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A classical revival: Human satellite DNAs enter the genomics era. Semin Cell Dev Biol 2022; 128:2-14. [PMID: 35487859 DOI: 10.1016/j.semcdb.2022.04.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022]
Abstract
The classical human satellite DNAs, also referred to as human satellites 1, 2 and 3 (HSat1, HSat2, HSat3, or collectively HSat1-3), occur on most human chromosomes as large, pericentromeric tandem repeat arrays, which together constitute roughly 3% of the human genome (100 megabases, on average). Even though HSat1-3 were among the first human DNA sequences to be isolated and characterized at the dawn of molecular biology, they have remained almost entirely missing from the human genome reference assembly for 20 years, hindering studies of their sequence, regulation, and potential structural roles in the nucleus. Recently, the Telomere-to-Telomere Consortium produced the first truly complete assembly of a human genome, paving the way for new studies of HSat1-3 with modern genomic tools. This review provides an account of the history and current understanding of HSat1-3, with a view towards future studies of their evolution and roles in health and disease.
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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: 167] [Impact Index Per Article: 83.5] [Reference Citation Analysis] [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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Hoyt SJ, Storer JM, Hartley GA, Grady PGS, Gershman A, de Lima LG, Limouse C, Halabian R, Wojenski L, Rodriguez M, Altemose N, Rhie A, Core LJ, Gerton JL, Makalowski W, Olson D, Rosen J, Smit AFA, Straight AF, Vollger MR, Wheeler TJ, Schatz MC, Eichler EE, Phillippy AM, Timp W, Miga KH, O’Neill RJ. From telomere to telomere: The transcriptional and epigenetic state of human repeat elements. Science 2022; 376:eabk3112. [PMID: 35357925 PMCID: PMC9301658 DOI: 10.1126/science.abk3112] [Citation(s) in RCA: 108] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mobile elements and repetitive genomic regions are sources of lineage-specific genomic innovation and uniquely fingerprint individual genomes. Comprehensive analyses of such repeat elements, including those found in more complex regions of the genome, require a complete, linear genome assembly. We present a de novo repeat discovery and annotation of the T2T-CHM13 human reference genome. We identified previously unknown satellite arrays, expanded the catalog of variants and families for repeats and mobile elements, characterized classes of complex composite repeats, and located retroelement transduction events. We detected nascent transcription and delineated CpG methylation profiles to define the structure of transcriptionally active retroelements in humans, including those in centromeres. These data expand our insight into the diversity, distribution, and evolution of repetitive regions that have shaped the human genome.
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Affiliation(s)
- Savannah J. Hoyt
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | | | - Gabrielle A. Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Patrick G. S. Grady
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | | | - Charles Limouse
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Reza Halabian
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Luke Wojenski
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Matias Rodriguez
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Nicolas Altemose
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Leighton J. Core
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
| | | | - Wojciech Makalowski
- Institute of Bioinformatics, Faculty of Medicine, University of Münster, Münster, Germany
| | - Daniel Olson
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | | | | | - Mitchell R. Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Travis J. Wheeler
- Department of Computer Science, University of Montana, Missoula, MT, USA
| | - Michael C. Schatz
- Department of Computer Science and 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, University of Washington, 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
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Karen H. Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, 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
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4
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Lopes M, Louzada S, Gama-Carvalho M, Chaves R. Genomic Tackling of Human Satellite DNA: Breaking Barriers through Time. Int J Mol Sci 2021; 22:4707. [PMID: 33946766 PMCID: PMC8125562 DOI: 10.3390/ijms22094707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 12/12/2022] Open
Abstract
(Peri)centromeric repetitive sequences and, more specifically, satellite DNA (satDNA) sequences, constitute a major human genomic component. SatDNA sequences can vary on a large number of features, including nucleotide composition, complexity, and abundance. Several satDNA families have been identified and characterized in the human genome through time, albeit at different speeds. Human satDNA families present a high degree of sub-variability, leading to the definition of various subfamilies with different organization and clustered localization. Evolution of satDNA analysis has enabled the progressive characterization of satDNA features. Despite recent advances in the sequencing of centromeric arrays, comprehensive genomic studies to assess their variability are still required to provide accurate and proportional representation of satDNA (peri)centromeric/acrocentric short arm sequences. Approaches combining multiple techniques have been successfully applied and seem to be the path to follow for generating integrated knowledge in the promising field of human satDNA biology.
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Affiliation(s)
- Mariana Lopes
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Sandra Louzada
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Margarida Gama-Carvalho
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
| | - Raquel Chaves
- Laboratory of Cytogenomics and Animal Genomics (CAG), Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal; (M.L.); (S.L.)
