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Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol 2023; 41:1474-1482. [PMID: 36797493 PMCID: PMC10427740 DOI: 10.1038/s41587-023-01662-6] [Citation(s) in RCA: 90] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 01/03/2023] [Indexed: 02/18/2023]
Abstract
The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio high-fidelity reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph by integrating ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.
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Affiliation(s)
- Mikko Rautiainen
- 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, UK
| | - Brian P Walenz
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - David Porubsky
- 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
| | - 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.
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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2
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Logsdon GA, Eichler EE. The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA. Genes (Basel) 2022; 14:92. [PMID: 36672831 PMCID: PMC9859433 DOI: 10.3390/genes14010092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 12/22/2022] [Accepted: 12/24/2022] [Indexed: 12/31/2022] Open
Abstract
The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our understanding of the genetic architecture and epigenetic properties of human centromeric DNA have advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex, saltatory mutational changes organized around distinct evolutionary layers. Pockets of regional hypomethylation within higher-order α-satellite DNA, termed centromere dip regions, appear to define the site of kinetochore attachment in all human chromosomes, although such epigenetic features can vary even within the same chromosome. Sequence resolution of satellite DNA is providing new insights into centromeric function with potential implications for improving our understanding of human biology and health.
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Affiliation(s)
- Glennis A. Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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3
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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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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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Ahmad SF, Singchat W, Jehangir M, Suntronpong A, Panthum T, Malaivijitnond S, Srikulnath K. Dark Matter of Primate Genomes: Satellite DNA Repeats and Their Evolutionary Dynamics. Cells 2020; 9:E2714. [PMID: 33352976 PMCID: PMC7767330 DOI: 10.3390/cells9122714] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
A substantial portion of the primate genome is composed of non-coding regions, so-called "dark matter", which includes an abundance of tandemly repeated sequences called satellite DNA. Collectively known as the satellitome, this genomic component offers exciting evolutionary insights into aspects of primate genome biology that raise new questions and challenge existing paradigms. A complete human reference genome was recently reported with telomere-to-telomere human X chromosome assembly that resolved hundreds of dark regions, encompassing a 3.1 Mb centromeric satellite array that had not been identified previously. With the recent exponential increase in the availability of primate genomes, and the development of modern genomic and bioinformatics tools, extensive growth in our knowledge concerning the structure, function, and evolution of satellite elements is expected. The current state of knowledge on this topic is summarized, highlighting various types of primate-specific satellite repeats to compare their proportions across diverse lineages. Inter- and intraspecific variation of satellite repeats in the primate genome are reviewed. The functional significance of these sequences is discussed by describing how the transcriptional activity of satellite repeats can affect gene expression during different cellular processes. Sex-linked satellites are outlined, together with their respective genomic organization. Mechanisms are proposed whereby satellite repeats might have emerged as novel sequences during different evolutionary phases. Finally, the main challenges that hinder the detection of satellite DNA are outlined and an overview of the latest methodologies to address technological limitations is presented.
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Affiliation(s)
- Syed Farhan Ahmad
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Maryam Jehangir
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Department of Structural and Functional Biology, Institute of Bioscience at Botucatu, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Thitipong Panthum
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
| | - Suchinda Malaivijitnond
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (S.F.A.); (W.S.); (M.J.); (A.S.); (T.P.)
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, Bangkok 10900, Thailand
- National Primate Research Center of Thailand, Chulalongkorn University, Saraburi 18110, Thailand;
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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6
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Bzikadze AV, Pevzner PA. Automated assembly of centromeres from ultra-long error-prone reads. Nat Biotechnol 2020; 38:1309-1316. [PMID: 32665660 PMCID: PMC10718184 DOI: 10.1038/s41587-020-0582-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 05/29/2020] [Indexed: 12/12/2022]
Abstract
Centromeric variation has been linked to cancer and infertility, but centromere sequences contain multiple tandem repeats and can only be assembled manually from long error-prone reads. Here we describe the centroFlye algorithm for centromere assembly using long error-prone reads, and apply it to assemble human centromeres on chromosomes 6 and X. Our analyses reveal putative breakpoints in the manual reconstruction of the human X centromere, demonstrate that human X chromosome is partitioned into repeat subfamilies and provide initial insights into centromere evolution. We anticipate that centroFlye could be applied to automatically close remaining multimegabase gaps in the reference human genome.
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Affiliation(s)
- Andrey V Bzikadze
- Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
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7
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Balzano E, Giunta S. Centromeres under Pressure: Evolutionary Innovation in Conflict with Conserved Function. Genes (Basel) 2020; 11:E912. [PMID: 32784998 PMCID: PMC7463522 DOI: 10.3390/genes11080912] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/22/2022] Open
Abstract
Centromeres are essential genetic elements that enable spindle microtubule attachment for chromosome segregation during mitosis and meiosis. While this function is preserved across species, centromeres display an array of dynamic features, including: (1) rapidly evolving DNA; (2) wide evolutionary diversity in size, shape and organization; (3) evidence of mutational processes to generate homogenized repetitive arrays that characterize centromeres in several species; (4) tolerance to changes in position, as in the case of neocentromeres; and (5) intrinsic fragility derived by sequence composition and secondary DNA structures. Centromere drive underlies rapid centromere DNA evolution due to the "selfish" pursuit to bias meiotic transmission and promote the propagation of stronger centromeres. Yet, the origins of other dynamic features of centromeres remain unclear. Here, we review our current understanding of centromere evolution and plasticity. We also detail the mutagenic processes proposed to shape the divergent genetic nature of centromeres. Changes to centromeres are not simply evolutionary relics, but ongoing shifts that on one side promote centromere flexibility, but on the other can undermine centromere integrity and function with potential pathological implications such as genome instability.
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Affiliation(s)
- Elisa Balzano
- Dipartimento di Biologia e Biotecnologie “Charles Darwin”, Sapienza Università di Roma, 00185 Roma, Italy;
| | - Simona Giunta
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
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8
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Miga KH. Centromere studies in the era of 'telomere-to-telomere' genomics. Exp Cell Res 2020; 394:112127. [PMID: 32504677 DOI: 10.1016/j.yexcr.2020.112127] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 05/23/2020] [Accepted: 05/30/2020] [Indexed: 12/17/2022]
Abstract
We are entering into an exciting era of genomics where truly complete, high-quality assemblies of human chromosomes are available end-to-end, or from 'telomere-to-telomere' (T2T). This technological advance offers a new opportunity to include endogenous human centromeric regions in high-resolution, sequence-based studies. These emerging reference maps are expected to reveal a new functional landscape in the human genome, where centromere proteins, transcriptional regulation, and spatial organization can be examined with base-level resolution across different stages of development and disease. Such studies will depend on innovative assembly methods of extremely long tandem repeats (ETRs), or satellite DNAs, paired with the development of new, orthogonal validation methods to ensure accuracy and completeness. This review reflects the progress in centromere genomics, credited by recent advancements in long-read sequencing and assembly methods. In doing so, I will discuss the challenges that remain and the promise for a new period of scientific discovery for satellite DNA biology and centromere function.
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Affiliation(s)
- Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, CA, 95064, USA.
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9
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Vondrak T, Ávila Robledillo L, Novák P, Koblížková A, Neumann P, Macas J. Characterization of repeat arrays in ultra-long nanopore reads reveals frequent origin of satellite DNA from retrotransposon-derived tandem repeats. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 101:484-500. [PMID: 31559657 PMCID: PMC7004042 DOI: 10.1111/tpj.14546] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/09/2019] [Accepted: 09/12/2019] [Indexed: 05/21/2023]
Abstract
Amplification of monomer sequences into long contiguous arrays is the main feature distinguishing satellite DNA from other tandem repeats, yet it is also the main obstacle in its investigation because these arrays are in principle difficult to assemble. Here we explore an alternative, assembly-free approach that utilizes ultra-long Oxford Nanopore reads to infer the length distribution of satellite repeat arrays, their association with other repeats and the prevailing sequence periodicities. Using the satellite DNA-rich legume plant Lathyrus sativus as a model, we demonstrated this approach by analyzing 11 major satellite repeats using a set of nanopore reads ranging from 30 to over 200 kb in length and representing 0.73× genome coverage. We found surprising differences between the analyzed repeats because only two of them were predominantly organized in long arrays typical for satellite DNA. The remaining nine satellites were found to be derived from short tandem arrays located within LTR-retrotransposons that occasionally expanded in length. While the corresponding LTR-retrotransposons were dispersed across the genome, this array expansion occurred mainly in the primary constrictions of the L. sativus chromosomes, which suggests that these genome regions are favourable for satellite DNA accumulation.
