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Gambelli A, Ferrando A, Boncristiani C, Schoeftner S. Regulation and function of R-loops at repetitive elements. Biochimie 2023; 214:141-155. [PMID: 37619810 DOI: 10.1016/j.biochi.2023.08.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/13/2023] [Accepted: 08/19/2023] [Indexed: 08/26/2023]
Abstract
R-loops are atypical, three-stranded nucleic acid structures that contain a stretch of RNA:DNA hybrids and an unpaired, single stranded DNA loop. R-loops are physiological relevant and can act as regulators of gene expression, chromatin structure, DNA damage repair and DNA replication. However, unscheduled and persistent R-loops are mutagenic and can mediate replication-transcription conflicts, leading to DNA damage and genome instability if left unchecked. Detailed transcriptome analysis unveiled that 85% of the human genome, including repetitive regions, hold transcriptional activity. This anticipates that R-loops management plays a central role for the regulation and integrity of genomes. This function is expected to have a particular relevance for repetitive sequences that make up to 75% of the human genome. Here, we review the impact of R-loops on the function and stability of repetitive regions such as centromeres, telomeres, rDNA arrays, transposable elements and triplet repeat expansions and discuss their relevance for associated pathological conditions.
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Affiliation(s)
- Alice Gambelli
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Alessandro Ferrando
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Chiara Boncristiani
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy
| | - Stefan Schoeftner
- Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Via E. Weiss 2, 34127, Trieste, Italy.
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2
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Mirceta M, Shum N, Schmidt MHM, Pearson CE. Fragile sites, chromosomal lesions, tandem repeats, and disease. Front Genet 2022; 13:985975. [PMID: 36468036 PMCID: PMC9714581 DOI: 10.3389/fgene.2022.985975] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 09/02/2022] [Indexed: 09/16/2023] Open
Abstract
Expanded tandem repeat DNAs are associated with various unusual chromosomal lesions, despiralizations, multi-branched inter-chromosomal associations, and fragile sites. Fragile sites cytogenetically manifest as localized gaps or discontinuities in chromosome structure and are an important genetic, biological, and health-related phenomena. Common fragile sites (∼230), present in most individuals, are induced by aphidicolin and can be associated with cancer; of the 27 molecularly-mapped common sites, none are associated with a particular DNA sequence motif. Rare fragile sites ( ≳ 40 known), ≤ 5% of the population (may be as few as a single individual), can be associated with neurodevelopmental disease. All 10 molecularly-mapped folate-sensitive fragile sites, the largest category of rare fragile sites, are caused by gene-specific CGG/CCG tandem repeat expansions that are aberrantly CpG methylated and include FRAXA, FRAXE, FRAXF, FRA2A, FRA7A, FRA10A, FRA11A, FRA11B, FRA12A, and FRA16A. The minisatellite-associated rare fragile sites, FRA10B, FRA16B, can be induced by AT-rich DNA-ligands or nucleotide analogs. Despiralized lesions and multi-branched inter-chromosomal associations at the heterochromatic satellite repeats of chromosomes 1, 9, 16 are inducible by de-methylating agents like 5-azadeoxycytidine and can spontaneously arise in patients with ICF syndrome (Immunodeficiency Centromeric instability and Facial anomalies) with mutations in genes regulating DNA methylation. ICF individuals have hypomethylated satellites I-III, alpha-satellites, and subtelomeric repeats. Ribosomal repeats and subtelomeric D4Z4 megasatellites/macrosatellites, are associated with chromosome location, fragility, and disease. Telomere repeats can also assume fragile sites. Dietary deficiencies of folate or vitamin B12, or drug insults are associated with megaloblastic and/or pernicious anemia, that display chromosomes with fragile sites. The recent discovery of many new tandem repeat expansion loci, with varied repeat motifs, where motif lengths can range from mono-nucleotides to megabase units, could be the molecular cause of new fragile sites, or other chromosomal lesions. This review focuses on repeat-associated fragility, covering their induction, cytogenetics, epigenetics, cell type specificity, genetic instability (repeat instability, micronuclei, deletions/rearrangements, and sister chromatid exchange), unusual heritability, disease association, and penetrance. Understanding tandem repeat-associated chromosomal fragile sites provides insight to chromosome structure, genome packaging, genetic instability, and disease.
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Affiliation(s)
- Mila Mirceta
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Natalie Shum
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Monika H. M. Schmidt
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Christopher E. Pearson
- Program of Genetics and Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, ON, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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3
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Telomeres and Their Neighbors. Genes (Basel) 2022; 13:genes13091663. [PMID: 36140830 PMCID: PMC9498494 DOI: 10.3390/genes13091663] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 11/21/2022] Open
Abstract
Telomeres are essential structures formed from satellite DNA repeats at the ends of chromosomes in most eukaryotes. Satellite DNA repeat sequences are useful markers for karyotyping, but have a more enigmatic role in the eukaryotic cell. Much work has been done to investigate the structure and arrangement of repetitive DNA elements in classical models with implications for species evolution. Still more is needed until there is a complete picture of the biological function of DNA satellite sequences, particularly when considering non-model organisms. Celebrating Gregor Mendel’s anniversary by going to the roots, this review is designed to inspire and aid new research into telomeres and satellites with a particular focus on non-model organisms and accessible experimental and in silico methods that do not require specialized equipment or expensive materials. We describe how to identify telomere (and satellite) repeats giving many examples of published (and some unpublished) data from these techniques to illustrate the principles behind the experiments. We also present advice on how to perform and analyse such experiments, including details of common pitfalls. Our examples are a selection of recent developments and underexplored areas of research from the past. As a nod to Mendel’s early work, we use many examples from plants and insects, especially as much recent work has expanded beyond the human and yeast models traditional in telomere research. We give a general introduction to the accepted knowledge of telomere and satellite systems and include references to specialized reviews for the interested reader.
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Thakur J, Packiaraj J, Henikoff S. Sequence, Chromatin and Evolution of Satellite DNA. Int J Mol Sci 2021; 22:ijms22094309. [PMID: 33919233 PMCID: PMC8122249 DOI: 10.3390/ijms22094309] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 12/15/2022] Open
Abstract
Satellite DNA consists of abundant tandem repeats that play important roles in cellular processes, including chromosome segregation, genome organization and chromosome end protection. Most satellite DNA repeat units are either of nucleosomal length or 5–10 bp long and occupy centromeric, pericentromeric or telomeric regions. Due to high repetitiveness, satellite DNA sequences have largely been absent from genome assemblies. Although few conserved satellite-specific sequence motifs have been identified, DNA curvature, dyad symmetries and inverted repeats are features of various satellite DNAs in several organisms. Satellite DNA sequences are either embedded in highly compact gene-poor heterochromatin or specialized chromatin that is distinct from euchromatin. Nevertheless, some satellite DNAs are transcribed into non-coding RNAs that may play important roles in satellite DNA function. Intriguingly, satellite DNAs are among the most rapidly evolving genomic elements, such that a large fraction is species-specific in most organisms. Here we describe the different classes of satellite DNA sequences, their satellite-specific chromatin features, and how these features may contribute to satellite DNA biology and evolution. We also discuss how the evolution of functional satellite DNA classes may contribute to speciation in plants and animals.
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Affiliation(s)
- Jitendra Thakur
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
- Correspondence:
| | - Jenika Packiaraj
- Department of Biology, Emory University, Atlanta, GA 30322, USA;
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA;
- Fred Hutchinson Cancer Research Center, Howard Hughes Medical Institute, Seattle, WA 98109, USA
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5
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Sugie K, Funaya S, Kawamura M, Nakamura T, Suzuki MG, Aoki F. Expression of Dux family genes in early preimplantation embryos. Sci Rep 2020; 10:19396. [PMID: 33173118 PMCID: PMC7655946 DOI: 10.1038/s41598-020-76538-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 10/27/2020] [Indexed: 12/31/2022] Open
Abstract
After fertilization, the zygotic genome is activated through two phases, minor zygotic activation (ZGA) and major ZGA.
Recently, it was suggested that DUX is expressed during minor ZGA and activates some genes during major ZGA. However, it has not been proven that Dux is expressed during minor ZGA and functions to activate major ZGA genes, because there are several Dux paralogs that may be expressed in zygotes instead of Dux. In this study, we found that more than a dozen Dux paralogs, as well as Dux, are expressed during minor ZGA. Overexpression of some of these genes induced increased expression of major ZGA genes. These results suggest that multiple Dux paralogs are expressed to ensure a sufficient amount of functional Dux and its paralogs which are generated during a short period of minor ZGA with a low transcriptional activity. The mechanism by which multiple Dux paralogs are expressed is discussed.
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Affiliation(s)
- Kenta Sugie
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Satoshi Funaya
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Machika Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Toshinobu Nakamura
- Department of Bio-Science, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Masataka G Suzuki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan
| | - Fugaku Aoki
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimei-Building 302, 5-1-5 Kashiwanoha, Kashiwa, 277-8562, Japan.