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal;
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5
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Giovannotti M, S'Khifa A, Nisi Cerioni P, Splendiani A, Slimani T, Fioravanti T, Olmo E, Caputo Barucchi V. Isolation and characterization of two satellite DNAs in Atlantolacerta andreanskyi (Werner, 1929) (Reptilia, Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:178-191. [PMID: 32061054 DOI: 10.1002/jez.b.22937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 11/29/2019] [Accepted: 01/30/2020] [Indexed: 11/07/2022]
Abstract
Two satellite DNAs (satDNAs) have been isolated and characterized from three populations of Atlantolacerta andreanskyi. One satDNA (AAN-TaqI) has been isolated here from the first time. It is characterized by a tendency to AT enrichment (AT = 54.2%) and monomer length ranging from 187 to 199 bp. FISH experiments showed that this element occurs in subterminal position on the short arms of all chromosomes of the complement. The analyses of genetic variability of AAN-TaqI showed that the concerted evolution is acting effectively on these repeats that form separate clusters consistent with the geographic origin in the phylogenetic tree, thus supporting the hypothesis that A. andreanskyi would be a species complex. In addition, in the population from Jbel Aoulime this satDNA is already differentiated into two subfamilies. The other satDNA belongs to the family of IMO-TaqI already isolated in other lacertids. Differently from AAN-TaqI, concerted evolution does not seem to act effectively on this element that is not differentiated between populations. These results confirm that IMO-TaqI (AT = 53.4%) is conserved in both chromosomal position and most of its sequence in the lacertids from which it has been characterized so far. Its remarkable evolutionary conservation for about 45 million years could indicate that this satDNA may have a functional role that future investigations could unveil. Once again, this study shows how satDNAs coexisting in the same genome may differ in their evolutionary pattern, even though the reasons underlying this phenomenon in the species here studied have still to be fully understood.
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Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Abderrahim S'Khifa
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Paola Nisi Cerioni
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Andrea Splendiani
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Tahar Slimani
- Laboratory Biodiversity and Ecosystem Dynamics, Faculty of Sciences Semlalia, Cadi Ayyad University, Boulevard Prince Moulay Abdellah, Marrakech, Morocco
| | - Tatiana Fioravanti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Ettore Olmo
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Vincenzo Caputo Barucchi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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6
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Ramos S, Rodríguez R, Castro O, Grether P, Molina B, Frias S. Presence of 15p Marker D15Z1 on the Short Arm of Acrocentric Chromosomes is Associated with Aneuploid Offspring in Mexican Couples. Int J Mol Sci 2019; 20:E5251. [PMID: 31652755 PMCID: PMC6862356 DOI: 10.3390/ijms20215251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/12/2023] Open
Abstract
Variation in the location of the 15p region D15Z1 is recognized as a polymorphism in several human populations. We used high-stringency Fluorescence In Situ Hybridization (FISH) to detect D15Z1 in a Mexican cohort. Here, we report the presence of extra D15Z1 sequences on the p-arm of acrocentric chromosomes other than 15 in two groups of Mexican couples, one with healthy offspring (n = 75) and the other with aneuploid offspring (n = 87), mainly trisomy 21. The additional D15Z1 polymorphism was significantly increased in individuals with aneuploid offspring (26.4%), in comparison to individuals with healthy offspring (14%). The most frequent acceptor chromosome of D15Z1 was chromosome 13p, followed by 14p, and finally, 21p. Our results show an overall frequency of 21.6% of this polymorphism in the Mexican population and suggest that its presence might be associated with the mis-segregation of other acrocentric chromosomes and aneuploid offspring. The high frequency of the polymorphism of the D15Z1 sequence on acrocentric chromosomes other than 15 suggests a sequence homogenization of the acrocentric p arms, related to the important function of the centromere and the nucleolar organization region, which flank satellite III DNA.
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Affiliation(s)
- Sandra Ramos
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, 04530 Mexico City, Mexico.
| | - Rebeca Rodríguez
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, 04530 Mexico City, Mexico.
| | - Oscar Castro
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, 04530 Mexico City, Mexico.
| | | | - Bertha Molina
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, 04530 Mexico City, Mexico.
| | - Sara Frias
- Laboratorio de Citogenética, Instituto Nacional de Pediatría, 04530 Mexico City, Mexico.
- Departamento de Medicina Genómica y Toxicología Ambiental, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de Mexico, 04510 Mexico City, Mexico.
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7
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Chiatante G, Giannuzzi G, Calabrese FM, Eichler EE, Ventura M. Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region. Mol Biol Evol 2017; 34:1669-1681. [PMID: 28333343 DOI: 10.1093/molbev/msx108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process.