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Affiliation(s)
- Tihana Vondrak
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Laura Ávila Robledillo
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
- Faculty of ScienceUniversity of South BohemiaČeské BudějoviceCzech Republic
| | - Petr Novák
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Andrea Koblížková
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Pavel Neumann
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
| | - Jiří Macas
- Biology CentreCzech Academy of SciencesBranišovská 31České BudějoviceCZ‐37005Czech Republic
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10
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Centromere Repeats: Hidden Gems of the Genome. Genes (Basel) 2019; 10:genes10030223. [PMID: 30884847 PMCID: PMC6471113 DOI: 10.3390/genes10030223] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 03/07/2019] [Accepted: 03/11/2019] [Indexed: 01/08/2023] Open
Abstract
Satellite DNAs are now regarded as powerful and active contributors to genomic and chromosomal evolution. Paired with mobile transposable elements, these repetitive sequences provide a dynamic mechanism through which novel karyotypic modifications and chromosomal rearrangements may occur. In this review, we discuss the regulatory activity of satellite DNA and their neighboring transposable elements in a chromosomal context with a particular emphasis on the integral role of both in centromere function. In addition, we discuss the varied mechanisms by which centromeric repeats have endured evolutionary processes, producing a novel, species-specific centromeric landscape despite sharing a ubiquitously conserved function. Finally, we highlight the role these repetitive elements play in the establishment and functionality of de novo centromeres and chromosomal breakpoints that underpin karyotypic variation. By emphasizing these unique activities of satellite DNAs and transposable elements, we hope to disparage the conventional exemplification of repetitive DNA in the historically-associated context of ‘junk’.
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11
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Cacheux L, Ponger L, Gerbault-Seureau M, Loll F, Gey D, Richard FA, Escudé C. The Targeted Sequencing of Alpha Satellite DNA in Cercopithecus pogonias Provides New Insight Into the Diversity and Dynamics of Centromeric Repeats in Old World Monkeys. Genome Biol Evol 2018; 10:1837-1851. [PMID: 29860303 PMCID: PMC6061836 DOI: 10.1093/gbe/evy109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/29/2018] [Indexed: 02/06/2023] Open
Abstract
Alpha satellite is the major repeated DNA element of primate centromeres. Specific evolutionary mechanisms have led to a great diversity of sequence families with peculiar genomic organization and distribution, which have till now been studied mostly in great apes. Using high throughput sequencing of alpha satellite monomers obtained by enzymatic digestion followed by computational and cytogenetic analysis, we compare here the diversity and genomic distribution of alpha satellite DNA in two related Old World monkey species, Cercopithecus pogonias and Cercopithecus solatus, which are known to have diverged about 7 Ma. Two main families of monomers, called C1 and C2, are found in both species. A detailed analysis of our data sets revealed the existence of numerous subfamilies within the centromeric C1 family. Although the most abundant subfamily is conserved between both species, our fluorescence in situ hybridization (FISH) experiments clearly show that some subfamilies are specific for each species and that their distribution is restricted to a subset of chromosomes, thereby pointing to the existence of recurrent amplification/homogenization events. The pericentromeric C2 family is very abundant on the short arm of all acrocentric chromosomes in both species, pointing to specific mechanisms that lead to this distribution. Results obtained using two different restriction enzymes are fully consistent with a predominant monomeric organization of alpha satellite DNA that coexists with higher order organization patterns in the C. pogonias genome. Our study suggests a high dynamics of alpha satellite DNA in Cercopithecini, with recurrent apparition of new sequence variants and interchromosomal sequence transfer.
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Affiliation(s)
- Lauriane Cacheux
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Loïc Ponger
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Michèle Gerbault-Seureau
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - François Loll
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Delphine Gey
- Service de Systématique Moléculaire, UMS 2700 CNRS, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
| | - Florence Anne Richard
- Département Origines et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
- Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Christophe Escudé
- Département Adaptations du Vivant, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum National d’Histoire Naturelle, Paris, France
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12
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Cacheux L, Ponger L, Gerbault-Seureau M, Richard FA, Escudé C. Diversity and distribution of alpha satellite DNA in the genome of an Old World monkey: Cercopithecus solatus. BMC Genomics 2016; 17:916. [PMID: 27842493 PMCID: PMC5109768 DOI: 10.1186/s12864-016-3246-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 11/02/2016] [Indexed: 11/10/2022] Open
Abstract
Background Alpha satellite is the major repeated DNA element of primate centromeres. Evolution of these tandemly repeated sequences has led to the existence of numerous families of monomers exhibiting specific organizational patterns. The limited amount of information available in non-human primates is a restriction to the understanding of the evolutionary dynamics of alpha satellite DNA. Results We carried out the targeted high-throughput sequencing of alpha satellite monomers and dimers from the Cercopithecus solatus genome, an Old World monkey from the Cercopithecini tribe. Computational approaches were used to infer the existence of sequence families and to study how these families are organized with respect to each other. While previous studies had suggested that alpha satellites in Old World monkeys were poorly diversified, our analysis provides evidence for the existence of at least four distinct families of sequences within the studied species and of higher order organizational patterns. Fluorescence in situ hybridization using oligonucleotide probes that are able to target each family in a specific way showed that the different families had distinct distributions on chromosomes and were not homogeneously distributed between chromosomes. Conclusions Our new approach provides an unprecedented and comprehensive view of the diversity and organization of alpha satellites in a species outside the hominoid group. We consider these data with respect to previously known alpha satellite families and to potential mechanisms for satellite DNA evolution. Applying this approach to other species will open new perspectives regarding the integration of satellite DNA into comparative genomic and cytogenetic studies. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3246-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lauriane Cacheux
- Département Régulations, Développement et Diversité Moléculaire, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France.,Département Systématique et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Loïc Ponger
- Département Régulations, Développement et Diversité Moléculaire, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Michèle Gerbault-Seureau
- Département Systématique et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France
| | - Florence Anne Richard
- Département Systématique et Evolution, Institut de Systématique, Evolution, Biodiversité, UMR 7205 MNHN, CNRS, UPMC, EPHE, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France.,Université Versailles St-Quentin, Montigny-le-Bretonneux, France
| | - Christophe Escudé
- Département Régulations, Développement et Diversité Moléculaire, Structure et Instabilité des Génomes, INSERM U1154, CNRS UMR7196, Sorbonne Universités, Muséum national d'Histoire naturelle, Paris, France.
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Morgan AP, Holt JM, McMullan RC, Bell TA, Clayshulte AMF, Didion JP, Yadgary L, Thybert D, Odom DT, Flicek P, McMillan L, de Villena FPM. The Evolutionary Fates of a Large Segmental Duplication in Mouse. Genetics 2016; 204:267-85. [PMID: 27371833 PMCID: PMC5012392 DOI: 10.1534/genetics.116.191007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 06/27/2016] [Indexed: 01/21/2023] Open
Abstract
Gene duplication and loss are major sources of genetic polymorphism in populations, and are important forces shaping the evolution of genome content and organization. We have reconstructed the origin and history of a 127-kbp segmental duplication, R2d, in the house mouse (Mus musculus). R2d contains a single protein-coding gene, Cwc22 De novo assembly of both the ancestral (R2d1) and the derived (R2d2) copies reveals that they have been subject to nonallelic gene conversion events spanning tens of kilobases. R2d2 is also a hotspot for structural variation: its diploid copy number ranges from zero in the mouse reference genome to >80 in wild mice sampled from around the globe. Hemizygosity for high copy-number alleles of R2d2 is associated in cis with meiotic drive; suppression of meiotic crossovers; and copy-number instability, with a mutation rate in excess of 1 per 100 transmissions in some laboratory populations. Our results provide a striking example of allelic diversity generated by duplication and demonstrate the value of de novo assembly in a phylogenetic context for understanding the mutational processes affecting duplicate genes.
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Affiliation(s)
- Andrew P Morgan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - J Matthew Holt
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Rachel C McMullan
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Timothy A Bell
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Amelia M-F Clayshulte
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - John P Didion
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Liran Yadgary
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - David Thybert
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom
| | - Duncan T Odom
- Cancer Research United Kingdom Cambridge Institute, University of Cambridge, CB2 0RE, United Kingdom Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Paul Flicek
- European Bioinformatics Institute, European Molecular Biology Laboratory, Wellcome Genome Campus, Cambridge, CB10 1SD, United Kingdom Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, CB10 1SA, United Kingdom
| | - Leonard McMillan
- Department of Computer Science, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Fernando Pardo-Manuel de Villena
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
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14
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Nambiar M, Smith GR. Repression of harmful meiotic recombination in centromeric regions. Semin Cell Dev Biol 2016; 54:188-97. [PMID: 26849908 DOI: 10.1016/j.semcdb.2016.01.042] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 01/27/2016] [Indexed: 11/16/2022]
Abstract
During the first division of meiosis, segregation of homologous chromosomes reduces the chromosome number by half. In most species, sister chromatid cohesion and reciprocal recombination (crossing-over) between homologous chromosomes are essential to provide tension to signal proper chromosome segregation during the first meiotic division. Crossovers are not distributed uniformly throughout the genome and are repressed at and near the centromeres. Rare crossovers that occur too near or in the centromere interfere with proper segregation and can give rise to aneuploid progeny, which can be severely defective or inviable. We review here how crossing-over occurs and how it is prevented in and around the centromeres. Molecular mechanisms of centromeric repression are only now being elucidated. However, rapid advances in understanding crossing-over, chromosome structure, and centromere functions promise to explain how potentially deleterious crossovers are avoided in certain chromosomal regions while allowing beneficial crossovers in others.
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Affiliation(s)
- Mridula Nambiar
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
| | - Gerald R Smith
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA, United States.