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6
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Rahnama M, Novikova O, Starnes JH, Zhang S, Chen L, Farman ML. Transposon-mediated telomere destabilization: a driver of genome evolution in the blast fungus. Nucleic Acids Res 2020; 48:7197-7217. [PMID: 32558886 PMCID: PMC7367193 DOI: 10.1093/nar/gkaa287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 04/03/2020] [Accepted: 04/14/2020] [Indexed: 01/01/2023] Open
Abstract
The fungus Magnaporthe oryzae causes devastating diseases of crops, including rice and wheat, and in various grasses. Strains from ryegrasses have highly unstable chromosome ends that undergo frequent rearrangements, and this has been associated with the presence of retrotransposons (Magnaporthe oryzae Telomeric Retrotransposons-MoTeRs) inserted in the telomeres. The objective of the present study was to determine the mechanisms by which MoTeRs promote telomere instability. Targeted cloning, mapping, and sequencing of parental and novel telomeric restriction fragments (TRFs), along with MinION sequencing of genomic DNA allowed us to document the precise molecular alterations underlying 109 newly-formed TRFs. These included truncations of subterminal rDNA sequences; acquisition of MoTeR insertions by 'plain' telomeres; insertion of the MAGGY retrotransposons into MoTeR arrays; MoTeR-independent expansion and contraction of subtelomeric tandem repeats; and a variety of rearrangements initiated through breaks in interstitial telomere tracts that are generated during MoTeR integration. Overall, we estimate that alterations occurred in approximately sixty percent of chromosomes (one in three telomeres) analyzed. Most importantly, we describe an entirely new mechanism by which transposons can promote genomic alterations at exceptionally high frequencies, and in a manner that can promote genome evolution while minimizing collateral damage to overall chromosome architecture and function.
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Affiliation(s)
- Mostafa Rahnama
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Olga Novikova
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - John H Starnes
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Shouan Zhang
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Li Chen
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
| | - Mark L Farman
- Department of Plant Pathology, University of Kentucky, 1405 Veteran's Dr., Lexington, KY 40546, USA
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7
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Aksenova AY, Mirkin SM. At the Beginning of the End and in the Middle of the Beginning: Structure and Maintenance of Telomeric DNA Repeats and Interstitial Telomeric Sequences. Genes (Basel) 2019; 10:genes10020118. [PMID: 30764567 PMCID: PMC6410037 DOI: 10.3390/genes10020118] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 02/07/2023] Open
Abstract
Tandem DNA repeats derived from the ancestral (TTAGGG)n run were first detected at chromosome ends of the majority of living organisms, hence the name telomeric DNA repeats. Subsequently, it has become clear that telomeric motifs are also present within chromosomes, and they were suitably called interstitial telomeric sequences (ITSs). It is well known that telomeric DNA repeats play a key role in chromosome stability, preventing end-to-end fusions and precluding the recurrent DNA loss during replication. Recent data suggest that ITSs are also important genomic elements as they confer its karyotype plasticity. In fact, ITSs appeared to be among the most unstable microsatellite sequences as they are highly length polymorphic and can trigger chromosomal fragility and gross chromosomal rearrangements. Importantly, mechanisms responsible for their instability appear to be similar to the mechanisms that maintain the length of genuine telomeres. This review compares the mechanisms of maintenance and dynamic properties of telomeric repeats and ITSs and discusses the implications of these dynamics on genome stability.
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Affiliation(s)
- Anna Y Aksenova
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia.
| | - Sergei M Mirkin
- Department of Biology, Tufts University, Medford, MA 02421, USA.
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8
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Choudhury SR, Cui Y, Narayanan A, Gilley DP, Huda N, Lo CL, Zhou FC, Yernool D, Irudayaraj J. Optogenetic regulation of site-specific subtelomeric DNA methylation. Oncotarget 2016; 7:50380-50391. [PMID: 27391261 PMCID: PMC5226589 DOI: 10.18632/oncotarget.10394] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/18/2016] [Indexed: 01/24/2023] Open
Abstract
Telomere length homeostasis, critical for chromosomal integrity and genome stability, is controlled by intricate molecular regulatory machinery that includes epigenetic modifications. Here, we examine site-specific and spatiotemporal alteration of the subtelomeric methylation of CpG islands using optogenetic tools to understand the epigenetic regulatory mechanisms of telomere length maintenance. Human DNA methyltransferase3A (DNMT3A) were assembled selectively at chromosome ends by fusion to cryptochrome 2 protein (CRY2) and its interacting complement, the basic helix loop helix protein-1 (CIB1). CIB1 was fused to the telomere-associated protein telomere repeat binding factor-1 (TRF1), which localized the protein complex DNMT3A-CRY2 at telomeric regions upon excitation by blue-light monitored by single-molecule fluorescence analyses. Increased methylation was achieved selectively at subtelomeric CpG sites on the six examined chromosome ends specifically after blue-light activation, which resulted in progressive increase in telomere length over three generations of HeLa cell replications. The modular design of the fusion constructs presented here allows for the selective substitution of other chromatin modifying enzymes and for loci-specific targeting to regulate the epigenetic pathways at telomeres and other selected genomic regions of interest.
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Affiliation(s)
- Samrat Roy Choudhury
- Department of Agricultural & Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Yi Cui
- Department of Agricultural & Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Anoop Narayanan
- Bindley Laboratory of Structural Biology, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - David P. Gilley
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Nazmul Huda
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Chiao-Ling Lo
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Feng C. Zhou
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Stark Institute of Neuroscience Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Dinesh Yernool
- Bindley Laboratory of Structural Biology, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA
| | - Joseph Irudayaraj
- Department of Agricultural & Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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9
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Mehdipour P, Javan F, Savad S, Karbassian H, Atri M. Personalized evolutionary hypothesis in genomics and auxiliary lymph node through diverse subtelomeric signal profile. Cell Biol Int 2015; 43:1353-1364. [PMID: 25644206 DOI: 10.1002/cbin.10448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/20/2015] [Indexed: 02/05/2023]
Abstract
Few available data on the genomic-somatic evolution in breast cancer create limitation to provide the appropriate clinical managements. As an example, human subtelomeres (ST) are diverse-prone and variable targets. STs, as hot spots, have positive and negative impacts on the status of health and malady. We showed higher subtelomere signal copy number (SCN) of specific chromosomes in genomics than in auxiliary lymph node (ALN). Dissimilarity of signal intensity (SI) is found for all chromosomes. Significantly higher SI in genomics than in ALN cells were specified as chromosomes 5, 6, 9-12, 16-19 for weak; 1, 5-9, 19, X for medium; and 2, 5, 9, 10, 16, 18 for strong SI. For lacking, and presence of one and two SCNs; p/q ratio reflected differences for all chromosomes; but, 2, 3, 5, 7, 8, 10, 16, 18, 20, and X chromosomes were involved for three SCN. Chromosomes 1, 4, 9, 12, 17-19 lacked three SCN in ALN and lymphocytes. Weak SI ratio was higher in p- than in q-arm in majority of chromosomes. Manner of evolution and diversity in p- and q-arms is expressive of a novel definition as two diverse domains with a personalized insight. These data have been accompanied by periodic charts as ST array profiles which provide specific and individualized pattern in breast neoplasm. Such profiling at genomics level could be considered as a prediction through the patients' life. Moreover, subtelomere territory by interacting with protein expression of Ki67, cyclin D1, and cyclin E; and molecular targets including telomere length at genomics and somatic level provides package of information to bridge cancer cell biology to the cancer clinic as "puzzling paradigm."
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Affiliation(s)
- Parvin Mehdipour
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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10
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Martin CL, Ledbetter DH. Molecular cytogenetic analysis of telomere rearrangements. CURRENT PROTOCOLS IN HUMAN GENETICS 2015; 84:8.11.1-8.11.15. [PMID: 25599669 PMCID: PMC4410364 DOI: 10.1002/0471142905.hg0811s84] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several methodologies that can be employed to study these unique regions of human chromosomes. It is a revision of the original version of the unit published in 2000, now including an introductory section describing advances in the discipline that have taken place since the original publication.
