1
|
Young E, Abid HZ, Kwok PY, Riethman H, Xiao M. Comprehensive Analysis of Human Subtelomeres by Whole Genome Mapping. PLoS Genet 2020; 16:e1008347. [PMID: 31986135 PMCID: PMC7004388 DOI: 10.1371/journal.pgen.1008347] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/06/2020] [Accepted: 10/15/2019] [Indexed: 12/03/2022] Open
Abstract
Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, we use high throughput optical mapping of large single DNA molecules in nanochannel arrays for 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (HG38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends we estimate a timeline for the spread of these duplication blocks.
Collapse
Affiliation(s)
- Eleanor Young
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Heba Z. Abid
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
| | - Pui-Yan Kwok
- Cardiovascular Research Institute, University of California–San Francisco, San Francisco, CA, United States of America
- Department of Dermatology, University of California–San Francisco, San Francisco, CA, United States of America
- Institute for Human Genetics, University of California–San Francisco, San Francisco, CA, United States of America
| | - Harold Riethman
- Medical Diagnostic & Translational Sciences, Old Dominium University, Norfolk, VA, United States of America
| | - Ming Xiao
- School of Biomedical Engineering, Drexel University, Philadelphia, PA, United States of America
- Institute of Molecular Medicine and Infectious Disease in the School of Medicine, Drexel University, Philadelphia, PA, United States of America
| |
Collapse
|
2
|
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.
Collapse
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
| | | | | | | |
Collapse
|
3
|
Recombinogenic telomeres in diploid Sorex granarius (Soricidae, Eulipotyphla) fibroblast cells. Mol Cell Biol 2014; 34:2786-99. [PMID: 24842907 DOI: 10.1128/mcb.01697-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The telomere structure in the Iberian shrew Sorex granarius is characterized by unique, striking features, with short arms of acrocentric chromosomes carrying extremely long telomeres (up to 300 kb) with interspersed ribosomal DNA (rDNA) repeat blocks. In this work, we investigated the telomere physiology of S. granarius fibroblast cells and found that telomere repeats are transcribed on both strands and that there is no telomere-dependent senescence mechanism. Although telomerase activity is detectable throughout cell culture and appears to act on both short and long telomeres, we also discovered that signatures of a recombinogenic activity are omnipresent, including telomere-sister chromatid exchanges, formation of alternative lengthening of telomeres (ALT)-associated PML-like bodies, production of telomere circles, and a high frequency of telomeres carrying marks of a DNA damage response. Our results suggest that recombination participates in the maintenance of the very long telomeres in normal S. granarius fibroblasts. We discuss the possible interplay between the interspersed telomere and rDNA repeats in the stabilization of the very long telomeres in this organism.
Collapse
|
4
|
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.
Collapse
Affiliation(s)
- Clara Novo
- Telomeres and Cancer laboratory, 'Equipe Labellisée Ligue contre le Cancer', UMR3244, Institut Curie, 26 rue d'Ulm, 75248 Paris, France
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Huang SL, Chou TC, Lin TH, Tsai MS, Wang SH. Gcse, a novel germ-cell-specific gene, is differentially expressed during meiosis and gametogenesis. Reprod Sci 2013; 20:1193-206. [PMID: 23456662 DOI: 10.1177/1933719113477490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Gametogenesis is a complex process wherein germ cells develop from primordial diploid cells into haploid gametes. To understand the mechanisms controlling gametogenesis, we identified a novel germ-cell-specific gene, Gcse. Gcse produces two major transcripts that are 1589 bp (Gcse-l) and 906 bp (Gcse-s) in length. Northern blotting and reverse transcription-polymerase chain reaction (RT-PCR) analyses of multiple tissues reveal that Gcse-l is expressed in both adult testes and ovaries, but Gcse-s is expressed only in adult testes. During female gonad development, Gcse-l is expressed from embryonic day 13.5 to adulthood, specifically in oocytes, and maintained in ovulated and fertilized eggs. However, Gcse-s signals were detected only in ovulated oocytes and fertilized eggs but not in adult ovary. During male gonad development, strong Gcse-l signals were detected in late pachytene spermatocytes and round spermatids. However, Gcse-s transcripts exist only in round spermatids. Furthermore, the expression of GCSE-L proteins and their subcellular localizations within cells are stage specific. GCSE-L is detected in the nucleus of late pachytene spermatocytes. During meiosis, GCSE-L is translocated to acrosome regions in spermatids and maintained in the acrosome of spermatozoa. GCSE-L colocalizes with acrosin and lectin peanut agglutinin in the Golgi apparatus. However, GCSE-S proteins are expressed only in the nucleus of spermatids. From these results, we suggest that GCSE proteins play roles in meiosis and may be involved in acrosome biogenesis during spermiogenesis.