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15
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Catacchio CR, Ragone R, Chiatante G, Ventura M. Organization and evolution of Gorilla centromeric DNA from old strategies to new approaches. Sci Rep 2015; 5:14189. [PMID: 26387916 PMCID: PMC4585704 DOI: 10.1038/srep14189] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/18/2015] [Indexed: 11/09/2022] Open
Abstract
The centromere/kinetochore interaction is responsible for the pairing and segregation of replicated chromosomes in eukaryotes. Centromere DNA is portrayed as scarcely conserved, repetitive in nature, quickly evolving and protein-binding competent. Among primates, the major class of centromeric DNA is the pancentromeric α-satellite, made of arrays of 171 bp monomers, repeated in a head-to-tail pattern. α-satellite sequences can either form tandem heterogeneous monomeric arrays or assemble in higher-order repeats (HORs). Gorilla centromere DNA has barely been characterized, and data are mainly based on hybridizations of human alphoid sequences. We isolated and finely characterized gorilla α-satellite sequences and revealed relevant structure and chromosomal distribution similarities with other great apes as well as gorilla-specific features, such as the uniquely octameric structure of the suprachromosomal family-2 (SF2). We demonstrated for the first time the orthologous localization of alphoid suprachromosomal families-1 and −2 (SF1 and SF2) between human and gorilla in contrast to chimpanzee centromeres. Finally, the discovery of a new 189 bp monomer type in gorilla centromeres unravels clues to the role of the centromere protein B, paving the way to solve the significance of the centromere DNA’s essential repetitive nature in association with its function and the peculiar evolution of the α-satellite sequence.
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Affiliation(s)
- C R Catacchio
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - R Ragone
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - G Chiatante
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
| | - M Ventura
- University of Bari Aldo Moro, Department of Biology, Via Orabona 4, Bari, 70125, Italy
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16
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Matylla-Kulinska K, Tafer H, Weiss A, Schroeder R. Functional repeat-derived RNAs often originate from retrotransposon-propagated ncRNAs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2014; 5:591-600. [PMID: 25045147 PMCID: PMC4233971 DOI: 10.1002/wrna.1243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/15/2014] [Accepted: 04/22/2014] [Indexed: 12/19/2022]
Abstract
The human genome is scattered with repetitive sequences, and the ENCODE project revealed that 60–70% of the genomic DNA is transcribed into RNA. As a consequence, the human transcriptome contains a large portion of repeat-derived RNAs (repRNAs). Here, we present a hypothesis for the evolution of novel functional repeat-derived RNAs from non-coding RNAs (ncRNAs) by retrotransposition. Upon amplification, the ncRNAs can diversify in sequence and subsequently evolve new activities, which can result in novel functions. Non-coding transcripts derived from highly repetitive regions can therefore serve as a reservoir for the evolution of novel functional RNAs. We base our hypothetical model on observations reported for short interspersed nuclear elements derived from 7SL RNA and tRNAs, α satellites derived from snoRNAs and SL RNAs derived from U1 small nuclear RNA. Furthermore, we present novel putative human repeat-derived ncRNAs obtained by the comparison of the Dfam and Rfam databases, as well as several examples in other species. We hypothesize that novel functional ncRNAs can derive also from other repetitive regions and propose Genomic SELEX as a tool for their identification.
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Affiliation(s)
- Katarzyna Matylla-Kulinska
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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17
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Miga KH, Newton Y, Jain M, Altemose N, Willard HF, Kent WJ. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res 2014; 24:697-707. [PMID: 24501022 PMCID: PMC3975068 DOI: 10.1101/gr.159624.113] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human genome sequence remains incomplete, with multimegabase-sized gaps representing the endogenous centromeres and other heterochromatic regions. Available sequence-based studies within these sites in the genome have demonstrated a role in centromere function and chromosome pairing, necessary to ensure proper chromosome segregation during cell division. A common genomic feature of these regions is the enrichment of long arrays of near-identical tandem repeats, known as satellite DNAs, which offer a limited number of variant sites to differentiate individual repeat copies across millions of bases. This substantial sequence homogeneity challenges available assembly strategies and, as a result, centromeric regions are omitted from ongoing genomic studies. To address this problem, we utilize monomer sequence and ordering information obtained from whole-genome shotgun reads to model two haploid human satellite arrays on chromosomes X and Y, resulting in an initial characterization of 3.83 Mb of centromeric DNA within an individual genome. To further expand the utility of each centromeric reference sequence model, we evaluate sites within the arrays for short-read mappability and chromosome specificity. Because satellite DNAs evolve in a concerted manner, we use these centromeric assemblies to assess the extent of sequence variation among 366 individuals from distinct human populations. We thus identify two satellite array variants in both X and Y centromeres, as determined by array length and sequence composition. This study provides an initial sequence characterization of a regional centromere and establishes a foundation to extend genomic characterization to these sites as well as to other repeat-rich regions within complex genomes.
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Affiliation(s)
- Karen H Miga
- Duke Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
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18
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Sharma A, Wolfgruber TK, Presting GG. Tandem repeats derived from centromeric retrotransposons. BMC Genomics 2013; 14:142. [PMID: 23452340 PMCID: PMC3648361 DOI: 10.1186/1471-2164-14-142] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/23/2013] [Indexed: 12/26/2022] Open
Abstract
Background Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotransposons, are enriched at centromeres. Some satellite repeats have homology to retrotransposons and several mechanisms have been proposed to explain the expansion, contraction as well as homogenization of tandem repeats. However, the origin and evolution of tandem repeat loci remain largely unknown. Results CRM1TR and CRM4TR are novel tandem repeats that we show to be entirely derived from CR elements belonging to two different subfamilies, CRM1 and CRM4. Although these tandem repeats clearly originated in at least two separate events, they are derived from similar regions of their respective parent element, namely the long terminal repeat (LTR) and untranslated region (UTR). The 5′ ends of the monomer repeat units of CRM1TR and CRM4TR map to different locations within their respective LTRs, while their 3′ ends map to the same relative position within a conserved region of their UTRs. Based on the insertion times of heterologous retrotransposons that have inserted into these tandem repeats, amplification of the repeats is estimated to have begun at least ~4 (CRM1TR) and ~1 (CRM4TR) million years ago. Distinct CRM1TR sequence variants occupy the two CRM1TR loci, indicating that there is little or no movement of repeats between loci, even though they are separated by only ~1.4 Mb. Conclusions The discovery of two novel retrotransposon derived tandem repeats supports the conclusions from earlier studies that retrotransposons can give rise to tandem repeats in eukaryotic genomes. Analysis of monomers from two different CRM1TR loci shows that gene conversion is the major cause of sequence variation. We propose that successive intrastrand deletions generated the initial repeat structure, and gene conversions increased the size of each tandem repeat locus.
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19
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Localization of centromeric breaks in head and neck squamous cell carcinoma. Cancer Genet 2012; 205:622-9. [DOI: 10.1016/j.cancergen.2012.10.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 10/01/2012] [Accepted: 10/02/2012] [Indexed: 11/20/2022]
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20
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Lan T, Albert VA. Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum, a lady's slipper orchid. BMC PLANT BIOLOGY 2011; 11:126. [PMID: 21910890 PMCID: PMC3184063 DOI: 10.1186/1471-2229-11-126] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/12/2011] [Indexed: 05/07/2023]
Abstract
Background Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. Results 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Conclusions Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of complex chromosomal evolution in plants.
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Affiliation(s)
- Tianying Lan
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
| | - Victor A Albert
- Department of Biological Sciences, University at Buffalo, Buffalo, NY 14260, USA
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21
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Lee HR, Hayden KE, Willard HF. Organization and molecular evolution of CENP-A--associated satellite DNA families in a basal primate genome. Genome Biol Evol 2011; 3:1136-49. [PMID: 21828373 PMCID: PMC3194837 DOI: 10.1093/gbe/evr083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Centromeric regions in many complex eukaryotic species contain highly repetitive satellite DNAs. Despite the diversity of centromeric DNA sequences among species, the functional centromeres in all species studied to date are marked by CENP-A, a centromere-specific histone H3 variant. Although it is well established that families of multimeric higher-order alpha satellite are conserved at the centromeres of human and great ape chromosomes and that diverged monomeric alpha satellite is found in old and new world monkey genomes, little is known about the organization, function, and evolution of centromeric sequences in more distant primates, including lemurs. Aye-Aye (Daubentonia madagascariensis) is a basal primate and is located at a key position in the evolutionary tree to study centromeric satellite transitions in primate genomes. Using the approach of chromatin immunoprecipitation with antibodies directed to CENP-A, we have identified two satellite families, Daubentonia madagascariensis Aye-Aye 1 (DMA1) and Daubentonia madagascariensis Aye-Aye 2 (DMA2), related to each other but unrelated in sequence to alpha satellite or any other previously described primate or mammalian satellite DNA families. Here, we describe the initial genomic and phylogenetic organization of DMA1 and DMA2 and present evidence of higher-order repeats in Aye-Aye centromeric domains, providing an opportunity to study the emergence of chromosome-specific modes of satellite DNA evolution in primate genomes.