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Affiliation(s)
- Giorgia Chiatante
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy.,Department of Biology, Anthropology Laboratories University of Florence, Florence, Italy
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA
| | - Mario Ventura
- Department of Biology, University of Bari "Aldo Moro", Bari, Italy
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8
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Maussion G, Cruceanu C, Rosenfeld JA, Bell SC, Jollant F, Szatkiewicz J, Collins RL, Hanscom C, Kolobova I, de Champfleur NM, Blumenthal I, Chiang C, Ota V, Hultman C, O'Dushlaine C, McCarroll S, Alda M, Jacquemont S, Ordulu Z, Marshall CR, Carter MT, Shaffer LG, Sklar P, Girirajan S, Morton CC, Gusella JF, Turecki G, Stavropoulos DJ, Sullivan PF, Scherer SW, Talkowski ME, Ernst C. Implication of LRRC4C and DPP6 in neurodevelopmental disorders. Am J Med Genet A 2016; 173:395-406. [PMID: 27759917 DOI: 10.1002/ajmg.a.38021] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/29/2016] [Indexed: 12/27/2022]
Abstract
We performed whole-genome sequencing on an individual from a family with variable psychiatric phenotypes that had a sensory processing disorder, apraxia, and autism. The proband harbored a maternally inherited balanced translocation (46,XY,t(11;14)(p12;p12)mat) that disrupted LRRC4C, a member of the highly specialized netrin G family of axon guidance molecules. The proband also inherited a paternally derived chromosomal inversion that disrupted DPP6, a potassium channel interacting protein. Copy Number (CN) analysis in 14,077 cases with neurodevelopmental disorders and 8,960 control subjects revealed that 60% of cases with exonic deletions in LRRC4C had a second clinically recognizable syndrome associated with variable clinical phenotypes, including 16p11.2, 1q44, and 2q33.1 CN syndromes, suggesting LRRC4C deletion variants may be modifiers of neurodevelopmental disorders. In vitro, functional assessments modeling patient deletions in LRRC4C suggest a negative regulatory role of these exons found in the untranslated region of LRRC4C, which has a single, terminal coding exon. These data suggest that the proband's autism may be due to the inheritance of disruptions in both DPP6 and LRRC4C, and may highlight the importance of the netrin G family and potassium channel interacting molecules in neurodevelopmental disorders. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gilles Maussion
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Cristiana Cruceanu
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington
| | - Scott C Bell
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Fabrice Jollant
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Nîmes Academic Hospital (CHU), Nîmes, France
| | - Jin Szatkiewicz
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Ryan L Collins
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Carrie Hanscom
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Ilaria Kolobova
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | | | - Ian Blumenthal
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - Colby Chiang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.,McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri
| | - Vanessa Ota
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | | | - Steve McCarroll
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Martin Alda
- Department of Psychiatry Halifax, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sebastien Jacquemont
- Department of Pediatrics, Sainte-Justine Hospital, University of Montreal, Montreal, Canada
| | - Zehra Ordulu
- Department of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Christian R Marshall
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Melissa T Carter
- Regional Genetics Program, The Children's Hospital of Eastern Ontario, Ottawa, Canada
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer, Inc., Spokane, Washington
| | - Pamela Sklar
- Departments of Neuroscience, Psychiatry and Genetics and Genome Sciences, Mount Sinai Hospital, New York, New York
| | - Santhosh Girirajan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania
| | - Cynthia C Morton
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Departments of Obstetrics, Gynecology, and Reproductive Biology and of Pathology, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts.,Manchester Academic Health Science Center, University of Manchester, Manchester, United Kingdom
| | - James F Gusella
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Genetics, Harvard Medical School, Boston, Massachusetts
| | - Gustavo Turecki
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
| | - Dimitri J Stavropoulos
- Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Patrick F Sullivan
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina
| | - Stephen W Scherer
- The Centre for Applied Genomics and Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Michael E Talkowski
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Department of Neurology, Harvard Medical School, Boston, Massachusetts
| | - Carl Ernst
- Department of Psychiatry, McGill Group for Suicide Studies, and Douglas Mental Health University Institute, Montreal, Canada.,Department of Human Genetics, McGill University, Montreal, Canada
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9
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Narrowing the localization of the region breakpoint in most frequent Robertsonian translocations. Chromosome Res 2014; 22:517-32. [PMID: 25179263 PMCID: PMC4257996 DOI: 10.1007/s10577-014-9439-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 06/27/2014] [Accepted: 08/04/2014] [Indexed: 11/23/2022]
Abstract
Despite that Robertsonian translocations (ROBs) are the most common chromosomal rearrangements in humans (1/1000 individuals), an exact breakpoint and the molecular mechanisms leading to their formation are still not well known. This is partly due to the fact that Human Genome Project did not provide any map or sequence for the acrocentric short arms. The main aim of our studies was to narrow the breakpoints in de novo arising and in familial cases of the most frequently occurring ROBs, using eight, previously not tested clones derived from 21p. Our results from PCR and FISH analysis showed that only the clones CR382285, CR382287, and a small fragment of CR382332 are retained in the examined ROBs. Moreover, interphase FISH on monochromosomal hybrids verified the orientation of studied clones in relation to centromeres of chromosomes 14 and 21. Given our results, we propose localization of the breakpoints in or nearby to clone CR382332. Summarizing, our results allowed to narrow the region where the breakpoints are localized and demonstrated that their position could be the same in all common ROBs.