Collapse
Affiliation(s)
- Shih-Ling Huang
- 1Department of Biomedical Sciences, Chung Shan Medical University, Taichung, Taiwan
| | | | | | | | | |
Collapse
|
6
|
Arnoult N, Schluth-Bolard C, Letessier A, Drascovic I, Bouarich-Bourimi R, Campisi J, Kim SH, Boussouar A, Ottaviani A, Magdinier F, Gilson E, Londoño-Vallejo A. Replication timing of human telomeres is chromosome arm-specific, influenced by subtelomeric structures and connected to nuclear localization. PLoS Genet 2010; 6:e1000920. [PMID: 20421929 PMCID: PMC2858680 DOI: 10.1371/journal.pgen.1000920] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 03/22/2010] [Indexed: 12/12/2022] Open
Abstract
The mechanisms governing telomere replication in humans are still poorly understood. To fill this gap, we investigated the timing of replication of single telomeres in human cells. Using in situ hybridization techniques, we have found that specific telomeres have preferential time windows for replication during the S-phase and that these intervals do not depend upon telomere length and are largely conserved between homologous chromosomes and between individuals, even in the presence of large subtelomeric segmental polymorphisms. Importantly, we show that one copy of the 3.3 kb macrosatellite repeat D4Z4, present in the subtelomeric region of the late replicating 4q35 telomere, is sufficient to confer both a more peripheral localization and a later-replicating property to a de novo formed telomere. Also, the presence of β-satellite repeats next to a newly created telomere is sufficient to delay its replication timing. Remarkably, several native, non-D4Z4–associated, late-replicating telomeres show a preferential localization toward the nuclear periphery, while several early-replicating telomeres are associated with the inner nuclear volume. We propose that, in humans, chromosome arm–specific subtelomeric sequences may influence both the spatial distribution of telomeres in the nucleus and their replication timing. Functional telomeres are essential for genome stability. While replication of telomeres has been extensively studied in model organisms such as the baker's yeast, little is known about the mechanisms that govern the replication of human telomeres. In this study, we have determined the timing of replication of telomeres of individual human chromosomes and its association with potential modulating factors such as particular subtelomeric sequences, the presence of heterochromatic regions, and nuclear localization. We have found that native telomeres associated with D4Z4 sequences—a macrosatellite naturally located in the subtelomeric regions of 4q, 10q, and acrocentric chromosome extremities—replicate later than others. We also present descriptive and experimental evidence indicating that nuclear localization influences the timing of telomere replication. These results contribute to our understanding of telomere metabolism in humans.
Collapse
Affiliation(s)
- Nausica Arnoult
- Telomeres and Cancer Laboratory, Institut Curie, CNRS, UPMC University Paris 06, Paris, France
| | - Caroline Schluth-Bolard
- Epigenetics and Telomere Regulation, CNRS ENS UCBL IFR128, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Anne Letessier
- Functional Organization and Plasticity of Mammalian Genomes, Institut Curie, UPMC University Paris 06, Paris, France
| | - Irena Drascovic
- Telomeres and Cancer Laboratory, Institut Curie, CNRS, UPMC University Paris 06, Paris, France
| | | | - Judith Campisi
- Lawrence Berkeley Laboratory, Berkeley, California, United States of America
- Buck Institute for Age Research, Novato, California, United States of America
| | - Sahn-ho Kim
- Lawrence Berkeley Laboratory, Berkeley, California, United States of America
| | - Amina Boussouar
- Epigenetics and Telomere Regulation, CNRS ENS UCBL IFR128, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Alexandre Ottaviani
- Epigenetics and Telomere Regulation, CNRS ENS UCBL IFR128, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Frédérique Magdinier
- Epigenetics and Telomere Regulation, CNRS ENS UCBL IFR128, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Eric Gilson
- Epigenetics and Telomere Regulation, CNRS ENS UCBL IFR128, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer Laboratory, Institut Curie, CNRS, UPMC University Paris 06, Paris, France
- * E-mail:
| |
Collapse
|
7
|
Probing PML body function in ALT cells reveals spatiotemporal requirements for telomere recombination. Proc Natl Acad Sci U S A 2009; 106:15726-31. [PMID: 19717459 DOI: 10.1073/pnas.0907689106] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Promyelocytic leukemia (PML) bodies (also called ND10) are dynamic nuclear structures implicated in a wide variety of cellular processes. ALT-associated PML bodies (APBs) are specialized PML bodies found exclusively in telomerase-negative tumors in which telomeres are maintained by recombination-based alternative (ALT) mechanisms. Although it has been suggested that APBs are directly implicated in telomere metabolism of ALT cells, their precise role and structure have remained elusive. Here we show that PML bodies in ALT cells associate with chromosome ends forming small, spatially well-defined clusters, containing on average 2-5 telomeres. Using an innovative approach that gently enlarges PML bodies in living cells while retaining their overall organization, we show that this physical enlargement of APBs spatially resolves the single telomeres in the cluster, but does not perturb the potential of the APB to recruit chromosome extremities. We show that telomere clustering in PML bodies is cell-cycle regulated and that unique telomeres within a cluster associate with recombination proteins. Enlargement of APBs induced the accumulation of telomere-telomere recombination intermediates visible on metaphase spreads and connecting heterologous chromosomes. The strand composition of these recombination intermediates indicated that this recombination is constrained to a narrow time window in the cell cycle following replication. These data provide strong evidence that PML bodies are not only a marker for ALT cells but play a direct role in telomere recombination, both by bringing together chromosome ends and by promoting telomere-telomere interactions between heterologous chromosomes.