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Affiliation(s)
- Hye-Ran Lee
- Genome Biology Group, Duke Institute for Genome Sciences & Policy, Duke University, USA
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22
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Koumbaris G, Hatzisevastou-Loukidou H, Alexandrou A, Ioannides M, Christodoulou C, Fitzgerald T, Rajan D, Clayton S, Kitsiou-Tzeli S, Vermeesch JR, Skordis N, Antoniou P, Kurg A, Georgiou I, Carter NP, Patsalis PC. FoSTeS, MMBIR and NAHR at the human proximal Xp region and the mechanisms of human Xq isochromosome formation. Hum Mol Genet 2011; 20:1925-36. [PMID: 21349920 PMCID: PMC3428953 DOI: 10.1093/hmg/ddr074] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The recently described DNA replication-based mechanisms of fork stalling and template switching (FoSTeS) and microhomology-mediated break-induced replication (MMBIR) were previously shown to catalyze complex exonic, genic and genomic rearrangements. By analyzing a large number of isochromosomes of the long arm of chromosome X (i(Xq)), using whole-genome tiling path array comparative genomic hybridization (aCGH), ultra-high resolution targeted aCGH and sequencing, we provide evidence that the FoSTeS and MMBIR mechanisms can generate large-scale gross chromosomal rearrangements leading to the deletion and duplication of entire chromosome arms, thus suggesting an important role for DNA replication-based mechanisms in both the development of genomic disorders and cancer. Furthermore, we elucidate the mechanisms of dicentric i(Xq) (idic(Xq)) formation and show that most idic(Xq) chromosomes result from non-allelic homologous recombination between palindromic low copy repeats and highly homologous palindromic LINE elements. We also show that non-recurrent-breakpoint idic(Xq) chromosomes have microhomology-associated breakpoint junctions and are likely catalyzed by microhomology-mediated replication-dependent recombination mechanisms such as FoSTeS and MMBIR. Finally, we stress the role of the proximal Xp region as a chromosomal rearrangement hotspot.
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Affiliation(s)
- George Koumbaris
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | | | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Marios Ioannides
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Christodoulos Christodoulou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Tomas Fitzgerald
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Diana Rajan
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Stephen Clayton
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Sophia Kitsiou-Tzeli
- Department of Medical Genetics, University of Athens, St Sophia Children’s Hospital, Athens 11527, Greece
| | - Joris R. Vermeesch
- Centre for Human Genetics, University Hospital, Catholic University of Leuven, 3000 Leuven, Belgium
| | - Nicos Skordis
- Pediatric Endocrine Unit, Makarios III Hospital, Nicosia 1474, Cyprus
| | - Pavlos Antoniou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
| | - Ants Kurg
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | | | - Nigel P. Carter
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Philippos C. Patsalis
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia 2370, Cyprus
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23
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Rocchi L, Braz C, Cattani S, Ramalho A, Christan S, Edlinger M, Ascenzioni F, Laner A, Kraner S, Amaral M, Schindelhauer D. Escherichia coli-cloned CFTR loci relevant for human artificial chromosome therapy. Hum Gene Ther 2010; 21:1077-92. [PMID: 20384480 DOI: 10.1089/hum.2009.225] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Classical gene therapy for cystic fibrosis has had limited success because of immune response against viral vectors and short-term expression of cDNA-based transgenes. These limitations could be overcome by delivering the complete genomic CFTR gene on nonintegrating human artificial chromosomes (HACs). Here, we report reconstruction of the genomic CFTR locus and analyze incorporation into HACs of three P1 phage-based and F factor bacteria-based artificial chromosomes (PACs/BACs) of various sizes: (1) 5A, a large, nonselectable BAC containing the entire wild-type CFTR locus extending into both adjacent genes (296.8-kb insert, from kb -58.4 to +51.4) containing all regulators; (2) CGT21, a small, selectable, telomerized PAC (134.7 kb, from kb -60.7 to + 2) containing a synthetic last exon joining exon 10, EGFP, exon 24, and the 3' untranslated region; and (3) CF225, a midsized, nonselectable PAC (225.3 kb, from kb -60.7 to +9.8) ligated from two PACs with optimized codons and a silent XmaI restriction variant to discriminate transgene from endogenous expression. Cotransfection with telomerized, blasticidin-S-selectable, centromere-proficient α-satellite constructs into HT1080 cells revealed a workable HAC formation rate of 1 per ∼25 lines when using CGT21 or 5A. CF225 was not incorporated into a de novo HAC in 122 lines analyzed, but integrants were expressed. Stability analyses suggest the feasibility of prefabricating a large, tagged CFTR transgene that stably replicates in the proximity of a functional centromere. Although definite conclusions about HAC-proficient construct configurations cannot be drawn at this stage, important transfer resources were generated and characterized, demonstrating the promise of de novo HACs as potentially ideal gene therapy vector systems.
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Affiliation(s)
- Lucia Rocchi
- Life Sciences Center Weihenstephan, Technical University Munich, Freising, Germany
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24
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Macas J, Neumann P, Novák P, Jiang J. Global sequence characterization of rice centromeric satellite based on oligomer frequency analysis in large-scale sequencing data. ACTA ACUST UNITED AC 2010; 26:2101-8. [PMID: 20616383 DOI: 10.1093/bioinformatics/btq343] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
MOTIVATION Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. RESULTS k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats.
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Affiliation(s)
- Jirí Macas
- Institute of Plant Molecular Biology, Biology Centre ASCR, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic.
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Pironon N, Puechberty J, Roizès G. Molecular and evolutionary characteristics of the fraction of human alpha satellite DNA associated with CENP-A at the centromeres of chromosomes 1, 5, 19, and 21. BMC Genomics 2010; 11:195. [PMID: 20331851 PMCID: PMC2853522 DOI: 10.1186/1471-2164-11-195] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2009] [Accepted: 03/23/2010] [Indexed: 11/15/2022] Open
Abstract
Background The mode of evolution of the highly homogeneous Higher-Order-Repeat-containing alpha satellite arrays is still subject to discussion. This is also true of the CENP-A associated repeats where the centromere is formed. Results In this paper, we show that the molecular mechanisms by which these arrays evolve are identical in multiple chromosomes: i) accumulation of crossovers that homogenise and expand the arrays into different domains and subdomains that are mostly unshared between homologues and ii) sporadic mutations and conversion events that simultaneously differentiate them from one another. Individual arrays are affected by these mechanisms to different extents that presumably increase with time. Repeats associated with CENP-A, where the centromere is formed, are subjected to the same evolutionary mechanisms, but constitute minor subsets that exhibit subtle sequence differences from those of the bulk repeats. While the DNA sequence per se is not essential for centromere localisation along an array, it appears that certain sequences can be selected against. On chromosomes 1 and 19, which are more affected by the above evolutionary mechanisms than are chromosomes 21 and 5, CENP-A associated repeats were also recovered from a second homogeneous array present on each chromosome. This could be a way for chromosomes to sustain mitosis and meiosis when the normal centromere locus is ineluctably undermined by the above mechanisms. Conclusion We discuss, in light of these observations, possible scenarios for the normal evolutionary fates of human centromeric regions.
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Affiliation(s)
- Nathalie Pironon
- Institut de Génétique Humaine, UPR 1142, CNRS, 141 Rue de Cardonille, 34396 Montpellier Cedex 5, France
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Abstract
Data from maize show that centromeres strongly suppress crossing over and instead undergo frequent genetic exchange in the form of gene conversion. Centromeres are the most dynamic regions of the genome, yet they are typified by little or no crossing over, making it difficult to explain the origin of this diversity. To address this question, we developed a novel CENH3 ChIP display method that maps kinetochore footprints over transposon-rich areas of centromere cores. A high level of polymorphism made it possible to map a total of 238 within-centromere markers using maize recombinant inbred lines. Over half of the markers were shown to interact directly with kinetochores (CENH3) by chromatin immunoprecipitation. Although classical crossing over is fully suppressed across CENH3 domains, two gene conversion events (i.e., non-crossover marker exchanges) were identified in a mapping population. A population genetic analysis of 53 diverse inbreds suggests that historical gene conversion is widespread in maize centromeres, occurring at a rate >1×10−5/marker/generation. We conclude that gene conversion accelerates centromere evolution by facilitating sequence exchange among chromosomes. Centromeres, which harbor the attachment points for microtubules during cell division, are characterized by repetitive DNA, paucity of genes, and almost complete suppression of crossing over. The repetitive DNA within centromeres appears to evolve much faster than would be expected for genetically inert regions, however. Current explanations for this rapid evolution tend to be theoretical. On the one hand there are arguments that subtle forms of selection on selfish repeat sequences can explain the rapid rate of change, while on the other hand it seems plausible that some form of accelerated neutral evolution is occurring. Here, we address this question in maize, which is known for its excellent genetic mapping resources. We first developed a method for identifying hundreds of single copy markers in centromeres and confirmed that they lie within functional domains by using a chromatin immunoprecipitation assay for kinetochore protein CENH3. All markers were mapped in relation to each other. The data show that, whereas classical crossing over is suppressed, there is extensive genetic exchange in the form of gene conversion (by which short segments of one chromosome are copied onto the other). These results were confirmed by demonstrating that similar short exchange tracts are common among the centromeres from multiple diverse inbred lines of maize. Our study suggests that centromere diversity can be at least partially attributed to a high rate of previously “hidden” genetic exchange within the core kinetochore domains.