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Affiliation(s)
- Christa Lese Martin
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
| | - David H Ledbetter
- Autism and Developmental Medicine Institute, Geisinger Health System, Danville, Pennsylvania
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11
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Stong N, Deng Z, Gupta R, Hu S, Paul S, Weiner AK, Eichler EE, Graves T, Fronick CC, Courtney L, Wilson RK, Lieberman PM, Davuluri RV, Riethman H. Subtelomeric CTCF and cohesin binding site organization using improved subtelomere assemblies and a novel annotation pipeline. Genome Res 2014; 24:1039-50. [PMID: 24676094 PMCID: PMC4032850 DOI: 10.1101/gr.166983.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 03/26/2014] [Indexed: 12/25/2022]
Abstract
Mapping genome-wide data to human subtelomeres has been problematic due to the incomplete assembly and challenges of low-copy repetitive DNA elements. Here, we provide updated human subtelomere sequence assemblies that were extended by filling telomere-adjacent gaps using clone-based resources. A bioinformatic pipeline incorporating multiread mapping for annotation of the updated assemblies using short-read data sets was developed and implemented. Annotation of subtelomeric sequence features as well as mapping of CTCF and cohesin binding sites using ChIP-seq data sets from multiple human cell types confirmed that CTCF and cohesin bind within 3 kb of the start of terminal repeat tracts at many, but not all, subtelomeres. CTCF and cohesin co-occupancy were also enriched near internal telomere-like sequence (ITS) islands and the nonterminal boundaries of subtelomere repeat elements (SREs) in transformed lymphoblastoid cell lines (LCLs) and human embryonic stem cell (ES) lines, but were not significantly enriched in the primary fibroblast IMR90 cell line. Subtelomeric CTCF and cohesin sites predicted by ChIP-seq using our bioinformatics pipeline (but not predicted when only uniquely mapping reads were considered) were consistently validated by ChIP-qPCR. The colocalized CTCF and cohesin sites in SRE regions are candidates for mediating long-range chromatin interactions in the transcript-rich SRE region. A public browser for the integrated display of short-read sequence-based annotations relative to key subtelomere features such as the start of each terminal repeat tract, SRE identity and organization, and subtelomeric gene models was established.
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Affiliation(s)
- Nicholas Stong
- Graduate Group in Genomics and Computational Biology, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Zhong Deng
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Ravi Gupta
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Sufen Hu
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | - Shiela Paul
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Tina Graves
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Catrina C. Fronick
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Laura Courtney
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
| | - Richard K. Wilson
- The Genome Institute, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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12
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Novo C, Arnoult N, Bordes WY, Castro-Vega L, Gibaud A, Dutrillaux B, Bacchetti S, Londoño-Vallejo A. The heterochromatic chromosome caps in great apes impact telomere metabolism. Nucleic Acids Res 2013; 41:4792-801. [PMID: 23519615 PMCID: PMC3643582 DOI: 10.1093/nar/gkt169] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In contrast with the limited sequence divergence accumulated after separation of higher primate lineages, marked cytogenetic variation has been associated with the genome evolution in these species. Studying the impact of such structural variations on defined molecular processes can provide valuable insights on how genome structural organization contributes to organismal evolution. Here, we show that telomeres on chromosome arms carrying subtelomeric heterochromatic caps in the chimpanzee, which are completely absent in humans, replicate later than telomeres on chromosome arms without caps. In gorilla, on the other hand, a proportion of the subtelomeric heterochromatic caps present in most chromosome arms are associated with large blocks of telomere-like sequences that follow a replication program different from that of bona fide telomeres. Strikingly, telomere-containing RNA accumulates extrachromosomally in gorilla mitotic cells, suggesting that at least some aspects of telomere-containing RNA biogenesis have diverged in gorilla, perhaps in concert with the evolution of heterochromatic caps in this species.
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Affiliation(s)
- Clara Novo
- Telomeres and Cancer laboratory, 'Equipe Labellisée Ligue contre le Cancer', UMR3244, Institut Curie, 26 rue d'Ulm, 75248 Paris, France
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Abstract
Anxiety comprises many clinical descriptions and phenotypes. A genetic predisposition to anxiety is undoubted; however, the nature and extent of that contribution is still unclear. Methods for the genetic analysis of such complex disorders is briefly reviewed, followed by a discussion of the comorbidity of anxiety with other psychiatric disorders and their possible common genetic etiology. Extensive genetic studies of the serotonin (5-hydroxytryptamine, 5-HT) transporter (5-HTT) gene have revealed how variation in gene expression can be correlated with anxiety phenotypes. Complete genome-wide linkage scans for panic disorder (PD) susceptibility genes have suggested a locus on chromosome arm 7p, and association studies have highlighted many candidate genes. A highly significant association between phobias, panic disorder, and a duplication at chromosomal region 15q24-26 is one of the most exciting findings to date. Emerging molecular genetic technologies and the use of increasingly sophisticated animal models of anxiety provide great promise for the future of the field.
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14
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Evolution of DUX gene macrosatellites in placental mammals. Chromosoma 2012; 121:489-97. [PMID: 22903800 DOI: 10.1007/s00412-012-0380-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/31/2012] [Accepted: 07/31/2012] [Indexed: 01/21/2023]
Abstract
Macrosatellites are large polymorphic tandem arrays. The human subtelomeric macrosatellite D4Z4 has 11-150 repeats, each containing a copy of the intronless DUX4 gene. DUX4 is linked to facioscapulohumeral muscular dystrophy, but its normal function is unknown. The DUX gene family includes DUX4, the intronless Dux macrosatellites in rat and mouse, as well as several intron-containing members (DUXA, DUXB, Duxbl, and DUXC). Here, we report that the genomic organization (though not the syntenic location) of primate DUX4 is conserved in the Afrotheria. In primates and Afrotheria, DUX4 arose by retrotransposition of an ancestral intron-containing DUXC, which is itself not found in these species. Surprisingly, we discovered a similar macrosatellite organization for DUXC in cow and other Laurasiatheria (dog, alpaca, dolphin, pig, and horse), and in Xenarthra (sloth). Therefore, DUX4 and Dux are not the only DUX gene macrosatellites. Our data suggest a new retrotransposition-displacement model for the evolution of intronless DUX macrosatellites.
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Chow EWL, Morrow CA, Djordjevic JT, Wood IA, Fraser JA. Microevolution of Cryptococcus neoformans driven by massive tandem gene amplification. Mol Biol Evol 2012; 29:1987-2000. [PMID: 22334577 DOI: 10.1093/molbev/mss066] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The subtelomeric regions of organisms ranging from protists to fungi undergo a much higher rate of rearrangement than is observed in the rest of the genome. While characterizing these ~40-kb regions of the human fungal pathogen Cryptococcus neoformans, we have identified a recent gene amplification event near the right telomere of chromosome 3 that involves a gene encoding an arsenite efflux transporter (ARR3). The 3,177-bp amplicon exists in a tandem array of 2-15 copies and is present exclusively in strains with the C. neoformans var. grubii subclade VNI A5 MLST profile. Strains bearing the amplification display dramatically enhanced resistance to arsenite that correlates with the copy number of the repeat; the origin of increased resistance was verified as transport-related by functional complementation of an arsenite transporter mutant of Saccharomyces cerevisiae. Subsequent experimental evolution in the presence of increasing concentrations of arsenite yielded highly resistant strains with the ARR3 amplicon further amplified to over 50 copies, accounting for up to ~1% of the whole genome and making the copy number of this repeat as high as that seen for the ribosomal DNA. The example described here therefore represents a rare evolutionary intermediate-an array that is currently in a state of dynamic flux, in dramatic contrast to relatively common, static relics of past tandem duplications that are unable to further amplify due to nucleotide divergence. Beyond identifying and engineering fungal isolates that are highly resistant to arsenite and describing the first reported instance of microevolution via massive gene amplification in C. neoformans, these results suggest that adaptation through gene amplification may be an important mechanism that C. neoformans employs in response to environmental stresses, perhaps including those encountered during infection. More importantly, the ARR3 array will serve as an ideal model for further molecular genetic analyses of how tandem gene duplications arise and expand.
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Affiliation(s)
- Eve W L Chow
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
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Kar A, Saha D, Purohit G, Singh A, Kumar P, Yadav VK, Kumar P, Thakur RK, Chowdhury S. Metastases suppressor NME2 associates with telomere ends and telomerase and reduces telomerase activity within cells. Nucleic Acids Res 2011; 40:2554-65. [PMID: 22135295 PMCID: PMC3315308 DOI: 10.1093/nar/gkr1109] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Analysis of chromatin-immunoprecipitation followed by sequencing (ChIP-seq) usually disregards sequence reads that do not map within binding positions (peaks). Using an unbiased approach, we analysed all reads, both that mapped and ones that were not included as part of peaks. ChIP-seq experiments were performed in human lung adenocarcinoma and fibrosarcoma cells for the metastasis suppressor non-metastatic 2 (NME2). Surprisingly, we identified sequence reads that uniquely represented human telomere ends in both cases. In vivo presence of NME2 at telomere ends was validated using independent methods and as further evidence we found intranuclear association of NME2 and the telomere repeat binding factor 2. Most remarkably, results demonstrate that NME2 associates with telomerase and reduces telomerase activity in vitro and in vivo, and sustained NME2 expression resulted in reduced telomere length in aggressive human cancer cells. Anti-metastatic function of NME2 has been demonstrated in human cancers, however, mechanisms are poorly understood. Together, findings reported here suggest a novel role for NME2 as a telomere binding protein that can alter telomerase function and telomere length. This presents an opportunity to investigate telomere-related interactions in metastasis suppression.