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10
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Altemose N, Miga KH, Maggioni M, Willard HF. Genomic characterization of large heterochromatic gaps in the human genome assembly. PLoS Comput Biol 2014; 10:e1003628. [PMID: 24831296 PMCID: PMC4022460 DOI: 10.1371/journal.pcbi.1003628] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 03/26/2014] [Indexed: 01/24/2023] Open
Abstract
The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats, Human Satellites 2 and 3 (HSat2,3). The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms, and as a result, the sequence composition and potential biological functions of these regions remain largely unexplored. Furthermore, existing genomic tools designed to predict consensus-based descriptions of repeat families cannot be readily applied to complex satellite repeats such as HSat2,3, which lack a consistent repeat unit reference sequence. Here we present an alignment-free method to characterize complex satellites using whole-genome shotgun read datasets. Utilizing this approach, we classify HSat2,3 sequences into fourteen subfamilies and predict their chromosomal distributions, resulting in a comprehensive satellite reference database to further enable genomic studies of heterochromatic regions. We also identify 1.3 Mb of non-repetitive sequence interspersed with HSat2,3 across 17 unmapped assembly scaffolds, including eight annotated gene predictions. Finally, we apply our satellite reference database to high-throughput sequence data from 396 males to estimate array size variation of the predominant HSat3 array on the Y chromosome, confirming that satellite array sizes can vary between individuals over an order of magnitude (7 to 98 Mb) and further demonstrating that array sizes are distributed differently within distinct Y haplogroups. In summary, we present a novel framework for generating initial reference databases for unassembled genomic regions enriched with complex satellite DNA, and we further demonstrate the utility of these reference databases for studying patterns of sequence variation within human populations. At least 5–10% of the human genome remains unassembled, unmapped, and poorly characterized. The reference assembly annotates these missing regions as multi-megabase heterochromatic gaps, found primarily near centromeres and on the short arms of the acrocentric chromosomes. This missing fraction of the genome consists predominantly of long arrays of near-identical tandem repeats called satellite DNA. Due to the repetitive nature of satellite DNA, sequence assembly algorithms cannot uniquely align overlapping sequence reads, and thus satellite-rich domains have been omitted from the reference assembly and from most genome-wide studies of variation and function. Existing methods for analyzing some satellite DNAs cannot be easily extended to a large portion of satellites whose repeat structures are complex and largely uncharacterized, such as Human Satellites 2 and 3 (HSat2,3). Here we characterize HSat2,3 using a novel approach that does not depend on having a well-defined repeat structure. By classifying genome-wide HSat2,3 sequences into subfamilies and localizing them to chromosomes, we have generated an initial HSat2,3 genomic reference, which serves as a critical foundation for future studies of variation and function in these regions. This approach should be generally applicable to other classes of satellite DNA, in both the human genome and other complex genomes.
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Affiliation(s)
- Nicolas Altemose
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
| | - Karen H. Miga
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
- * E-mail:
| | - Mauro Maggioni
- Department of Mathematics, Duke University, Durham, North Carolina, United States of America
| | - Huntington F. Willard
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina, United States of America
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11
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Giovannotti M, Rojo V, Nisi Cerioni P, González-Tizón A, Martínez-Lage A, Splendiani A, Naveira H, Ruggeri P, Arribas Ó, Olmo E, Caputo Barucchi V. Isolation and characterization of two satellite DNAs in some Iberian rock lizards (Squamata, Lacertidae). JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2013; 322:13-26. [PMID: 24014193 DOI: 10.1002/jez.b.22530] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 07/29/2013] [Accepted: 07/31/2013] [Indexed: 01/15/2023]
Abstract
Satellite DNAs represent a large portion of all high eukaryotic genomes. They consist of numerous very similar repeated sequences, tandemly arranged in large clusters up to 100 million base pairs in length, usually located in the heterochromatic parts of chromosomes. The biological significance of satDNAs is still under discussion, but most of their proposed functions are related to heterochromatin and/or centromere formation and function. Because information about the structure of reptilian satDNA is far from exhaustive, we present a molecular and cytogenetic characterization of two satDNA families in four lacertid species. Two families of tandemly repeated DNAs, namely TaqI and HindIII satDNAs, have been cloned and sequenced from four species belonging to the genus Iberolacerta. These satDNAs are characterized by a monomer length of 171-188 and 170-172 bp, and by an AT content of 60.5% and 58.1%, respectively. FISH experiments with TaqI satDNA probe produced bright signals in pericentromeric regions of a subset of chromosomes whereas all the centromeres were marked by HindIII probe. The results obtained in this study suggest that chromosome location and abundance of satDNAs influence the evolution of these elements, with centromeric families evolving tenfold faster than interstitial/pericentromeric ones. Such different rates render different satellites useful for phylogenetic investigation at different taxonomic ranks.