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Plohl M, Petrović V, Luchetti A, Ricci A, Satović E, Passamonti M, Mantovani B. Long-term conservation vs high sequence divergence: the case of an extraordinarily old satellite DNA in bivalve mollusks. Heredity (Edinb) 2009; 104:543-51. [PMID: 19844270 DOI: 10.1038/hdy.2009.141] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (Protobranchia, Pteriomorphia and Heteroconchia). BIV160 monomers are similar in repeat size and nucleotide sequence to satDNAs described earlier in oysters and in the clam Donax trunculus. The broad distribution of BIV160 satDNA indicates that similar variants existed in the ancestral bivalve species that lived about 540 million years ago; this makes BIV160 the most ancient satDNA described so far. In the species examined, monomer variants are distributed in quite a complex pattern. This pattern includes (i) species characterized by a specific group of variants, (ii) species that share distinct group(s) of variants and (iii) species with both specific and shared types. The evolutionary scenario suggested by these data reconciles sequence uniformity in homogenization-maintained satDNA arrays with the genomic richness of divergent monomer variants formed by diversification of the same ancestral satDNA sequence. Diversified repeats can continue to evolve in a non-concerted manner and behave as independent amplification-contraction units in the framework of a 'library of satDNA variants' representing a permanent source of monomers that can be amplified into novel homogeneous satDNA arrays. On the whole, diversification of satDNA monomers and copy number fluctuations provide a highly dynamic genomic environment able to form and displace satDNA sequence variants rapidly in evolution.
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Affiliation(s)
- M Plohl
- Department of Molecular Biology, Ruder Bosković Institute, Zagreb, Croatia.
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Bulazel KV, Ferreri GC, Eldridge MDB, O'Neill RJ. Species-specific shifts in centromere sequence composition are coincident with breakpoint reuse in karyotypically divergent lineages. Genome Biol 2008; 8:R170. [PMID: 17708770 PMCID: PMC2375000 DOI: 10.1186/gb-2007-8-8-r170] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2007] [Accepted: 08/20/2007] [Indexed: 11/12/2022] Open
Abstract
The evolution of three classes of centromere sequences across nine species of macropodine marsupials were compared with that of other genes, showing that each species has experienced differential expansion and contraction of individual classes. Background It has been hypothesized that rapid divergence in centromere sequences accompanies rapid karyotypic change during speciation. However, the reuse of breakpoints coincident with centromeres in the evolution of divergent karyotypes poses a potential paradox. In distantly related species where the same centromere breakpoints are used in the independent derivation of karyotypes, centromere-specific sequences may undergo convergent evolution rather than rapid sequence divergence. To determine whether centromere sequence composition follows the phylogenetic history of species evolution or patterns of convergent breakpoint reuse through chromosome evolution, we examined the phylogenetic trajectory of centromere sequences within a group of karyotypically diverse mammals, macropodine marsupials (wallabies, wallaroos and kangaroos). Results The evolution of three classes of centromere sequences across nine species within the genus Macropus (including Wallabia) were compared with the phylogenetic history of a mitochondrial gene, Cytochrome b (Cyt b), a nuclear gene, selenocysteine tRNA (TRSP), and the chromosomal histories of the syntenic blocks that define the different karyotype arrangements. Convergent contraction or expansion of predominant satellites is found to accompany specific karyotype rearrangements. The phylogenetic history of these centromere sequences includes the convergence of centromere composition in divergent species through convergent breakpoint reuse between syntenic blocks. Conclusion These data support the 'library hypothesis' of centromere evolution within this genus as each species possesses all three satellites yet each species has experienced differential expansion and contraction of individual classes. Thus, we have identified a correlation between the evolution of centromere satellite sequences, the reuse of syntenic breakpoints, and karyotype convergence in the context of a gene-based phylogeny.
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Affiliation(s)
- Kira V Bulazel
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Gianni C Ferreri
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
| | - Mark DB Eldridge
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia
- Molecular Biology, Australian Museum, College St, Sydney, NSW 2010, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Mansfield Rd, University of Connecticut, Storrs, CT 06269, USA
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Intraspecific concerted evolution of the rDNA ITS1 in Anopheles farauti sensu stricto (Diptera: Culicidae) reveals recent patterns of population structure. J Mol Evol 2008; 67:397-411. [PMID: 18818859 PMCID: PMC9931795 DOI: 10.1007/s00239-008-9161-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 06/18/2008] [Accepted: 08/28/2008] [Indexed: 10/21/2022]
Abstract
We examined the intraindividual variation present in the first ribosomal internal transcribed spacer (ITS1) of Anopheles farauti to determine the level of divergence among populations for this important malarial vector. We isolated 187 clones from 70 individuals and found regional variation among four internal tandem repeats. The data were partitioned prior to analysis given the presence of a paralogous ITS2 sequence, called the 5'-subrepeat, inserted in the ITS1 of most clones. A high level of homogenization and population differentiation was observed for this repeat, which indicates a higher rate of turnover relative to the adjacent 'core' region. Bayesian analysis was performed using several substitutional models on both a combined and a partitioned data set. On the whole, the ITS1 phylogeny and geographic origin of the samples appear to be congruent. Some interesting exceptions indicate the spread of variant repeats between populations and the retention of ancestral polymorphism. Our data clearly demonstrate concerted evolution at the intraspecific level despite intraindividual variation and a complex internal repeat structure from a species that occupies a continuous coastal distribution. A high rate of genomic turnover in combination with a high level of sequence divergence appears to be a major factor leading to its concerted evolution within these populations.
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30
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Plohl M, Luchetti A, Mestrović N, Mantovani B. Satellite DNAs between selfishness and functionality: structure, genomics and evolution of tandem repeats in centromeric (hetero)chromatin. Gene 2007; 409:72-82. [PMID: 18182173 DOI: 10.1016/j.gene.2007.11.013] [Citation(s) in RCA: 234] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2007] [Revised: 11/08/2007] [Accepted: 11/20/2007] [Indexed: 12/21/2022]
Abstract
Satellite DNAs (tandemly repeated, non-coding DNA sequences) stretch over almost all native centromeres and surrounding pericentromeric heterochromatin. Once considered as inert by-products of genome dynamics in heterochromatic regions, recent studies showed that satellite DNA evolution is interplay of stochastic events and selective pressure. This points to a functional significance of satellite sequences, which in (peri)centromeres may play some fundamental functional roles. First, specific interactions with DNA-binding proteins are proposed to complement sequence-independent epigenetic processes. The second role is achieved through RNAi mechanism, in which transcripts of satellite sequences initialize heterochromatin formation. In addition, satellite DNAs in (peri)centromeric regions affect chromosomal dynamics and genome plasticity. Paradoxically, while centromeric function is conserved through eukaryotes, the profile of satellite DNAs in this region is almost always species-specific. We argue that tandem repeats may be advantageous forms of DNA sequences in (peri)centromeres due to concerted evolution, which maintains high intra-array and intrapopulation sequence homogeneity of satellite arrays, while allowing rapid changes in nucleotide sequence and/or composition of satellite repeats. This feature may be crucial for long-term stability of DNA-protein interactions in centromeric regions.
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Affiliation(s)
- Miroslav Plohl
- Department of Molecular Genetics, Ruder Bosković Institute, Bijenicka 54, HR-10002 Zagreb, Croatia.
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31
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Luchetti A, Scanabissi F, Mantovani B. Evolution of LEP150 sub-repeat array within the ribosomal IGS of the clam shrimp Leptestheria dahalacensis (Crustacea Branchiopoda Conchostraca). Gene 2007; 400:174-80. [PMID: 17651923 DOI: 10.1016/j.gene.2007.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2007] [Revised: 06/14/2007] [Accepted: 06/19/2007] [Indexed: 11/28/2022]
Abstract
Leptestheria dahalacensis genome harbours repeats of the LEP150 satellite DNA family linked to 5S gene, within the ribosomal intergenic spacer. In genetically isolated samples, the sequence analysis of the region (5S, flanking region, first satellite monomer: unit A, second satellite monomer: unit B) evidenced three 5S variants. The alpha and gamma variants share a greater homology. They co-occur in the Central European samples, while in the Italian one, the highly divergent alpha and beta variants are present. In phylogenetic analyses, A and B LEP150 monomers show a peculiar clustering; this was further confirmed through the sequencing for the alpha variant of four monomers at the 5' and 3' tails (units A, B, C, D and D', C', B', A', respectively). Horizontal homogenisation was observed only across C, D, C' and D' units. Furthermore, repeat sequence diversity decrease toward terminal repeats, at variance of literature data. The pattern of variation observed is explained taking into account the presence at the LEP150 array borders of two loci under natural selection: the 5S rRNA gene, upstream, and the rDNA transcription promoter, downstream. These elements may drive the dynamics of flanking regions and linked repeats in a process similar to selective sweep. At variance of classical genetic hitchhiking, the selective sweep here scored should be realized and maintained through an interplay of selection and molecular drive.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Biologia E. S., Università degli Studi di Bologna, Bologna, Italy.