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Affiliation(s)
- Anirban Kar
- Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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Hirschfeldova K, Baxova A, Kebrdlova V, Solc R, Mihalova R, Lnenicka P, Vesela K, Stekrova J. Cryptic Chromosomal Rearrangements in Children with Idiopathic Mental Retardation in the Czech Population. Genet Test Mol Biomarkers 2011; 15:607-11. [DOI: 10.1089/gtmb.2010.0218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Affiliation(s)
- Katerina Hirschfeldova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Alice Baxova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Vera Kebrdlova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Roman Solc
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Romana Mihalova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Petr Lnenicka
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Kamila Vesela
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
| | - Jitka Stekrova
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine and General Teaching Hospital, Charles University in Prague, Prague, Czech Republic
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Theisen A, Shaffer LG. Disorders caused by chromosome abnormalities. APPLICATION OF CLINICAL GENETICS 2010; 3:159-74. [PMID: 23776360 PMCID: PMC3681172 DOI: 10.2147/tacg.s8884] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Many human genetic disorders result from unbalanced chromosome abnormalities, in which there is a net gain or loss of genetic material. Such imbalances often disrupt large numbers of dosage-sensitive, developmentally important genes and result in specific and complex phenotypes. Alternately, some chromosomal syndromes may be caused by a deletion or duplication of a single gene with pleiotropic effects. Traditionally, chromosome abnormalities were identified by visual inspection of the chromosomes under a microscope. The use of molecular cytogenetic technologies, such as fluorescence in situ hybridization and microarrays, has allowed for the identification of cryptic or submicroscopic imbalances, which are not visible under the light microscope. Microarrays have allowed for the identification of numerous new syndromes through a genotype-first approach in which patients with the same or overlapping genomic alterations are identified and then the phenotypes are described. Because many chromosomal alterations are large and encompass numerous genes, the ascertainment of individuals with overlapping deletions and varying clinical features may allow researchers to narrow the region in which to search for candidate genes.
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Dhillon B, Cavaletto JR, Wood KV, Goodwin SB. Accidental amplification and inactivation of a methyltransferase gene eliminates cytosine methylation in Mycosphaerella graminicola. Genetics 2010; 186:67-77. [PMID: 20610411 PMCID: PMC2940312 DOI: 10.1534/genetics.110.117408] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A de novo search for repetitive elements in the genome sequence of the wheat pathogen Mycosphaerella graminicola identified a family of repeats containing a DNA cytosine methyltransferase sequence (MgDNMT). All 23 MgDNMT sequences identified carried signatures of repeat induced point mutation (RIP). All copies were subtelomeric in location except for one on chromosome 6. Synteny with M. fijiensis implied that the nontelomeric copy on chromosome 6 served as a template for subsequent amplifications. Southern analysis revealed that the MgDNMT sequence also was amplified in 15 additional M. graminicola isolates from various geographical regions. However, this amplification event was specific to M. graminicola; a search for MgDNMT homologs identified only a single, unmutated copy in the genomes of 11 other ascomycetes. A genome-wide methylation assay revealed that M. graminicola lacks cytosine methylation, as expected if its MgDNMT gene is inactivated. Methylation was present in several other species tested, including the closest known relatives of M. graminicola, species S1 and S2. Therefore, the observed changes most likely occurred within the past 10,500 years since the divergence between M. graminicola and S1. Our data indicate that the recent amplification of a single-copy MgDNMT gene made it susceptible to RIP, resulting in complete loss of cytosine methylation in M. graminicola.
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Affiliation(s)
- Braham Dhillon
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana 47907, USA
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Soto J, Peña Á, Salcedo M, Domínguez MC, Sánchez A, García-Vallejo F. Caracterización genómica de la integración in vitro del VIH-1 en células mononucleares de sangre periférica, macrófagos y células T de Jurkat. INFECTIO 2010. [DOI: 10.1016/s0123-9392(10)70089-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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In Saccharomyces cerevisiae, yKu and subtelomeric core X sequences repress homologous recombination near telomeres as part of the same pathway. Genetics 2009; 183:441-51, 1SI-12SI. [PMID: 19652177 DOI: 10.1534/genetics.109.106674] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Unlike in meiosis where recombination near telomeres is repressed, subtelomeric regions appear to recombine with each other frequently in vegetative cells with no detrimental consequences. To test whether or not such recombination is prevented in the core of chromosomes for maintenance of genome stability, we measured allelic homologous recombination (HR) along chromosome arms and between different ectopic locations. We found that there is an increase of recombination at telomeres in wild-type cells compared with sequences at proximal subtelomeric and interstitial regions of the genome. We also screened for mutations that result in an increase in HR between a telomeric sequence and a more internal sequence, which normally exhibit very low rates of HR. YKU80 was hit most frequently in our screen, and we show that the yKu heterodimer specifically represses HR in the vicinity of telomeres. This repression of HR is not explained solely by the role of yKu in maintaining telomere length, silencing, or tethering to the nuclear periphery. Analysis of mutant strains harboring deleted core X sequences revealed a role for this subtelomeric element in preventing telomeric recombination. Furthermore, core X bestowed this protection as part of the same pathway as yKu. Our findings implicate a role for both yKu and core X in stabilizing the genome against recombination events involving telomeric sequences.
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22
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Costa V, Casamassimi A, Roberto R, Gianfrancesco F, Matarazzo MR, D'Urso M, D'Esposito M, Rocchi M, Ciccodicola A. DDX11L: a novel transcript family emerging from human subtelomeric regions. BMC Genomics 2009; 10:250. [PMID: 19476624 PMCID: PMC2705379 DOI: 10.1186/1471-2164-10-250] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Accepted: 05/28/2009] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND The subtelomeric regions of human chromosomes exhibit an extraordinary plasticity. To date, due to the high GC content and to the presence of telomeric repeats, the subtelomeric sequences are underrepresented in the genomic libraries and consequently their sequences are incomplete in the finished human genome sequence, and still much remains to be learned about subtelomere organization, evolution and function. Indeed, only in recent years, several studies have disclosed, within human subtelomeres, novel gene family members. RESULTS During a project aimed to analyze genes located in the telomeric region of the long arm of the human X chromosome, we have identified a novel transcript family, DDX11L, members of which map to 1pter, 2q13/14.1, 2qter, 3qter, 6pter, 9pter/9qter, 11pter, 12pter, 15qter, 16pter, 17pter, 19pter, 20pter/20qter, Xpter/Xqter and Yqter. Furthermore, we partially sequenced the underrepresented subtelomeres of human chromosomes showing a common evolutionary origin. CONCLUSION Our data indicate that an ancestral gene, originated as a rearranged portion of the primate DDX11 gene, and propagated along many subtelomeric locations, is emerging within subtelomeres of human chromosomes, defining a novel gene family. These findings support the possibility that the high plasticity of these regions, sites of DNA exchange among different chromosomes, could trigger the emergence of new genes.
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Affiliation(s)
- Valerio Costa
- Institute of Genetics and Biophysics A, Buzzati-Traverso , CNR, 80131 Naples, Italy.
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23
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Yatsenko SA, Brundage EK, Roney EK, Cheung SW, Chinault AC, Lupski JR. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet 2009; 18:1924-36. [PMID: 19293338 DOI: 10.1093/hmg/ddp114] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We characterized at the molecular level the genomic rearrangements in 28 unrelated patients with 9q34.3 subtelomeric deletions. Four distinct categories were delineated: terminal deletions, interstitial deletions, derivative chromosomes and complex rearrangements; each results in haploinsufficiency of the EHMT1 gene and a characteristic phenotype. Interestingly, 25% of our patients had de novo interstitial deletions, 25% were found with derivative chromosomes and complex rearrangements and only 50% were bona fide terminal deletions. In contrast to genomic disorders that are often associated with recurrent rearrangements, breakpoints involving the 9q34.3 subtelomere region are highly variable. Molecular studies identified three regions of breakpoint grouping. Interspersed repetitive elements such as Alu, LINE, long-terminal repeats and simple tandem repeats are frequently observed at the breakpoints. Such repetitive elements may play an important role by providing substrates with a specific DNA secondary structure that stabilizes broken chromosomes or assist in either DNA double-strand break repair or repair of single double-strand DNA ends generated by collapsed forks. Sequence analyses of the breakpoint junctions suggest that subtelomeric deletions can be stabilized by both homologous and nonhomologous recombination mechanisms, through a telomere-capture event, by de novo telomere synthesis, or multistep breakage-fusion-bridge cycles.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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24
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Riethman H. Human subtelomeric copy number variations. Cytogenet Genome Res 2009; 123:244-52. [PMID: 19287161 DOI: 10.1159/000184714] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/23/2008] [Indexed: 01/15/2023] Open
Abstract
Copy number variation is a defining characteristic of human subtelomeres. Human subtelomeric segmental duplication regions ('Subtelomeric Repeats') comprise about 25% of the most distal 500 kb and 80% of the most distal 100 kb in human DNA. Huge allelic disparities seen in subtelomeric DNA sequence content and organization are postulated to have an impact on the dosage of transcripts embedded within the duplicated sequences, on the transcription of genes in adjacent single copy DNA regions, and on the chromatin structures mediating telomere functions including chromosome stability. In addition to the complex duplicon substructure and huge allelic variations in extended subtelomere regions, both copy number variation and alternative sequence organizations for DNA characterize the sequences immediately adjacent to terminal (TTAGGG)n tracts ('subterminal DNA'). The structural variation in subterminal DNA is likely to have important consequences for expression of subterminal transcripts such as a newly-discovered gene family encoding actin-interacting proteins and a non-coding telomeric repeat containing RNA (TERRA) transcript family critical for telomere integrity. Major immediate challenges include discovering the full extent and nature of subtelomeric structural and copy number variation in humans, and developing methods for tracking individual allelic variants in the context of total genomic DNA.