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Affiliation(s)
- Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona, Italy
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12
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Ventura M, Catacchio CR, Sajjadian S, Vives L, Sudmant PH, Marques-Bonet T, Graves TA, Wilson RK, Eichler EE. The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2. Genome Res 2012; 22:1036-49. [PMID: 22419167 PMCID: PMC3371704 DOI: 10.1101/gr.136556.111] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chimpanzee and gorilla chromosomes differ from human chromosomes by the presence of large blocks of subterminal heterochromatin thought to be composed primarily of arrays of tandem satellite sequence. We explore their sequence composition and organization and show a complex organization composed of specific sets of segmental duplications that have hyperexpanded in concert with the formation of subterminal satellites. These regions are highly copy number polymorphic between and within species, and copy number differences involving hundreds of copies can be accurately estimated by assaying read-depth of next-generation sequencing data sets. Phylogenetic and comparative genomic analyses suggest that the structures have arisen largely independently in the two lineages with the exception of a few seed sequences present in the common ancestor of humans and African apes. We propose a model where an ancestral human-chimpanzee pericentric inversion and the ancestral chromosome 2 fusion both predisposed and protected the chimpanzee and human genomes, respectively, to the formation of subtelomeric heterochromatin. Our findings highlight the complex interplay between duplicated sequences and chromosomal rearrangements that rapidly alter the cytogenetic landscape in a short period of evolutionary time.
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Affiliation(s)
- Mario Ventura
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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13
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Warburton PE, Hasson D, Guillem F, Lescale C, Jin X, Abrusan G. Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics 2008; 9:533. [PMID: 18992157 PMCID: PMC2588610 DOI: 10.1186/1471-2164-9-533] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2008] [Accepted: 11/07/2008] [Indexed: 01/26/2023] Open
Abstract
Background Tandemly Repeated DNA represents a large portion of the human genome, and accounts for a significant amount of copy number variation. Here we present a genome wide analysis of the largest tandem repeats found in the human genome sequence. Results Using Tandem Repeats Finder (TRF), tandem repeat arrays greater than 10 kb in total size were identified, and classified into simple sequence e.g. GAATG, classical satellites e.g. alpha satellite DNA, and locus specific VNTR arrays. Analysis of these large sequenced regions revealed that several "simple sequence" arrays actually showed complex domain and/or higher order repeat organization. Using additional methods, we further identified a total of 96 additional arrays with tandem repeat units greater than 2 kb (the detection limit of TRF), 53 of which contained genes or repeated exons. The overall size of an array of tandem 12 kb repeats which spanned a gap on chromosome 8 was found to be 600 kb to 1.7 Mbp in size, representing one of the largest non-centromeric arrays characterized. Several novel megasatellite tandem DNA families were observed that are characterized by repeating patterns of interspersed transposable elements that have expanded presumably by unequal crossing over. One of these families is found on 11 different chromosomes in >25 arrays, and represents one of the largest most widespread megasatellite DNA families. Conclusion This study represents the most comprehensive genome wide analysis of large tandem repeats in the human genome, and will serve as an important resource towards understanding the organization and copy number variation of these complex DNA families.
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Affiliation(s)
- Peter E Warburton
- Deptartment of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA.
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14
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Gene dosage change of TPTE and BAGE2 and breakpoint analysis in Robertsonian Down syndrome. J Hum Genet 2007; 53:136-143. [DOI: 10.1007/s10038-007-0229-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Accepted: 11/13/2007] [Indexed: 10/22/2022]
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15
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Jarmuz M, Glotzbach CD, Bailey KA, Bandyopadhyay R, Shaffer LG. The Evolution of satellite III DNA subfamilies among primates. Am J Hum Genet 2007; 80:495-501. [PMID: 17273970 PMCID: PMC1821104 DOI: 10.1086/512132] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Accepted: 12/16/2006] [Indexed: 01/30/2023] Open
Abstract
We demonstrate that satellite III (SatIII) DNA subfamilies cloned from human acrocentric chromosomes arose in the Hominoidea superfamily. Two groups, distinguished by sequence composition, evolved nonconcurrently, with group 2 evolving 16-23 million years ago (MYA) and the more recent group 1 sequences emerging approximately 4.5 MYA. We also show the relative order of emergence of each group 2 subfamily in the various primate species. Our results show that each SatIII subfamily is an independent evolutionary unit, that the rate of evolution is not uniform between species, and that the evolution within a species is not uniform between chromosomes.
