satellite DNAs.
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Affiliation(s)
- L Y Romanova
- National Research Center of Mental Health, Moscow, Russia
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17
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Romanova LY, Alexandrov IA, Schwab G, Hilbert DM, Mushinski JF, Nordan RP. Mechanism of apoptosis suppression by phorbol ester in IL-6-starved murine plasmacytomas: role of PKC modulation and cell cycle. Biochemistry 1996; 35:9900-6. [PMID: 8703964 DOI: 10.1021/bi9525886] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We show here that the mode of cell death in IL-6-starved T1165 and T1198 plasmacytoma cell lines is apoptosis, and that it can be suppressed by phorbol ester (PMA) treatment in a protein kinase C (PKC)-mediated process that involves alpha and/or delta isozymes. PMA-induced PKC activation, but not the depletion that follows it, participates in the suppression of apoptosis. Extended PKC activation is necessary but not sufficient for the apoptosis suppression. In addition, the cells must be in a "competent" state, which appears not to be determined by PKC. We observed two points of "competence" during the time between withdrawal of IL-6 and the start of massive cell death: one, immediately after withdrawal, and another, just before onset of apoptosis, at the time corresponding to maximal accumulation of cells in a G0/G1 block imposed by IL-6 withdrawal. Treatment with PMA and other PKC activators resulted in a shift of the cell population to S phase, lifting the G0/G1 block. We propose a model in which cells are rescued in a certain stage of the G1 phase of cell cycle. Death suppression occurs when a transient PMA-induced PKC activation occurs when a significant number of cells are in this part of G1, allowing them to pass the restriction point safely without initiating the cell death program.
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Affiliation(s)
- L Y Romanova
- Laboratory of Genetics, National Cancer Institute, NIH, Bethesda, Maryland, USA
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18
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Mashkova TD, Akopian TA, Romanova LY, Mitkevich SP, Yurov YB, Kisselev LL, Alexandrov IA. Genomic organization, sequence and polymorphism of the human chromosome 4-specific alpha-satellite DNA. Gene 1994; 140:211-7. [PMID: 7908273 DOI: 10.1016/0378-1119(94)90546-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two alpha-satellite fragments specific for human chromosome 4 have been cloned and characterized. Under stringent annealing conditions, they hybridized in situ only to the pericentromeric region of chromosome 4, but under non-stringent conditions they hybridized to all chromosomes containing the sequences of alpha-satellite suprachromosomal family 2 (viz., chromosomes 2, 4, 8, 9, 13, 14, 15, 18, 20, 21 and 22). Southern blot analysis reveals the 3.2-kb higher-order repeated unit which exists in two forms: as a single MspI fragment or a combination of the 2.6-kb and 0.6-kb MspI fragments. The two chromosome-4-specific cloned sequences appear to be different parts of this repeated unit. Taken together they constitute about 60% of its length. The primary structure of the higher-order repeated unit is characterized by a dimeric periodicity of the D1-D2 type which is usual to suprachromosomal family 2. At least in one site this regularity is disrupted by monomer deletion leading to the D2-D2 monomeric order. The most likely mechanism of this monomer excision is homologous unequal crossing-over. These sequences may serve as both cytogenetic and restriction-fragment length polymorphism (RFLP) markers for the pericentromeric region of chromosome 4.
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Affiliation(s)
- T D Mashkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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19
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Alexandrov IA, Mashkova TD, Romanova LY, Yurov YB, Kisselev LL. Segment substitutions in alpha satellite DNA. Unusual structure of human chromosome 3-specific alpha satellite repeat unit. J Mol Biol 1993; 231:516-20. [PMID: 8510162 DOI: 10.1006/jmbi.1993.1302] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have sequenced the full-length copy of the alpha satellite higher-order repeated unit characteristic of human chromosome 3. Its internal structure, the regular alterations of J1 and J2 type monomers, is typical of the alphoid suprachromosomal family 1. This dimeric order is disrupted by the substitution of one J1 unit by an alien dimer which is not clearly related to any of the established monomeric types. We have also observed some other similar cases of segment substitutions in alpha satellite DNA. They probably represent a special type of molecular event which could be generated by gene conversion. Segment substitutions may be one of the important factors responsible for the extreme variability of localization patterns and actual sequences of alpha satellite DNA that should be taken into account in reconstructions of alpha satellite evolution.
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Affiliation(s)
- I A Alexandrov
- Laboratory of Cytogenetics, National Research Center of Mental Health, Moscow, Russia
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20
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Alexandrov IA, Medvedev LI, Mashkova TD, Kisselev LL, Romanova LY, Yurov YB. Definition of a new alpha satellite suprachromosomal family characterized by monomeric organization. Nucleic Acids Res 1993; 21:2209-15. [PMID: 8502563 PMCID: PMC309486 DOI: 10.1093/nar/21.9.2209] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
We have analyzed more than 500 alphoid monomers either sequenced in our laboratory or available in the literature. Most of them belonged to the well studied suprachromosomal families 1, 2 and 3 characterized by dimeric (1 and 2) and pentameric (3) ancestral periodicities. The sequences that did not belong to the previously known families were subjected to further analysis. About a half of them formed a relatively homogenous family. Its members were on average 80.5% identical and 89.5% homologous to the M1 consensus sequence derived from this group (39 monomers). In the genome they do not form any ancestral periodicities other than a monomeric one, and are found at least in chromosomes 13, 14, 15, 21, 22 and Y. The newly defined family was termed suprachromosomal family 4. Comparison of all 10 alphoid monomeric groups identified so far showed that the M1 sequence is closely related to the J1-D2-W4-W5 homology grouping. Notably the African Green Monkey alpha satellite, also characterized by monomeric construction, appears to be a member of the same group.