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32
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Kawabe A, Charlesworth D. Patterns of DNA variation among three centromere satellite families in Arabidopsis halleri and A. lyrata. J Mol Evol 2006; 64:237-47. [PMID: 17160639 DOI: 10.1007/s00239-006-0097-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2006] [Accepted: 10/03/2006] [Indexed: 11/28/2022]
Abstract
We describe patterns of DNA variation among the three centromeric satellite families in Arabidopsis halleri and lyrata. The newly studied subspecies (A. halleri ssp. halleri and A. lyrata ssp. lyrata and petraea), like the previously studied A. halleri ssp. gemmifera and A. lyrata ssp. kawasakiana, have three different centromeric satellite families, the older pAa family (also present in A. arenosa) and two families, pAge1 and pAge2, that probably evolved more recently. Sequence variability is high in all three satellite families, and the pAa sequences do not cluster by their species of origin. Diversity in the pAge2 family is complex, and different from variation among copies of the other two families, showing clear evidence for exchange events among family members, especially in A. halleri ssp. halleri. In A. lyrata ssp. lyrata there is some evidence for recent rapid spread of pAge2 variants, suggesting selection favoring these sequences.
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Affiliation(s)
- Akira Kawabe
- Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories King's Buildings, West Mains Road, Edinburgh, EH9 3JT, UK.
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Dawe RK, Henikoff S. Centromeres put epigenetics in the driver's seat. Trends Biochem Sci 2006; 31:662-9. [PMID: 17074489 DOI: 10.1016/j.tibs.2006.10.004] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2006] [Revised: 09/19/2006] [Accepted: 10/20/2006] [Indexed: 01/01/2023]
Abstract
A defining feature of chromosomes is the centromere, the site for spindle attachment at mitosis and meiosis. Intriguingly, centromeres of plants and animals are maintained by both sequence-specific and sequence-independent (epigenetic) processes. Epigenetic inheritance might enable kinetochores (the structures that attach centromeres to spindles) to maintain an optimal size. However, centromeres are susceptible to the evolution of "selfish" DNA repeats that bind to kinetochore proteins. We argue that such sequence-specific interactions are evolutionarily unstable because they enable repeat arrays to influence kinetochore size. Changes in kinetochore size could affect the interaction of kinetochores with the spindle and, in principle, skew Mendelian segregation. We propose that key kinetochore proteins have adapted to disrupt such sequence-specific interactions and restore epigenetic inheritance.
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Affiliation(s)
- R Kelly Dawe
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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34
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Rosandić M, Paar V, Basar I, Gluncić M, Pavin N, Pilas I. CENP-B box and pJalpha sequence distribution in human alpha satellite higher-order repeats (HOR). Chromosome Res 2006; 14:735-53. [PMID: 17115329 DOI: 10.1007/s10577-006-1078-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2005] [Accepted: 06/03/2006] [Indexed: 01/13/2023]
Abstract
Using our Key String Algorithm (KSA) to analyze Build 35.1 assembly we determined consensus alpha satellite higher-order repeats (HOR) and consensus distributions of CENP-B box and pJalpha motif in human chromosomes 1, 4, 5, 7, 8, 10, 11, 17, 19, and X. We determined new suprachromosomal family (SF) assignments: SF5 for 13mer (2211 bp), SF5 for 13mer (2214 bp), SF2 for 11mer (1869 bp), SF1 for 18mer (3058 bp), SF3 for 12mer (2047 bp), SF3 for 14mer (2379 bp), and SF5 for 17mer (2896 bp) in chromosomes 4, 5, 8, 10, 11, 17, and 19, respectively. In chromosome 5 we identified SF5 13mer without any CENP-B box and pJalpha motif, highly homologous (96%) to 13mer in chromosome 19. Additionally, in chromosome 19 we identified new SF5 17mer with one CENP-B box and pJalpha motif, aligned to 13mer by deleting four monomers. In chromosome 11 we identified SF3 12mer, homologous to 12mer in chromosome X. In chromosome 10 we identified new SF1 18mer with eight CENP-B boxes in every other monomer (except one). In chromosome 4 we identified new SF5 13mer with CENP-B box in three consecutive monomers. We found four exceptions to the rule that CENP-B box belongs to type B and pJalpha motif to type A monomers.
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Affiliation(s)
- Marija Rosandić
- Department of Internal Medicine, University Hospital Rebro, University of Zagreb, 10000, Zagreb, Croatia
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35
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Abstract
Centromeres are the elements of chromosomes that assemble the proteinaceous kinetochore, maintain sister chromatid cohesion, regulate chromosome attachment to the spindle, and direct chromosome movement during cell division. Although the functions of centromeres and the proteins that contribute to their complex structure and function are conserved in eukaryotes, centromeric DNA diverges rapidly. Human centromeres are particularly complicated. Here, we review studies on the organization of homogeneous arrays of chromosome-specific alpha-satellite repeats and evolutionary links among eukaryotic centromeric sequences. We also discuss epigenetic mechanisms of centromere identity that confer structural and functional features of the centromere through DNA-protein interactions and post-translational modifications, producing centromere-specific chromatin signatures. The assembly and organization of human centromeres, the contributions of satellite DNA to centromere identity and diversity, and the mechanism whereby centromeres are distinguished from the rest of the genome reflect ongoing puzzles in chromosome biology.
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Affiliation(s)
- Mary G Schueler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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36
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Feliciello I, Picariello O, Chinali G. Intra-specific variability and unusual organization of the repetitive units in a satellite DNA from Rana dalmatina: molecular evidence of a new mechanism of DNA repair acting on satellite DNA. Gene 2006; 383:81-92. [PMID: 16956734 DOI: 10.1016/j.gene.2006.07.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Revised: 07/06/2006] [Accepted: 07/13/2006] [Indexed: 10/24/2022]
Abstract
We have characterized the S1 satellite from eight European populations of Rana dalmatina by Southern blot, cloning and a new method that determines the sequence variability of repetitive units in the genome. This report completes our previous studies on this satellite DNA family, thus providing the first characterization of the overall variability of the structure and genomic organization of a satellite DNA within a species and among related species. The S1 satellite from R. dalmatina has a pericentromeric location on ten chromosome pairs and presents two homologous repeats S1a (494 bp) and S1b (332 bp), mostly organized as composite S1a-S1b repetitive units. In other brown frog species, both repeats have different sequences and locations, and are usually organized as separate arrays, although composite S1a-S1b repeats represent a minor, widely variable component in Rana italica. The average genomic sequences indicate that the species contains an enormous number of variants of each repeat derived from a unique, species-specific common sequence. The repeat variability is restricted to specific base changes in specific sequence positions in all population samples. Our data show that the structure and evolution of S1 satellite family is not due to crossing-over and gene conversion, but to a mechanism that maintains the ability of the satellite DNA to assemble in constitutive heterochromatin by replacing altered satellite segments with new arrays generated by rolling circle amplification. The mode of action of this repair process not only directly explains the intra- and inter-specific variability of the structure and organization of the S1 satellite repeats from European brown frogs, but also accounts for all general features of satellite DNA in eukaryotes, including its discontinuous evolution. This repair mechanism can maintain the satellite structure in a species indefinitely, but also promote a rapid generation of new variants or types of satellite DNA when environmental conditions favor the formation of new species.
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Affiliation(s)
- Isidoro Feliciello
- Dipartimento di Medicina Clinica e Sperimentale, Università di Napoli Federico II, Via Pansini 5, I-80131 Napoli, Italy
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37
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Macas J, Navrátilová A, Koblízková A. Sequence homogenization and chromosomal localization of VicTR-B satellites differ between closely related Vicia species. Chromosoma 2006; 115:437-47. [PMID: 16788823 DOI: 10.1007/s00412-006-0070-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2006] [Revised: 05/04/2006] [Accepted: 05/05/2006] [Indexed: 11/28/2022]
Abstract
Satellite sequences of the VicTR-B family are specific for the genus Vicia (Leguminosae), but their abundance varies among the species, being the highest in Vicia sativa and Vicia grandiflora. In this study, we have sequenced multiple randomly cloned VicTR-B fragments from these two species and analyzed their sequence variability, periodicity, and chromosomal localization. We have found that V. sativa VicTR-B sequences are homogeneous with respect to their nucleotide sequences and periodicity (monomers of 38 bp), whereas V. grandiflora repeats are considerably more variable, occurring in at least four distinct sequence subfamilies. Although the periodicity of 38 bp was conserved in most of the V. grandiflora sequences, one of the subfamilies was composed of higher-order repeats of 186 bp, which originated from a pentamer of the basic repeated unit. Individual VicTR-B subfamilies were preferentially located in either intercalary or subtelomeric regions of chromosomes. Interestingly, two V. grandiflora subfamilies with the highest similarity to V. sativa VicTR-B sequences were located in intercalary heterochromatic bands, showing similar chromosomal distribution as the majority of VicTR-B repeats in V. sativa. The other two V. grandiflora subfamilies showing a considerable divergence from V. sativa sequences were found to be accumulated at subtelomeric regions of V. grandiflora chromosomes.