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Affiliation(s)
- Malgorzata Jarmuz
- Health Research and Education Center, Washington State University, Spokane 99210, USA
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16
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Babcock M, Yatsenko S, Stankiewicz P, Lupski JR, Morrow BE. AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. Genome Res 2007; 17:451-60. [PMID: 17284672 PMCID: PMC1832092 DOI: 10.1101/gr.5651507] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Low copy repeats (LCRs; segmental duplications) constitute approximately 5% of the sequenced human genome. Nonallelic homologous recombination events between LCRs during meiosis can lead to chromosomal rearrangements responsible for many genomic disorders. The 22q11.2 region is susceptible to recurrent and nonrecurrent deletions, duplications as well as translocations that are mediated by LCRs termed LCR22s. One particular DNA structural element, a palindromic AT-rich repeat (PATRR) present within LCR22-3a, is responsible for translocations. Similar AT-rich repeats are present within the two largest LCR22s, LCR22-2 and LCR22-4. We provide direct sequence evidence that the AT-rich repeats have altered LCR22 organization during primate evolution. The AT-rich repeats are surrounded by a subtype of human satellite I (HSAT I), and an AluSc element, forming a 2.4-kb tripartite structure. Besides 22q11.2, FISH and PCR mapping localized the tripartite repeat within heterochromatic, unsequenced regions of the genome, including the pericentromeric regions of the acrocentric chromosomes and the heterochromatic portion of Yq12 in humans. The repeat is also present on autosomes but not on chromosome Y in other hominoid species, suggesting that it has duplicated on Yq12 after speciation of humans from its common ancestor. This demonstrates that AT-rich repeats have shaped or altered the structure of the genome during evolution.
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Affiliation(s)
- Melanie Babcock
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Svetlana Yatsenko
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pawel Stankiewicz
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bernice E. Morrow
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding author.E-mail ; fax (718) 430-8778
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17
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Valgardsdottir R, Chiodi I, Giordano M, Cobianchi F, Riva S, Biamonti G. Structural and functional characterization of noncoding repetitive RNAs transcribed in stressed human cells. Mol Biol Cell 2005; 16:2597-604. [PMID: 15788562 PMCID: PMC1142408 DOI: 10.1091/mbc.e04-12-1078] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Thermal and chemical stresses induce the formation in human cells of novel and transient nuclear structures called nuclear stress bodies (nSBs). These contain heat shock factor 1 (HSF-1) and a specific subset of pre-mRNA processing factors. Nuclear stress bodies are assembled on specific pericentromeric heterochromatic domains containing satellite III (SatIII) DNA. In response to stress, these domains change their epigenetic status from heterochromatin to euchromatin and are transcribed in poly-adenylated RNAs that remain associated with nSBs. In this article, we describe the cloning, sequencing, and functional characterization of these transcripts. They are composed of SatIII repeats and originate from the transcription of multiple sites within the SatIII arrays. Interestingly, the level of SatIII RNAs can be down-regulated both by antisense oligonucleotides and small interfering RNAs (siRNA). Knockdown of SatIII RNA by siRNAs requires the activity of Argonaute 2, a component of the RNA-induced silencing complex. Down-regulation of satellite III RNAs significantly affects the recruitment of RNA processing factors to nSBs without altering the association of HSF-1 with these structures nor the presence of acetylated histones within nSBs. Thus, satellite III RNAs have a major role in the formation of nSBs.
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MESH Headings
- Animals
- Argonaute Proteins
- Cell Fusion
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus Structures/metabolism
- Coculture Techniques
- DNA, Satellite/chemistry
- DNA, Satellite/metabolism
- DNA-Binding Proteins
- Dose-Response Relationship, Drug
- Down-Regulation
- Euchromatin/genetics
- Euchromatin/metabolism
- Eukaryotic Initiation Factor-2
- HeLa Cells
- Heat Shock Transcription Factors
- Heat-Shock Response
- Heterochromatin/genetics
- Heterochromatin/metabolism
- Humans
- Mice
- NIH 3T3 Cells
- Oligonucleotides, Antisense/pharmacology
- Peptide Initiation Factors/metabolism
- RNA, Small Interfering/pharmacology
- RNA, Untranslated/chemistry
- RNA, Untranslated/genetics
- RNA, Untranslated/metabolism
- RNA-Induced Silencing Complex
- Sequence Analysis, RNA
- Stress, Physiological/genetics
- Stress, Physiological/metabolism
- Transcription Factors
- Transcription, Genetic
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Affiliation(s)
- Rut Valgardsdottir
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, 27100 Pavia, Italy
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18
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Cardone MF, Ballarati L, Ventura M, Rocchi M, Marozzi A, Ginelli E, Meneveri R. Evolution of beta satellite DNA sequences: evidence for duplication-mediated repeat amplification and spreading. Mol Biol Evol 2004; 21:1792-9. [PMID: 15201396 DOI: 10.1093/molbev/msh190] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
In this article, we report studies on the evolutionary history of beta satellite repeats (BSR) in primates. In the orangutan genome, the bulk of BSR sequences was found organized as very short stretches of approximately 100 to 170 bp, embedded in a 60-kb to 80-kb duplicated DNA segment. The estimated copy number of the duplicon that carries BSR sequences ranges from 70 to 100 per orangutan haploid genome. In both macaque and gibbon, the duplicon mapped to a single chromosomal region at the boundary of the rDNA on the marker chromosome (chromosome 13 and 12, respectively). However, only in the gibbon, the duplicon comprised 100 bp of beta satellite. Thus, the ancestral copy of the duplicon appeared in Old World monkeys ( approximately 25 to approximately 35 MYA), whereas the prototype of beta satellite repeats took place in a gibbon ancestor, after apes/Old World monkeys divergence ( approximately 25 MYA). Subsequently, a burst in spreading of the duplicon that carries the beta satellite was observed in the orangutan, after lesser apes divergence from the great apes-humans lineage ( approximately 18 MYA). The analysis of the orangutan genome also indicated the existence of two variants of the duplication that differ for the length (100 or 170 bp) of beta satellite repeats. The latter organization was probably generated by nonhomologous recombination between two 100-bp repeated regions, and it likely led to the duplication of the single Sau3A site present in the 100-bp variant, which generated the prototype of Sau3A 68-bp beta satellite tandem organization. The two variants of the duplication, although with a different ratios, characterize the hominoid genomes from the orangutan to humans, preferentially involving acrocentric chromosomes. At variance to alpha satellite, which appeared before the divergence of New World and Old World monkeys, the beta satellite evolutionary history began in apes ancestor, where we have first documented a low-copy, nonduplicated BSR sequence. The first step of BSR amplification and spreading occurred, most likely, because the BSR was part of a large duplicon, which underwent a burst dispersal in great apes' ancestor after the lesser apes' branching. Then, after orangutan divergence, BSR acquired the clustered structural organization typical of satellite DNA.