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Affiliation(s)
- H Riethman
- The Wistar Institute, Philadelphia, PA, USA
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25
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Subtelomeric DNA hypomethylation is not required for telomeric sister chromatid exchanges in ALT cells. Oncogene 2009; 28:1682-93. [PMID: 19252523 DOI: 10.1038/onc.2009.23] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Most human tumor cells acquire immortality by activating the expression of telomerase, a ribonucleoprotein that maintains stable telomere lengths at chromosome ends throughout cell divisions. Other tumors use an alternative mechanism of telomere lengthening (ALT), characterized by high frequencies of telomeric sister chromatid exchanges (T-SCEs). Mechanisms of ALT activation are still poorly understood, but recent studies suggest that DNA hypomethylation of chromosome ends might contribute to the process by facilitating T-SCEs. Here, we show that ALT/T-SCE(high) tumor cells display low DNA-methylation levels at the D4Z4 and DNF92 subtelomeric sequences. Surprisingly, however, the same sequences retained high methylation levels in ALT/T-SCE(high) SV40-immortalized fibroblasts. Moreover, T-SCE rates were efficiently reduced by ectopic expression of active telomerase in ALT tumor cells, even though subtelomeric sequences remained hypomethylated. We also show that hypomethylation of subtelomeric sequences in ALT tumor cells is correlated with genome-wide hypomethylation of Alu repeats and pericentromeric Sat2 DNA sequences. Overall, this study suggests that, although subtelomeric DNA hypomethylation is often coincident with the ALT process in human tumor cells, it is not required for T-SCE.
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Abstract
Human telomeric DNA is complex and highly variable. Subterminal sequences are associated with cis-acting determinants of allele-specific (TTAGGG)n tract length regulation and may modulate susceptibility of (TTAGGG)n tracts to rapid deletion events. More extensive subtelomeric DNA tracts are filled with segmental duplications and segments that vary in copy number, leading to highly variable subtelomeric allele structures in the human population. RNA transcripts encoded in telomere regions include multicopy protein-encoding gene families and a variety of noncoding RNAs. One recently described family of (UUAGGG)n-containing subterminal RNAs appears to be critical for telomere integrity; these RNAs associate with telomeric chromatin and are regulated by RNA surveillance factors including human homologs of the yeast Est1p protein. An increasingly detailed and complete picture of telomeric DNA sequence organization and structural variation is essential for understanding and tracking allele-specific subterminal and subtelomeric features critical for human biology.
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Affiliation(s)
- Harold Riethman
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
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27
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Lese CM, Ledbetter DH. Molecular cytogenetic analysis of telomere rearrangements. ACTA ACUST UNITED AC 2008; Chapter 8:Unit 8.11. [PMID: 18428312 DOI: 10.1002/0471142905.hg0811s24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genomic imbalances involving the telomeric regions of human chromosomes, which contain the highest gene concentration in the genome, are proposed to have severe phenotypic consequences. For this reason, it is important to identify telomere rearrangements and assess their contribution to human pathology. This unit describes the structure and function of human telomeres and outlines several FISH-based methodologies that can be employed to study these unique regions of human chromosomes.
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Affiliation(s)
- C M Lese
- The University of Chicago, Chicago, Illinois, USA
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28
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Abstract
DNA sequence surveys in yeast and humans suggest that the forces shaping telomeric polymorphism and divergence are distinctly more dynamic than those in the euchromatic, gene-rich regions of the chromosomes. However, the generality of this pattern across outbreeding, multicellular eukaryotes has not been determined. To characterize the structure and evolution of Drosophila telomeres, we collected and analyzed molecular population genetics data from the X chromosome subtelomere in 58 lines of North American Drosophila melanogaster and 29 lines of African D. melanogaster. We found that Drosophila subtelomeres exhibit high levels of both structural and substitutional polymorphism relative to linked euchromatic regions. We also observed strikingly different patterns of variation in the North American and African samples. Moreover, our analyses of the polymorphism data identify a localized hotspot of recombination in the most-distal portion of the X subtelomere. While the levels of polymorphism decline sharply and in parallel with rates of crossing over per physical length over the distal first euchromatic megabase pairs of the X chromosome, our data suggest that they rise again sharply in the subtelomeric region (approximately 80 kbp). These patterns of historical recombination and geographic differentiation indicate that, similar to yeast and humans, Drosophila subtelomeric DNA is evolving very differently from euchromatic DNA.
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29
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Ambrosini A, Paul S, Hu S, Riethman H. Human subtelomeric duplicon structure and organization. Genome Biol 2008; 8:R151. [PMID: 17663781 PMCID: PMC2323237 DOI: 10.1186/gb-2007-8-7-r151] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 06/25/2007] [Accepted: 07/30/2007] [Indexed: 01/27/2023] Open
Abstract
The sequence divergence within subtelomeric duplicon families varies considerably, as does the organization of duplicon blocks at subtelomere alleles; a class of duplicon blocks was identified that are subtelomere-specific. Background Human subtelomeric segmental duplications ('subtelomeric repeats') comprise about 25% of the most distal 500 kb and 80% of the most distal 100 kb in human DNA. A systematic analysis of the duplication substructure of human subtelomeric regions was done in order to develop a detailed understanding of subtelomeric sequence organization and a nucleotide sequence-level characterization of subtelomeric duplicon families. Results The extent of nucleotide sequence divergence within subtelomeric duplicon families varies considerably, as does the organization of duplicon blocks at subtelomere alleles. Subtelomeric internal (TTAGGG)n-like tracts occur at duplicon boundaries, suggesting their involvement in the generation of the complex sequence organization. Most duplicons have copies at both subtelomere and non-subtelomere locations, but a class of duplicon blocks is identified that are subtelomere-specific. In addition, a group of six subterminal duplicon families are identified that, together with six single-copy telomere-adjacent segments, include all of the (TTAGGG)n-adjacent sequence identified so far in the human genome. Conclusion Identification of a class of duplicon blocks that is subtelomere-specific will facilitate high-resolution analysis of subtelomere repeat copy number variation as well as studies involving somatic subtelomere rearrangements. The significant levels of nucleotide sequence divergence within many duplicon families as well as the differential organization of duplicon blocks on subtelomere alleles may provide opportunities for allele-specific subtelomere marker development; this is especially true for subterminal regions, where divergence and organizational differences are the greatest. These subterminal sequence families comprise the immediate cis-elements for (TTAGGG)n tracts, and are prime candidates for subtelomeric sequences regulating telomere-specific (TTAGGG)n tract length in humans.
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Affiliation(s)
- Anthony Ambrosini
- The Wistar Institute, Spruce St, Philadelphia, PA 19104, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Sheila Paul
- The Wistar Institute, Spruce St, Philadelphia, PA 19104, USA
| | - Sufen Hu
- The Wistar Institute, Spruce St, Philadelphia, PA 19104, USA
| | - Harold Riethman
- The Wistar Institute, Spruce St, Philadelphia, PA 19104, USA
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Endings in the middle: current knowledge of interstitial telomeric sequences. Mutat Res 2007; 658:95-110. [PMID: 17921045 DOI: 10.1016/j.mrrev.2007.08.006] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 08/28/2007] [Accepted: 08/30/2007] [Indexed: 01/24/2023]
Abstract
Interstitial telomeric sequences (ITSs) consist of tandem repeats of the canonical telomeric repeat and are common in mammals. They are localized at intrachromosomal sites, including those repeats located close to the centromeres and those found at interstitial sites, i.e., between the centromeres and the telomeres. ITSs might originate from ancestral intrachromosomal rearrangements (inversions and fusions), from differential crossing-over or from the repair of double-strand break during evolution. Three classes of ITSs have been described in the human genome, namely, short ITSs, long subtelomeric ITSs and fusion ITSs. The fourth class of ITSs, pericentromeric ITSs, has been found in other species. The function of ITSs can be inferred from the association of heritable diseases with ITS polymorphic variants, both in copy number and sequence. This is one of the most attractive aspects of ITS studies because it leads to new and useful markers for genetic linkage studies, forensic applications, and detection of genetic instability in tumors. Some ITSs also might be hotspots of chromosome breakage, rearrangement and amplification sites, based on the type of clastogens and the nature of ITSs. This study will contribute new knowledge with respect to ITSs' biology and mechanism, prevalence of diseases, risk evaluation and prevention of related diseases, thus facilitates the design of early detection markers for diseases caused by genomic instability.