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Affiliation(s)
- I A Alexandrov
- National Research Center of Mental Health, Moscow, Russia
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21
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Alexandrov IA, Mashkova TD, Akopian TA, Medvedev LI, Kisselev LL, Mitkevich SP, Yurov YB. Chromosome-specific alpha satellites: two distinct families on human chromosome 18. Genomics 1991; 11:15-23. [PMID: 1765373 DOI: 10.1016/0888-7543(91)90097-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Two types of human chromosome 18-specific alpha satellite fragments have been cloned and sequenced. They represent closely related but distinct alphoid families formed by two different types of the higher-order repeated units (1360-bp EcoRI and 1700-bp HindIII fragments) that do not alternate in the genome. The individual repeats within each family are 99% identical and interfamily homology is about 78%. Sequence analysis shows that both repeats belong to alphoid suprachromosomal family 2, but their homology is not higher than that of family members located on different chromosomes. Therefore, the two repeats shared a common origin in the recent past, although they are not the direct offspring of one ancestral sequence. Our data indicate that these two 18-specific domains have appeared as a result of two separate amplification events. Despite the high degree of homology, they are not undergoing intrachromosomal homogenization, although some variation of this process might take place within each domain.
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Affiliation(s)
- I A Alexandrov
- All-Union Research Center of Mental Health, Moscow, USSR
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22
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Abstract
The chromosomal distribution of sequences homologous to 18 coned alpha satellite fragments was established by in situ hybridization. It appeared that all the cloned sequences were members of small repeated families located on single chromosome pairs. Among the sequences studied specific molecular markers for chromosomes 3, 4, 10, 11, 17, 18 and X were found. Comparison of the hybridization spectra obtained under non-stringent conditions and of restriction site periodicities in different chromosome-specific families allowed the identification of three "suprachromosomal" families, each located on a characteristic set of chromosomes. The three families together cover all the autosomes and the X chromosome. These data plus those reported previously allow part of the phylogenetic tree of chromosome-specific alpha satellite repeats to be drawn. Each suprachromosomal family has presumably originated from a distinct ancestral sequence and consists of certain types of monomers. Ancestral sequences have evolved into a number of chromosome-specific families by cycles of interchromosomal transfers and subsequent amplification events. The high homogeneity of chromosome-specific families may be a result of intrachromosomal homogenization of amplification units in chromosome-specific alpha satellite domains.
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Affiliation(s)
- I A Alexandrov
- All Union Research Center of Mental Health, Academy of Medical Sciences of USSR, Moscow
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23
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Yurov YB, Mitkevich SP, Alexandrov IA. Application of cloned satellite DNA sequences to molecular-cytogenetic analysis of constitutive heterochromatin heteromorphisms in man. Hum Genet 1987; 76:157-64. [PMID: 3475246 DOI: 10.1007/bf00284914] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The cloned alpha-satellite DNA sequences were used to evaluate the specificity and possible variability of repetitive DNA in constitutive heterochromatin of human chromosomes. Five probes with high specificity to individual chromosomes (chromosomes 3, 11, 17, 18, and X) were in situ hybridized to metaphase chromosomes of different individuals. The stable position of alpha-satellite DNA sequences in heterochromatic regions of particular chromosomes was found. Therefore, the chromosome-specific alpha-satellite DNA sequences may be used as molecular markers for heterochromatic regions of certain human chromosomes. The homologous chromosomes of many individuals were characterized by cytologically visible heteromorphisms of hybridization intensity with chromosome-specific alpha-satellite DNA sequences. A special analysis of hybridization between homologues with morphological differences provided the evidence for a high resolution power of the in situ hybridization technique for evaluation of chromosome heteromorphisms. The approaches for detection of heteromorphisms in cases without morphological differences between homologues are discussed. The results obtained indicate that constitutive heterochromatin of human chromosomes has a variable amount of alpha-satellite DNA sequences. In situ hybridization of cloned satellite DNA sequences may be used as a new general approach to analysis of chromosome heteromorphisms in man.
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MESH Headings
- Base Sequence
- Chromosome Mapping
- Chromosomes, Human, Pair 11
- Chromosomes, Human, Pair 17
- Chromosomes, Human, Pair 18
- Chromosomes, Human, Pair 3
- Cloning, Molecular
- DNA, Satellite/genetics
- Genetic Markers
- Heterochromatin/genetics
- Humans
- Karyotyping
- Nucleic Acid Hybridization
- Polymorphism, Genetic
- X Chromosome
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24
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Vorsanova SG, Yurov YB, Alexandrov IA, Demidova IA, Mitkevich SP, Tirskaia AF. 18p- syndrome: an unusual case and diagnosis by in situ hybridization with chromosome 18-specific alphoid DNA sequence. Hum Genet 1986; 72:185-7. [PMID: 3753696 DOI: 10.1007/bf00283945] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A patient with an atypical clinical picture of 18p- syndrome is described. By the in situ hybridization technique we localized the chromosome 18-specific cloned repetitive sequence to metaphase chromosomes of the patient. The predominant hybridization of the probe was found in pericentromeric regions of homologous chromosomes 18. The amount of pericentromeric DNA measured by in situ hybridization differed between homologous chromosomes; and the number of radioactive grains was statistically greater in the normal chromosome 18 than in the aberrant chromosome 18p-. The results indicate that this probe may be useful in clinical cytogenetics for identification of aberrant chromosomes, localization of breakpoints, and studies of C-band DNA polymorphism of chromosome 18.
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