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Affiliation(s)
- M F Cardone
- Dipartimento di Anatomia Patologica e Genetica, Sezione di Genetica, Bari, Italy
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19
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Cheng EY, Naluai-Cecchini T. FISHing for acrocentric associations between chromosomes 14 and 21 in human oogenesis. Am J Obstet Gynecol 2004; 190:1781-5; discussion 1785-7. [PMID: 15284799 DOI: 10.1016/j.ajog.2004.02.062] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
OBJECTIVE The purpose of this study was to search for cytologic evidence of robertsonian translocation formation that involves chromosomes 14q and 21q in human oogenesis with the use of dual color fluorescent in situ hybridization with whole chromosome paints. STUDY DESIGN The oocytes from a chromosomally normal fetus at 23.5 weeks of gestation underwent cohybridization with chromosome specific DNA libraries from chromosomes 14 and 21. The nuclei were scored for the proportion of meiosis I prophase substages and for hybridization efficiency and were evaluated for the presence of hybridization signals that were suggestive of heterologous associations between chromosomes 14q and 21q in zygotene, pachytene, and diplotene. RESULTS A total of 1769 meiotic nuclei were analyzed. Of 272 informative nuclei at zygotene, pachytene, and diplotene, 1 nucleus at pachytene demonstrated hybridization signals for chromosomes 14 and 21 that could be consistent with a robertsonian translocation. CONCLUSION A heterologous association between chromosomes 14q and 21q that possibly represent robertsonian translocation formation was observed cytologically with the use of fluorescent in situ hybridization.
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Affiliation(s)
- Edith Y Cheng
- Departments of Obstetrics and Gynecology and Medicine, University of Washington, Seattle, 98195-6460, USA.
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20
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Sucgang R, Chen G, Liu W, Lindsay R, Lu J, Muzny D, Shaulsky G, Loomis W, Gibbs R, Kuspa A. Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium. Nucleic Acids Res 2003; 31:2361-8. [PMID: 12711681 PMCID: PMC154234 DOI: 10.1093/nar/gkg348] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are encoded by multicopy families of identical genes. In Dictyostelium and other protists, the rDNA is carried on extrachromosomal palindromic elements that comprise up to 20% of the nuclear DNA. We present the sequence of the 88 kb Dictyostelium rDNA element, noting that the rRNA genes are likely to be the only transcribed regions. By interrogating a library of ordered YAC clones, we provide evidence for a chromosomal copy of the rDNA on chromosome 4. This locus may provide master copies for the stable transmission of the extrachromosomal elements. The extrachromosomal elements were also found to form chromosome-sized clusters of DNA within nuclei of nocodazole-treated cells arrested in mitosis. These clusters resemble true chromosomes and may allow the efficient segregation of the rDNA during mitosis. These rDNA clusters may also explain the cytological observations of a seventh chromosome in this organism.