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31
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Farman ML. Telomeres in the rice blast fungus Magnaporthe oryzae: the world of the end as we know it. FEMS Microbiol Lett 2007; 273:125-32. [PMID: 17610516 DOI: 10.1111/j.1574-6968.2007.00812.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
The subtelomeres of many microbial eukaryotes are highly enriched in genes with roles in niche adaptation. Host and cultivar specificity genes in the rice blast fungus Magnaporthe oryzae also tend to be located near telomeres. In addition, the M. oryzae telomeres are highly variable chromosome regions. These observations suggested that plant pathogenic fungi might also use subtelomere regions for the amplification of genes with adaptive significance. Targeted sequencing of the M. oryzae telomeres provided an opportunity to test this hypothesis, and has yielded valuable insights into the organization and dynamics of these important chromosome regions.
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Affiliation(s)
- Mark L Farman
- Department of Plant Pathology, University of Kentucky, Lexington, KY 40503, USA.
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32
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Zhdanova NS, Rubtsov NB, Minina YM. Terminal regions of mammal chromosomes: Plasticity and role in evolution. RUSS J GENET+ 2007. [DOI: 10.1134/s1022795407070022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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33
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Hills M, Jeyapalan JN, Foxon JL, Royle NJ. Mutation mechanisms that underlie turnover of a human telomere-adjacent segmental duplication containing an unstable minisatellite. Genomics 2007; 89:480-9. [PMID: 17270395 DOI: 10.1016/j.ygeno.2006.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2006] [Revised: 11/02/2006] [Accepted: 12/30/2006] [Indexed: 11/29/2022]
Abstract
Subterminal regions, juxtaposed to telomeres on human chromosomes, contain a high density of segmental duplications, but relatively little is known about the evolutionary processes that underlie sequence turnover in these regions. We have characterized a segmental duplication adjacent to the Xp/Yp telomere, each copy containing a hypervariable array of the DXYS14 minisatellite. Both DXYS14 repeat arrays mutate at a high rate (0.3 and 0.2% per gamete) but linkage disequilibrium analysis across 27 SNPs and a direct crossover assay show that recombination during meiosis is suppressed. Therefore instability at DXYS14a and b is dominated by intra-allelic processes or possibly conversion limited to the repeat arrays. Furthermore some chromosomes (14%) carry only one copy of the duplicon, including one DXYS14 repeat array that is also highly mutable (1.2% per gamete). To explain these and other observations, we propose there is another low-rate mutation process that causes copy number change in part or all of the duplicon.
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Affiliation(s)
- Mark Hills
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
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Mignon-Ravix C, Depetris D, Luciani JJ, Cuoco C, Krajewska-Walasek M, Missirian C, Collignon P, Delobel B, Croquette MF, Moncla A, Kroisel PM, Mattei MG. Recurrent rearrangements in the proximal 15q11–q14 region: a new breakpoint cluster specific to unbalanced translocations. Eur J Hum Genet 2007; 15:432-40. [PMID: 17264869 DOI: 10.1038/sj.ejhg.5201775] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Unbalanced translocations, that involve the proximal chromosome 15 long arm and the telomeric region of a partner chromosome, result in a karyotype of 45 chromosomes with monosomy of the proximal 15q imprinted region. Here, we present our analysis of eight such unbalanced translocations that, depending on the parental origin of the rearranged chromosome, were associated with either Prader-Willi or Angelman syndrome. First, using FISH with specific BAC clones, we characterized the chromosome 15 breakpoint of each translocation and demonstrate that four of them are clustered in a small 460 kb interval located in the proximal 15q14 band. Second, analyzing the sequence of this region, we demonstrate the proximity of a low-copy repeat 15 (LCR15)-duplicon element that is known to facilitate recombination events at meiosis and to promote rearrangements. The presence, in this region, of both a cluster of translocation breakpoints and a LCR15-duplicon element defines a new breakpoint cluster (BP6), which, to our knowledge, is the most distal breakpoint cluster described in proximal 15q. Third, we demonstrate that the breakpoints for other rearrangements including large inv dup (15) chromosomes do not map to BP6, suggesting that it is specific to translocations. Finally, the translocation breakpoints located within BP6 result in very large proximal 15q deletions providing new informative genotype-phenotype correlations.
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Affiliation(s)
- Cécile Mignon-Ravix
- INSERM U491, Université de la Méditerranée, Faculté de Médecine de la Timone, Marseille, France
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35
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Rehmeyer C, Li W, Kusaba M, Kim YS, Brown D, Staben C, Dean R, Farman M. Organization of chromosome ends in the rice blast fungus, Magnaporthe oryzae. Nucleic Acids Res 2006; 34:4685-701. [PMID: 16963777 PMCID: PMC1635262 DOI: 10.1093/nar/gkl588] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Eukaryotic pathogens of humans often evade the immune system by switching the expression of surface proteins encoded by subtelomeric gene families. To determine if plant pathogenic fungi use a similar mechanism to avoid host defenses, we sequenced the 14 chromosome ends of the rice blast pathogen, Magnaporthe oryzae. One telomere is directly joined to ribosomal RNA-encoding genes, at the end of the ∼2 Mb rDNA array. Two are attached to chromosome-unique sequences, and the remainder adjoin a distinct subtelomere region, consisting of a telomere-linked RecQ-helicase (TLH) gene flanked by several blocks of tandem repeats. Unlike other microbes, M.oryzae exhibits very little gene amplification in the subtelomere regions—out of 261 predicted genes found within 100 kb of the telomeres, only four were present at more than one chromosome end. Therefore, it seems unlikely that M.oryzae uses switching mechanisms to evade host defenses. Instead, the M.oryzae telomeres have undergone frequent terminal truncation, and there is evidence of extensive ectopic recombination among transposons in these regions. We propose that the M.oryzae chromosome termini play more subtle roles in host adaptation by promoting the loss of terminally-positioned genes that tend to trigger host defenses.
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Affiliation(s)
- Cathryn Rehmeyer
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Weixi Li
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Motoaki Kusaba
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Yun-Sik Kim
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
| | - Doug Brown
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Chuck Staben
- Department of Biology, University of KentuckyLexington, KY 40546 USA
| | - Ralph Dean
- Center for Integrated Fungal Research, North Carolina State UniversityRaleigh, NC 27695 USA
| | - Mark Farman
- Department of Plant Pathology, University of KentuckyLexington, KY 40546 USA
- To whom correspondence should be addressed. Tel: 859 257 7445, ext. 80728; Fax: 859 323 1961;
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Kuo HF, Olsen KM, Richards EJ. Natural variation in a subtelomeric region of Arabidopsis: implications for the genomic dynamics of a chromosome end. Genetics 2006; 173:401-17. [PMID: 16547105 PMCID: PMC1461430 DOI: 10.1534/genetics.105.055202] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2005] [Accepted: 03/07/2006] [Indexed: 11/18/2022] Open
Abstract
We investigated genome dynamics at a chromosome end in the model plant Arabidopsis thaliana through a study of natural variation in 35 wild accessions. We focused on the single-copy subtelomeric region of chromosome 1 north (approximately 3.5 kb), which represents the relatively simple organization of subtelomeric regions in this species. PCR fragment-length variation across the subtelomeric region indicated that the 1.4-kb distal region showed elevated structural variation relative to the centromere-proximal region. Examination of nucleotide sequences from this 1.4-kb region revealed diverse DNA rearrangements, including an inversion, several deletions, and an insertion of a retrotransposon LTR. The structures at the deletion and inversion breakpoints are characteristic of simple deletion-associated nonhomologous end-joining (NHEJ) events. There was strong linkage disequilibrium between the distal subtelomeric region and the proximal telomere, which contains degenerate and variant telomeric repeats. Variation in the proximal telomere was characterized by the expansion and deletion of blocks of repeats. Our sample of accessions documented two independent chromosome-healing events associated with terminal deletions of the subtelomeric region as well as the capture of a scrambled mitochondrial DNA segment in the proximal telomeric array. This natural variation study highlights the variety of genomic events that drive the fluidity of chromosome termini.