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Affiliation(s)
- Jirí Macas
- Institute of Plant Molecular Biology, Branisovská 31, Ceské Budejovice, 37005, Czech Republic.
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38
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Roizès G. Human centromeric alphoid domains are periodically homogenized so that they vary substantially between homologues. Mechanism and implications for centromere functioning. Nucleic Acids Res 2006; 34:1912-24. [PMID: 16598075 PMCID: PMC1447651 DOI: 10.1093/nar/gkl137] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Sequence analysis of alphoid repeats from human chromosomes 17, 21 and 13 reveals recurrent diagnostic variant nucleotides. Their combinations define haplotypes, with higher order repeats (HORs) containing identical or closely-related haplotypes tandemly arranged into separate domains. The haplotypes found on homologues can be totally different, while HORs remain 99.8% homogeneous both intrachromosomally and between homologues. These results support the hypothesis, never before demonstrated, that unequal crossovers between sister chromatids accumulate to produce homogenization and amplification into tandem alphoid repeats. I propose that the molecular basis of this involves the diagnostic variant nucleotides, which enable pairing between HORs with identical or closely-related haplotypes. Domains are thus periodically renewed to maintain high intrachromosomal and interhomologue homogeneity. The capacity of a domain to form an active centromere is maintained as long as neither retrotransposons nor significant numbers of mutations affect it. In the presented model, a chromosome with an altered centromere can be transiently rescued by forming a neocentromere, until a restored, fully-competent domain is amplified de novo or rehomogenized through the accumulation of unequal crossovers.
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Affiliation(s)
- Gérard Roizès
- Institut de Génétique Humaine, UPR 1142, CNRS, 141 Rue de la Cardonille, 34396 Montpellier Cedex 5, France.
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Abstract
Alpha-satellite is a family of tandemly repeated sequences found at all normal human centromeres. In addition to its significance for understanding centromere function, alpha-satellite is also a model for concerted evolution, as alpha-satellite repeats are more similar within a species than between species. There are two types of alpha-satellite in the human genome; while both are made up of approximately 171-bp monomers, they can be distinguished by whether monomers are arranged in extremely homogeneous higher-order, multimeric repeat units or exist as more divergent monomeric alpha-satellite that lacks any multimeric periodicity. In this study, as a model to examine the genomic and evolutionary relationships between these two types, we have focused on the chromosome 17 centromeric region that has reached both higher-order and monomeric alpha-satellite in the human genome assembly. Monomeric and higher-order alpha-satellites on chromosome 17 are phylogenetically distinct, consistent with a model in which higher-order evolved independently of monomeric alpha-satellite. Comparative analysis between human chromosome 17 and the orthologous chimpanzee chromosome indicates that monomeric alpha-satellite is evolving at approximately the same rate as the adjacent non-alpha-satellite DNA. However, higher-order alpha-satellite is less conserved, suggesting different evolutionary rates for the two types of alpha-satellite.
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Affiliation(s)
- M Katharine Rudd
- Institute for Genome Sciences & Policy, Duke University, Durham, North Carolina 27708, USA
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40
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Kolas NK, Svetlanov A, Lenzi ML, Macaluso FP, Lipkin SM, Liskay RM, Greally J, Edelmann W, Cohen PE. Localization of MMR proteins on meiotic chromosomes in mice indicates distinct functions during prophase I. ACTA ACUST UNITED AC 2005; 171:447-58. [PMID: 16260499 PMCID: PMC2171243 DOI: 10.1083/jcb.200506170] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mammalian MutL homologues function in DNA mismatch repair (MMR) after replication errors and in meiotic recombination. Both functions are initiated by a heterodimer of MutS homologues specific to either MMR (MSH2-MSH3 or MSH2-MSH6) or crossing over (MSH4-MSH5). Mutations of three of the four MutL homologues (Mlh1, Mlh3, and Pms2) result in meiotic defects. We show herein that two distinct complexes involving MLH3 are formed during murine meiosis. The first is a stable association between MLH3 and MLH1 and is involved in promoting crossing over in conjunction with MSH4-MSH5. The second complex involves MLH3 together with MSH2-MSH3 and localizes to repetitive sequences at centromeres and the Y chromosome. This complex is up-regulated in Pms2-/- males, but not females, providing an explanation for the sexual dimorphism seen in Pms2-/- mice. The association of MLH3 with repetitive DNA sequences is coincident with MSH2-MSH3 and is decreased in Msh2-/- and Msh3-/- mice, suggesting a novel role for the MMR family in the maintenance of repeat unit integrity during mammalian meiosis.
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Affiliation(s)
- Nadine K Kolas
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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41
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Petrović V, Plohl M. Sequence divergence and conservation in organizationally distinct subfamilies of Donax trunculus satellite DNA. Gene 2005; 362:37-43. [PMID: 16216450 DOI: 10.1016/j.gene.2005.06.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2005] [Accepted: 06/03/2005] [Indexed: 10/25/2022]
Abstract
Characterization of a low-copy number DTF1 satellite DNA detected in the bivalve mollusk Donax trunculus revealed extensive grouping of monomer sequence variants into subfamilies identified by distinctive combinations of diagnostic nucleotides. It can be anticipated that a large number of subfamilies exists in the genome. In addition to the tandem organization of 169 bp long monomers, at least one subfamily was created through amplification of adjacent repeats in a higher order register. This complex satellite unit consists of two distinctive monomer variants that differ both in specific nucleotide changes and in a deleted segment partially substituted with a short unrelated sequence element. Most of the nucleotide substitutions differing between subfamilies are highly homogenized within a corresponding group of monomer variants, and intra-subfamily variability in general is low. Nucleotide diversity analysis of all sequenced variants of DTF1 satellite revealed the presence of two conserved segments, while the rest of the monomer sequence shows uniform and considerably higher level of variability. The persistence of conserved segments stands in contrast to the sequence and organizational divergence of monomer variant groups, and may indicate constraints in the evolution of DTF1 satellite repeats.
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Affiliation(s)
- Vlatka Petrović
- Ruder Bosković Institute, Department of Molecular Biology, Bijenicka 54, HR-10002, Zagreb, Croatia
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Schueler MG, Dunn JM, Bird CP, Ross MT, Viggiano L, Rocchi M, Willard HF, Green ED. Progressive proximal expansion of the primate X chromosome centromere. Proc Natl Acad Sci U S A 2005; 102:10563-8. [PMID: 16030148 PMCID: PMC1180780 DOI: 10.1073/pnas.0503346102] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous studies of the pericentromeric region of the human X chromosome short arm (Xp) revealed an age gradient from ancient DNA that contains expressed genes to recent human-specific DNA at the functional centromere. We analyzed the finished sequence of this human genomic region to investigate its evolutionary history. Phylogenetic analysis of >1,500 alpha-satellite monomers from the region revealed the presence of five physical domains, each containing monomers from a distinct phylogenetic clade. The most distal domain contains long interspersed nucleotide element repeats that were active >35 million years ago, whereas the four proximal domains contain more recently active long interspersed nucleotide element repeats. An out-of-register, unequal recombination (i.e., crossover) detected at the edge of the X chromosome-specific alpha-satellite array (DXZ1) may reflect the most recent of a series of punctuating events during evolution that resulted in a proximal physical expansion of the X centromere. The first 18 kb of this array has 97-99% pairwise identity among all 2-kb repeat units. To perform more detailed evolutionary comparisons, we sequenced the junction between the ancient DNA of Xp and the primate-specific alpha satellite in chimpanzee, gorilla, orangutan, vervet, macaque, and baboon. The striking conservation found in all cases supports the ancestral nature of the alpha satellite at this location. These studies demonstrate that the primate X centromere appears to have evolved through repeated expansion events occurring within the central, active region of centromeric DNA, with the newly added sequences then conferring centromere function.
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Affiliation(s)
- Mary G Schueler
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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43
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Laner A, Goussard S, Ramalho AS, Schwarz T, Amaral MD, Courvalin P, Schindelhauer D, Grillot-Courvalin C. Bacterial transfer of large functional genomic DNA into human cells. Gene Ther 2005; 12:1559-72. [PMID: 15973438 DOI: 10.1038/sj.gt.3302576] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Efficient transfer of chromosome-based vectors into mammalian cells is difficult, mostly due to their large size. Using a genetically engineered invasive Escherichia coli vector, alpha satellite DNA cloned in P1-based artificial chromosome was stably delivered into the HT1080 cell line and efficiently generated human artificial chromosomes de novo. Similarly, a large genomic cystic fibrosis transmembrane conductance regulator (CFTR) construct of 160 kb containing a portion of the CFTR gene was stably propagated in the bacterial vector and transferred into HT1080 cells where it was transcribed, and correctly spliced, indicating transfer of an intact and functional locus of at least 80 kb. These results demonstrate that bacteria allow the cloning, propagation and transfer of large intact and functional genomic DNA fragments and their subsequent direct delivery into cells for functional analysis. Such an approach opens new perspectives for gene therapy.