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Affiliation(s)
- Richard Sucgang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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21
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Berend SA, Page SL, Atkinson W, McCaskill C, Lamb NE, Sherman SL, Shaffer LG. Obligate short-arm exchange in de novo Robertsonian translocation formation influences placement of crossovers in chromosome 21 nondisjunction. Am J Hum Genet 2003; 72:488-95. [PMID: 12506337 PMCID: PMC379241 DOI: 10.1086/367547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2002] [Accepted: 11/18/2002] [Indexed: 11/03/2022] Open
Abstract
Robertsonian translocations (ROBs) involving chromosome 21 are found in approximately 5% of patients with Down syndrome (DS). The most common nonhomologous ROB in DS is rob(14q21q). Aberrant recombination is associated with nondisjunction (NDJ) leading to trisomy 21. Haplotype analysis of 23 patients with DS and de novo rob(14q21q) showed that all translocations and all nondisjoined chromosomes 21 were maternally derived. Meiosis II NDJ occurred in 21 of 23 families. For these, a ROB DS chromosome 21 genetic map was constructed and compared to a normal female map and a published trisomy 21 map derived from meiosis II NDJ. The location of exchanges differed significantly from both maps, with a significant shift to a more distal interval in the ROB DS map. The shift may perturb segregation, leading to the meiosis II NDJ in this study, and is further evidence for crossover interference. More importantly, because the event in the short arms that forms the de novo ROB influences the placement of chiasmata in the long arm, it is most likely that the translocation formation occurs through a recombination pathway in meiosis. Additionally, we have demonstrated that events that occur in meiosis I can influence events, such as chromatid segregation in meiosis II, many decades later.
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MESH Headings
- Chromosome Aberrations
- Chromosomes, Human, Pair 14
- Chromosomes, Human, Pair 21
- Crossing Over, Genetic
- Down Syndrome/genetics
- Female
- Genetic Markers
- Genome, Human
- Haplotypes
- Humans
- Male
- Meiosis
- Microsatellite Repeats
- Models, Genetic
- Nondisjunction, Genetic
- Pedigree
- Polymorphism, Genetic
- Recombination, Genetic
- Translocation, Genetic
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Affiliation(s)
- Sue Ann Berend
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - Scott L. Page
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - William Atkinson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - Christopher McCaskill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - Neil E. Lamb
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - Stephanie L. Sherman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
| | - Lisa G. Shaffer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Stowers Institute for Medical Research, Kansas City, MO; Department of Genetics, Emory University, Atlanta; and Genzyme Genetics, Santa Fe
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22
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Bandyopadhyay R, Heller A, Knox-DuBois C, McCaskill C, Berend SA, Page SL, Shaffer LG. Parental origin and timing of de novo Robertsonian translocation formation. Am J Hum Genet 2002; 71:1456-62. [PMID: 12424707 PMCID: PMC378592 DOI: 10.1086/344662] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2002] [Accepted: 09/05/2002] [Indexed: 11/03/2022] Open
Abstract
Robertsonian translocations (ROBs) are the most common chromosomal rearrangements in humans. ROBs are whole-arm rearrangements between the acrocentric chromosomes 13-15, 21, and 22. ROBs can be classified into two groups depending on their frequency of occurrence, common (rob(13q14q) and rob(14q21q)), and rare (all remaining possible nonhomologous combinations). Herein, we have studied 29 case subjects of common and rare de novo ROBs to determine their parental origins and timing of formation. We compared these case subjects to 35 published case subjects of common ROBs and found that most common ROBs apparently have the same breakpoints and arise mainly during oogenesis (50/54). These probably form through a common mechanism and have been termed "class 1." Collectively, rare ROBs also occur mostly during oogenesis (7/10) but probably arise through a more "random" mechanism or a variety of mechanisms and have been termed "class 2." Thus, we demonstrate that although both classes of ROBs occur predominantly during meiosis, the common, class 1 ROBs occur primarily during oogenesis and likely form through a mechanism distinct from that forming class 2 ROBs.
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Affiliation(s)
- Ruma Bandyopadhyay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Anita Heller
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Cami Knox-DuBois
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Christopher McCaskill
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Sue Ann Berend
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Scott L. Page
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
| | - Lisa G. Shaffer
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston; Institute for Human Genetics and Anthropology, Jena, Germany; Genzyme Genetics, Santa Fe; and Stowers Institute for Medical Research, Kansas City, MO
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23
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Bandyopadhyay R, Berend SA, Page SL, Choo KH, Shaffer LG. Satellite III sequences on 14p and their relevance to Robertsonian translocation formation. Chromosome Res 2001; 9:235-42. [PMID: 11330398 DOI: 10.1023/a:1016652621226] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Robertsonian translocations (ROBs) are the most common rearrangements in humans, contributing significantly to genetic imbalance, fetal wastage, mental retardation and birth defects. Rob(14q21q) and rob(13q14q), which are formed predominantly during female meiosis, comprise the majority (approximately 85%) of all ROBs. Previous studies have shown that the breakpoints are consistently located within specific regions of the proximal short arms of chromosomes 13, 14, and 21. The high prevalence of these translocations, the consistent breakpoints found, and the fact that roughly 50% of cases occur sporadically suggest that the sequences at or near the breakpoints confer susceptibility to chromosome rearrangement and that the rearrangements occur through a specific mechanism. To investigate this hypothesis, we developed hamster-human somatic cell hybrids derived from de novo rob(14q21q) patients that contained the translocated chromosome segregated from the other acrocentric chromosomes. We determined the physical order of five satellite III subfamilies on 14p, and investigated their involvement in formation of these de novo translocations.
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Affiliation(s)
- R Bandyopadhyay
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
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