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Affiliation(s)
- Hui-Fen Kuo
- Department of Biology, Washington University, St. Louis, Missouri 63130, USA
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Gignac J, Danis K, Tihy F, Lemyre E. Prenatal detection of subtelomeric rearrangements by multi-subtelomere FISH in a cohort of fetuses with major malformations. Am J Med Genet A 2006; 140:2768-75. [PMID: 17103433 DOI: 10.1002/ajmg.a.31472] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Cryptic unbalanced subtelomeric rearrangements have been identified as an important contributor ( approximately 6%) to the etiology of mental retardation and dysmorphism. Our objective was to study the role of these rearrangements in the development of fetal malformations. Multi-subtelomere FISH was performed on cells from 48 fetuses with major malformations diagnosed by prenatal ultrasound with a normal karyotype at a minimal 400 band resolution. We developed a method of performing multi-subtelomere FISH on a single slide of amniocyte metaphase spreads. We identified five subtelomeric abnormalities: two derivative chromosomes inherited from a parent carrying a balanced translocation, two known polymorphisms, and one novel familial variant. These results show a similar frequency (4%) of clinically significant subtelomeric rearrangements to that found in children with multiple malformations. This study adds to a growing number of reports of cryptic subtelomeric rearrangements associated with congenital malformations and highlights the relevance and technical feasibility of multi-subtelomere FISH screening of prenatal samples.
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Affiliation(s)
- Jennifer Gignac
- Laboratoire de Cytogénétique Prénatale, Service de Génétique Médicale, CHU Sainte-Justine, Montréal, Québec, Canada
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Abstract
Work towards completion of the human reference genome sequence has revealed a great deal of complexity and plasticity in human subtelomeric regions. The highly variable subtelomeric repeat regions are filled with recently shuffled genomic segments, many of which contain sequences matching transcripts and transcript fragments; the rapid duplication and combinatorial evolution of these regions has generated an extremely diverse set of subtelomeric alleles in the human species, the complexity and potential significance of which is only beginning to be understood. This review summarizes recent progress in analyzing human subtelomeric sequence assemblies and large-scale variation in human subtelomere regions.
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Affiliation(s)
- H Riethman
- Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA.
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Amiel A, Goldzak G, Gaber E, Yosef G, Fejgin MD, Yukla M, Lishner M. Random aneuploidy and telomere capture in chronic lymphocytic leukemia and chronic myeloid leukemia patients. ACTA ACUST UNITED AC 2005; 163:12-6. [PMID: 16271950 DOI: 10.1016/j.cancergencyto.2005.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 04/12/2005] [Accepted: 04/13/2005] [Indexed: 11/25/2022]
Abstract
Telomeric regions of the human genome are of particular interest, because rearrangements of these regions are difficult to identify by conventional chromosome banding technology. With the advent of molecular cytogenetic techniques such as fluorescence in situ hybridization (FISH), it has been possible to investigate the terminus in cytogenetically visible terminal deletions and telomere rearrangements. We investigated telomere capture and aneuploidy rates in chronic lymphocytic leukemia (CLL) and chronic myeloid leukemia (CML) patients, as well as in healthy control subsets. Using a FISH technique, we estimated the random aneuploidy and telomere capture of the 21q22, SNRPN, and 15qter loci. Higher aneuploidy rates were found in the leukocytes of CLL and CML patients, compared with the control group, for the 21q22 and SNRPN loci. There was no difference in the aneuploidy rate between the CML and CLL groups. Telomere capture was found in the two groups (CLL and CML), but not in the control group. We propose that the telomere capture phenomenon is much more common than has been reported in the literature; however, its prognostic significance is yet to be established.
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MESH Headings
- Aged
- Aged, 80 and over
- Aneuploidy
- Bone Marrow Cells/pathology
- Chromosome Mapping
- Chromosomes, Human, Pair 15
- Chromosomes, Human, Pair 21
- Humans
- In Situ Hybridization, Fluorescence
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Middle Aged
- Telomere/genetics
- Translocation, Genetic
- Trisomy
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Affiliation(s)
- A Amiel
- Genetic Institute, Meir Medical Center, Kfar-Saba 44281, Israel.
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Pinson L, Perrin A, Plouzennec C, Parent P, Metz C, Collet M, Le Bris MJ, Douet-Guilbert N, Morel F, De Braekeleer M. Detection of an unexpected subtelomeric 15q26.2 --> qter deletion in a little girl: clinical and cytogenetic studies. Am J Med Genet A 2005; 138A:160-5. [PMID: 16114049 DOI: 10.1002/ajmg.a.30939] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Unlike the small proximal 15q deletions causing Prader-Willi and/or Angelman syndrome, distal deletions of the terminal long arm of chromosome 15 have rarely been described. To the best of our knowledge, only four patients with a pure terminal 15q deletion have been documented in the literature. We report here on an unexpected abnormal hybridization pattern for the 15q specific subtelomeric control probe (clone 154P1) of the commercial SNRPN probe in a girl referred for suspicion of Angelman syndrome. Investigation by fluorescent in situ hybridization (FISH) using bacterial artificial chromosome (BAC) clones defined a partial monosomy 15q26.2 --> 15qter for a minimal critical region of approximately 5.7 Mb, which is the most distal de novo 15qter deletion reported to date. All the de novo 15qter deletion cases, including ours, presented with pre- and post-natal growth retardation related to the loss of one copy of the IGF1R gene. Based on the comparaison with the previous published cases and owing to the clinical phenotype of our patient, we define a new subtelomeric 15qter syndrome which would be characterized by intrauterine growth retardation and global post-natal growth failure, variable mental retardation, facial anomalies including relative micrognathia and triangular facies and minor malformations of the extremities including proximally placed thumbs, cubitus valgus, and brachydactyly with tappering of the digits.
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Affiliation(s)
- L Pinson
- Laboratoire d'Histologie, Embryologie et Cytogénétique, Faculté de Médecine et des Sciences de la Santé, Université de Bretagne Occidentale, Brest, France
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41
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Linardopoulou EV, Williams EM, Fan Y, Friedman C, Young JM, Trask BJ. Human subtelomeres are hot spots of interchromosomal recombination and segmental duplication. Nature 2005; 437:94-100. [PMID: 16136133 PMCID: PMC1368961 DOI: 10.1038/nature04029] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2005] [Accepted: 07/05/2005] [Indexed: 01/09/2023]
Abstract
Human subtelomeres are polymorphic patchworks of interchromosomal segmental duplications at the ends of chromosomes. Here we provide evidence that these patchworks arose recently through repeated translocations between chromosome ends. We assess the relative contribution of the principal mechanisms of ectopic DNA repair to the formation of subtelomeric duplications and find that non-homologous end-joining predominates. Once subtelomeric duplications arise, they are prone to homology-based sequence transfers as shown by the incongruent phylogenetic relationships of neighbouring sections. Interchromosomal recombination of subtelomeres is a potent force for recent change. Cytogenetic and sequence analyses reveal that pieces of the subtelomeric patchwork have changed location and copy number with unprecedented frequency during primate evolution. Half of the known subtelomeric sequence has formed recently, through human-specific sequence transfers and duplications. Subtelomeric dynamics result in a gene duplication rate significantly higher than the genome average and could have both advantageous and pathological consequences in human biology. More generally, our analyses suggest an evolutionary cycle between segmental polymorphisms and genome rearrangements.
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Affiliation(s)
- Elena V. Linardopoulou
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
- Department of Bioengineering, University of Washington, Box 357962, Seattle, Washington 98195-7962, USA
| | - Eleanor M. Williams
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
| | - Yuxin Fan
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
| | - Cynthia Friedman
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
| | - Janet M. Young
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
| | - Barbara J. Trask
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, Seattle, Washington 98109, USA
- Department of Bioengineering, University of Washington, Box 357962, Seattle, Washington 98195-7962, USA
- Department of Genome Sciences, University of Washington, Box 357730, Seattle, Washington 98195-7730, USA
- Correspondence and requests for materials should be addressed to B.J.T. (e-mail:
)
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42
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Abstract
The structures of specific chromosome regions, centromeres and telomeres, present a number of puzzles. As functions performed by these regions are ubiquitous and essential, their DNA, proteins and chromatin structure are expected to be conserved. Recent studies of centromeric DNA from human, Drosophila and plant species have demonstrated that a hidden universal centromere-specific sequence is highly unlikely. The DNA of telomeres is more conserved consisting of a tandemly repeated 6-8 bp Arabidopsis-like sequence in a majority of organisms as diverse as protozoan, fungi, mammals and plants. However, there are alternatives to short DNA repeats at the ends of chromosomes and for telomere elongation by telomerase. Here we focus on the similarities and diversity that exist among the structural elements, DNA sequences and proteins, that make up terminal domains (telomeres and subtelomeres), and how organisms use these in different ways to fulfil the functions of end-replication and end-protection.