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MESH Headings
- Cell Line, Tumor/metabolism
- Cell Line, Tumor/microbiology
- Chromosomes, Artificial, Bacterial
- Chromosomes, Artificial, Human
- Clone Cells
- DNA, Recombinant/metabolism
- Electroporation
- Escherichia coli/genetics
- Flow Cytometry
- Gene Expression
- Genetic Therapy/methods
- Genetic Vectors/administration & dosage
- Genome, Bacterial
- Humans
- In Situ Hybridization, Fluorescence
- Lung Neoplasms
- Recombination, Genetic
- Reverse Transcriptase Polymerase Chain Reaction
- Sarcoma
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Affiliation(s)
- A Laner
- Department of Medical Genetics, Childrens Hospital, Ludwig Maximilians University, Munich, Germany
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44
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Hall SE, Luo S, Hall AE, Preuss D. Differential rates of local and global homogenization in centromere satellites from Arabidopsis relatives. Genetics 2005; 170:1913-27. [PMID: 15937135 PMCID: PMC1449784 DOI: 10.1534/genetics.104.038208] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Higher eukaryotic centromeres contain thousands of satellite repeats organized into tandem arrays. As species diverge, new satellite variants are homogenized within and between chromosomes, yet the processes by which particular sequences are dispersed are poorly understood. Here, we isolated and analyzed centromere satellites in plants separated from Arabidopsis thaliana by 5-20 million years, uncovering more rapid satellite divergence compared to primate alpha-satellite repeats. We also found that satellites derived from the same genomic locus were more similar to each other than satellites derived from disparate genomic regions, indicating that new sequence alterations were homogenized more efficiently at a local, rather than global, level. Nonetheless, the presence of higher-order satellite arrays, similar to those identified in human centromeres, indicated limits to local homogenization and suggested that sequence polymorphisms may play important functional roles. In two species, we defined more extensive polymorphisms, identifying physically separated and highly distinct satellite types. Taken together, these data show that there is a balance between plant satellite homogenization and the persistence of satellite variants. This balance could ultimately generate sufficient sequence divergence to cause mating incompatibilities between plant species, while maintaining adequate conservation within a species for centromere activity.
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MESH Headings
- Amino Acid Sequence
- Arabidopsis/genetics
- Base Sequence
- Centromere/genetics
- Chromatin Immunoprecipitation
- Consensus Sequence
- DNA, Plant/analysis
- DNA, Satellite/genetics
- DNA, Satellite/metabolism
- Fluorescein-5-isothiocyanate
- Fluorescent Antibody Technique, Direct
- Fluorescent Dyes
- Genome, Plant
- Heterochromatin/metabolism
- In Situ Hybridization, Fluorescence
- Indoles
- Microscopy, Fluorescence
- Molecular Sequence Data
- Phylogeny
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
- Sequence Homology, Nucleic Acid
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Affiliation(s)
- Sarah E Hall
- Howard Hughes Medical Institute, University of Chicago, Chicago, Illinois 60637, USA
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45
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Luchetti A, Marino A, Scanabissi F, Mantovani B. Genomic dynamics of a low-copy-number satellite DNA family in Leptestheria dahalacensis (Crustacea, Branchiopoda, Conchostraca). Gene 2004; 342:313-20. [PMID: 15527990 DOI: 10.1016/j.gene.2004.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 08/06/2004] [Accepted: 08/19/2004] [Indexed: 10/26/2022]
Abstract
The LEP150 satellite DNA (satDNA) family found in Leptestheria dahalacensis (Ruppel, 1837) (Conchostraca) is a low-copy-number satellite with a canonical monomer of 150 bp. Nucleotide variation analyses suggest a 14-bp palindromic region as a possible protein binding site with constraints acting on the whole sequence but a 25-bp variable box. Besides the head-to-tail arrangement of 150 bp monomers, multimers analyses evidenced incomplete monomers, one duplication event, and three inversions. Both observed rearrangements and the higher values of sequence variability scored suggest that rearranged monomers reside in regions with a lower degree of homogenisation efficiency. Sixty-seven percent of the breakpoints occurs at kinkable dinucleotides, thus supporting their role in rearrangements as documented in alphoid satDNA recombination events. Monomers of different lengths may result from crossing over between repeats misaligned through the direct and inverted subrepeats of LEP150 monomers. ANOVA results indicate that the same range of sequence diversity is experienced at the individual and population ranks; therefore, the evolution of the L. dahalacensis satDNA is concerted.
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Affiliation(s)
- Andrea Luchetti
- Dipartimento di Biologia Evoluzionistica Sperimentale, Università di Bologna, Via Selmi 3, Bologna 40126, Italy
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46
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Rudd MK, Schueler MG, Willard HF. Sequence organization and functional annotation of human centromeres. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:141-9. [PMID: 15338612 DOI: 10.1101/sqb.2003.68.141] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- M K Rudd
- Institute for Genome Sciences & Policy, Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA
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47
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Laner A, Schwarz T, Christan S, Schindelhauer D. Suitability of a CMV/EGFP cassette to monitor stable expression from human artificial chromosomes but not transient transfer in the cells forming viable clones. Cytogenet Genome Res 2004; 107:9-13. [PMID: 15305049 DOI: 10.1159/000079564] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 05/28/2004] [Indexed: 11/19/2022] Open
Abstract
Human artificial chromosomes (HACs) were generated by transfer of telomerized PAC constructs containing alpha satellite DNA of various human chromosomes. To monitor which cells took up constructs and subsequently formed stable clones under blasticidin S (BS) selection, a CMV/EGFP expression cassette was inserted into a HAC construct based on chromosome 5 alpha satellite DNA (142 kb). Lipofection into HT1080 cells resulted in a small proportion of cells exhibiting bright green fluorescence on day 1. Areas containing such early green cells were marked, and plates monitored over 2 weeks. In only one out of 41 marked areas, a viable clone developed. In the remaining 40 areas, the green cells ceased division at 1-8 cells. In contrast, outside the marked areas, 16 stable clones formed which did not exhibit green fluorescence during the first cell divisions, but all cells of each became green around day 4-6. Fluorescence in situ hybridization (FISH) analysis of isolated clonal lines demonstrated low copy HAC formation without integration. We conclude that transient expression of an EGFP marker on HAC DNA is not a suitable means for the identification of the proportion of transfected cells which are capable of forming viable clones. One explanation could be that the high copy number required to consistently detect transient EGFP expression (Schindelhauer and Laner, 2002) impairs viability and clone formation.
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Affiliation(s)
- A Laner
- Medical Genetics, Childrens Hospital, Ludwig Maximilians University, Munich, Germany
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48
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Hall AE, Keith KC, Hall SE, Copenhaver GP, Preuss D. The rapidly evolving field of plant centromeres. CURRENT OPINION IN PLANT BIOLOGY 2004; 7:108-14. [PMID: 15003208 DOI: 10.1016/j.pbi.2004.01.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Meiotic and mitotic chromosome segregation are highly conserved in eukaryotic organisms, yet centromeres--the chromosomal sites that mediate segregation--evolve extremely rapidly. Plant centromeres have DNA elements that are shared across species, yet they diverge rapidly through large- and small-scale changes. Over evolutionary time-scales, centromeres migrate to non-centromeric regions and, in plants, heterochromatic knobs can acquire centromere activity. Discerning the functional significance of these changes will require comparative analyses of closely related species. Combined with functional assays, continued efforts in plant genomics will uncover key DNA elements that allow centromeres to retain their role in chromosome segregation while allowing rapid evolution.
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Affiliation(s)
- Anne E Hall
- Department of Molecular Genetics and Cell Biology, The University of Chicago, Chicago, Illinois 60637, USA
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49
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Rudd MK, Mays RW, Schwartz S, Willard HF. Human artificial chromosomes with alpha satellite-based de novo centromeres show increased frequency of nondisjunction and anaphase lag. Mol Cell Biol 2003; 23:7689-97. [PMID: 14560014 PMCID: PMC207596 DOI: 10.1128/mcb.23.21.7689-7697.2003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human artificial chromosomes have been used to model requirements for human chromosome segregation and to explore the nature of sequences competent for centromere function. Normal human centromeres require specialized chromatin that consists of alpha satellite DNA complexed with epigenetically modified histones and centromere-specific proteins. While several types of alpha satellite DNA have been used to assemble de novo centromeres in artificial chromosome assays, the extent to which they fully recapitulate normal centromere function has not been explored. Here, we have used two kinds of alpha satellite DNA, DXZ1 (from the X chromosome) and D17Z1 (from chromosome 17), to generate human artificial chromosomes. Although artificial chromosomes are mitotically stable over many months in culture, when we examined their segregation in individual cell divisions using an anaphase assay, artificial chromosomes exhibited more segregation errors than natural human chromosomes (P < 0.001). Naturally occurring, but abnormal small ring chromosomes derived from chromosome 17 and the X chromosome also missegregate more than normal chromosomes, implicating overall chromosome size and/or structure in the fidelity of chromosome segregation. As different artificial chromosomes missegregate over a fivefold range, the data suggest that variable centromeric DNA content and/or epigenetic assembly can influence the mitotic behavior of artificial chromosomes.
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Affiliation(s)
- M Katharine Rudd
- Department of Genetics, Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA
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