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Affiliation(s)
- Edward J Louis
- Department of Genetics, University of Leicester, Leicester UK.
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43
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Velagaleti GVN, Robinson SS, Rouse BM, Tonk VS, Lockhart LH. Subtelomeric rearrangements in idiopathic mental retardation. Indian J Pediatr 2005; 72:679-85. [PMID: 16131774 DOI: 10.1007/bf02724077] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
OBJECTIVE To estimate the frequency of subtelomeric rearrangements in patients with sporadic and non-syndromic idiopathic mental retardation (IMR). METHODS A total of 18 IMR patients were taken for the study. Selection criteria included no known syndromes or chromosomes abnormalities and known causes of IMR. All patients signed an informed consent to participate. Chromosome analysis was carried out on all patients to rule out gross chromosome abnormalities. Lymphocyte cultures were initiated and harvested using standard protocols. For fluorescence in situ hybridization (FISH), Chromoprobe Multiprobe-T system was used. This system consists of 24 embossed areas with each area having one reversibly bound subtelomere probe for a specific chromosome. The subtelomere probes were differentially labeled with green fluorescence for short arm and orange for the long arm. Hybridization, washing and staining are done using standard protocols. A minimum of 5 metaphases were analyzed per chromosome per patient. RESULTS A total of 2 subtelomeric rearrangements were detected (11.1%). Case 1 involved a 17-year-old with severe MR, profound deafness and dysmorphic features with reciprocal translocation t(3;7)(q26.2; p15.1). The second case involved a 4.6-year-old with mild developmental delay and a terminal deletion of the long arm of chromosome 2, del(2) (q37.3). The frequency of abnormalities detected in our study is in agreement with published reports. CONCLUSION Subtelomeric screening with FISH is a useful tool for investigation of IMR, however, it is not cost effective in all cases. Conventional chromosome analysis coupled with targeted FISH testing might be the optimal strategy for investigation of IMR.
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44
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van der Maarel SM, Frants RR. The D4Z4 repeat-mediated pathogenesis of facioscapulohumeral muscular dystrophy. Am J Hum Genet 2005; 76:375-86. [PMID: 15674778 PMCID: PMC1196390 DOI: 10.1086/428361] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2004] [Indexed: 01/19/2023] Open
Affiliation(s)
- Silvère M van der Maarel
- Leiden University Medical Center, Center for Human and Clinical Genetics, Leiden, The Netherlands.
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45
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Mewborn SK, Lese Martin C, Ledbetter DH. The dynamic nature and evolutionary history of subtelomeric and pericentromeric regions. Cytogenet Genome Res 2004; 108:22-5. [PMID: 15545712 DOI: 10.1159/000080798] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Accepted: 02/06/2004] [Indexed: 02/02/2023] Open
Abstract
The organization and evolution of the subtelomeric and pericentromeric regions of human chromosomes exhibit unique characteristics compared to other regions of the genome. As shown in Fig. 1 the functional elements of the centromere and telomere are comprised of highly repetitive DNA sequences, which are responsible for carrying out the main mechanistic duties of these two regions: chromosome segregation and end replication, respectively. The nature of the repeats in these two regions and their function have been reviewed separately and, therefore, will not be discussed in more detail here (Sullivan et al., 1996, 2001; McEachern et al., 2000; Henikoff et al., 2001). Adjacent to these functional element regions, the centromere and telomere regions share an interesting architecture as depicted in Fig. 1. For both pericentromeric and subtelomeric regions, blocks of recent genomic duplications form a zone of shared sequence homologies between certain subsets of human chromosomes. The dynamic nature and evolutionary history of these regions and the unique DNA sequence adjacent to them will be the focus of this review.
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Affiliation(s)
- S K Mewborn
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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46
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Riethman H, Ambrosini A, Castaneda C, Finklestein JM, Hu XL, Paul S, Wei J. Human subtelomeric DNA. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2004; 68:39-47. [PMID: 15338601 DOI: 10.1101/sqb.2003.68.39] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- H Riethman
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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47
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Londoño-Vallejo JA. Telomere length heterogeneity and chromosome instability. Cancer Lett 2004; 212:135-44. [PMID: 15341022 DOI: 10.1016/j.canlet.2004.05.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2004] [Accepted: 05/12/2004] [Indexed: 01/04/2023]
Abstract
Chromosome aberrations are the hallmark of cancer cells. Although a few specific chromosome aberrations are frequently detected in some types of cancer, the majority of karyotypic abnormalities tend to differ between different histological types and between individuals with the same type of cancer. Recent work indicates that telomeres may be directly involved in shaping the karyotypes of tumor cells. In particular, the heterogeneity of telomere lengths within cells may have direct influence on the frequency with which chromosomes engage in telomeric fusions and in subsequent breakage-fusion-bridge cycles. Since telomere length distribution among chromosome arms is a polymorphic trait, difference in distributions between individuals may account, at least in part, for the karyotypic differences found among tumors of the same type. Conversely, if single telomere lengths happen to be inherited, the segregation of particularly short telomeres in families may increase the incidence of specific chromosome aberrations during tumor evolution, and perhaps contribute, along with other factors, to cancer pre-disposition.
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48
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Stewart DR, Huang A, Faravelli F, Anderlid BM, Medne L, Ciprero K, Kaur M, Rossi E, Tenconi R, Nordenskjöld M, Gripp KW, Nicholson L, Meschino WS, Capua E, Quarrell OWJ, Flint J, Irons M, Giampietro PF, Schowalter DB, Zaleski CA, Malacarne M, Zackai EH, Spinner NB, Krantz ID. Subtelomeric deletions of chromosome 9q: A novel microdeletion syndrome. Am J Med Genet A 2004; 128A:340-51. [PMID: 15264279 DOI: 10.1002/ajmg.a.30136] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Fluorescent in situ hybridization (FISH) screening of subtelomeric rearrangements has resulted in the identification of previously unrecognized chromosomal causes of mental retardation with and without dysmorphic features. This article reports the phenotypic and molecular breakpoint characterization in a cohort of 12 patients with subtelomeric deletions of chromosome 9q34. The phenotypic findings are consistent amongst these individuals and consist of mental retardation, distinct facial features and congenital heart defects (primarily conotruncal defects). Detailed breakpoint mapping by FISH, microsatellite and single nucleotide polymorphism (SNP) genotyping analysis has narrowed the commonly deleted region to an approximately 1.2 Mb interval containing 14 known transcripts. The majority of the proximal deletion breakpoints fall within a 400 kb interval between SNP markers C12020842 proximally and C80658 distally suggesting a common breakpoint in this interval.
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Affiliation(s)
- Douglas R Stewart
- Division of Human Genetics and Molecular Biology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
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49
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Riethman H, Ambrosini A, Castaneda C, Finklestein J, Hu XL, Mudunuri U, Paul S, Wei J. Mapping and initial analysis of human subtelomeric sequence assemblies. Genome Res 2004; 14:18-28. [PMID: 14707167 PMCID: PMC314271 DOI: 10.1101/gr.1245004] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within approximately 10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions.
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Affiliation(s)
- Harold Riethman
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
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50
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Lowell JE, Roughton AI, Lundblad V, Pillus L. Telomerase-independent proliferation is influenced by cell type in Saccharomyces cerevisiae. Genetics 2003; 164:909-21. [PMID: 12871903 PMCID: PMC1462614 DOI: 10.1093/genetics/164.3.909] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Yeast strains harboring mutations in genes required for telomerase function (TLC1 and the EST genes) exhibit progressive shortening of telomeric DNA and replicative senescence. A minority of cells withstands loss of telomerase through RAD52-dependent amplification of telomeric and subtelomeric sequences; such survivors are now capable of long-term propagation with telomeres maintained by recombination rather than by telomerase. Here we report that simultaneous expression in haploid cells of both MATa and MATalpha information suppresses the senescence of telomerase-deficient mutants, with suppression occurring via the RAD52-dependent survivor pathway(s). Such suppression can be mimicked by deletion of SIR1-SIR4, genes that function in transcriptional silencing of several loci including the silent mating-type loci. Furthermore, telomerase-defective diploid strains that express only MATa or MATalpha information senesce at a faster rate than telomerase-defective diploids that are heterozygous at the MAT locus. This suggests that the RAD52-dependent pathway(s) for telomere maintenance respond to changes in the levels of recombination, a process regulated in part by the hierarchy of gene control that includes MAT regulation. We propose that cell-type-specific regulation of recombination at human telomeres may similarly contribute to the tissue-specific patterns of disease found in telomerase-deficient tumors.
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Affiliation(s)
- Joanna E Lowell
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, USA
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