Collapse
|
8
|
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.
Collapse
Affiliation(s)
- H Riethman
- The Wistar Institute, Philadelphia, PA, USA
| |
Collapse
|
9
|
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.
Collapse
|
10
|
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.
Collapse
Affiliation(s)
- Harold Riethman
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
De La Chesnaye E, Kerr B, Paredes A, Merchant-Larios H, Méndez JP, Ojeda SR. Fbxw15/Fbxo12J is an F-box protein-encoding gene selectively expressed in oocytes of the mouse ovary. Biol Reprod 2007; 78:714-25. [PMID: 18094359 DOI: 10.1095/biolreprod.107.063826] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
In recent years, several factors required for follicular assembly and/or early growth of newly formed primordial follicles have been characterized, but additional factors likely remain to be identified. We have used cDNA arrays to compare gene expression in the neonatal mouse ovary at 48 h (when primordial follicles are being assembled) and at 96 h (when early follicular growth is taking place) after birth to that of ovaries collected <24 h after birth (when follicles have not yet been formed). Segregating genes according to their pattern of expression revealed the presence of one cluster of 24 genes for which expression consistently increased at 48 and 96 h. The top increaser in this cluster encodes a approximately 1.5-kb mRNA containing an open reading frame of 1401 bp that encodes a protein of 466 amino acids. The predicted 52.3-kDa protein is a member of the F-box-only (FBXO) protein family, termed FBXW15 or FBXO12J. It has a cytoplasmic localization that includes the endoplasmic reticulum. Expression of Fbxw15/Fbxp12J mRNA is oocyte-specific; the mRNA is first detected on Gestational Day 18, decreasing thereafter to minimal levels on the day of birth. The prevalence of Fbxw15/Fbxp12J mRNA increases again at 48 and 96 h after birth, coinciding with the time of follicular assembly and the initiation of early follicular growth, respectively. The specific expression of Fbxw15/Fbxp12J in oocytes and its developmental pattern of expression suggest a role for this gene in the regulation of oocyte physiology.
Collapse
Affiliation(s)
- Elsa De La Chesnaye
- UIM en Biología del Desarrollo, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | | | | | | | | |
Collapse
|
13
|
Zhdanova NS, Minina JM, Karamisheva TV, Draskovic I, Rubtsov NB, Londoño-Vallejo JA. The very long telomeres in Sorex granarius (Soricidae, Eulipothyphla) contain ribosomal DNA. Chromosome Res 2007; 15:881-90. [PMID: 17899406 DOI: 10.1007/s10577-007-1170-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2007] [Revised: 08/03/2007] [Accepted: 08/03/2007] [Indexed: 01/13/2023]
Abstract
Two closely related shrew species, Sorex granarius and Sorex araneus, in which Robertsonian rearrangements have played a primary role in karyotype evolution, present very distinct telomere length patterns. S. granarius displays hyperlong telomeres specifically associated with the short arms of acrocentrics, whereas telomere lengths in S. araneus are rather short and homogenous. Using a combined approach of chromosome and fibre FISH, modified Q-FISH, 3D-FISH, Ag-NOR staining and TRF analysis, we carried out a comparative analysis of telomeric repeats and rDNA distribution on chromosome ends of Sorex granarius. Our results show that rDNA sequences forming active nuclear organizing regions are interspersed with the long telomere tracts of all short arms of acrocentrics. These observations suggest that the major rearrangements that gave rise to today's karyotype in S. granarius were accompanied by a profound reorganization of chromosome ends, which comprised extensive amplification of telomeric and rDNA repeats on the short arms of acrocentrics and finally contributed to the stabilization of telomeres. This is the first time that such telomeric structures have been observed in any mammalian species.
Collapse
Affiliation(s)
- Natalia S Zhdanova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | | | | | | | | | | |
Collapse
|
14
|
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]
|
15
|
Graakjaer J, Der-Sarkissian H, Schmitz A, Bayer J, Thomas G, Kolvraa S, Londoño-Vallejo JA. Allele-specific relative telomere lengths are inherited. Hum Genet 2006; 119:344-50. [PMID: 16440201 DOI: 10.1007/s00439-006-0137-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 01/02/2006] [Indexed: 10/25/2022]
Abstract
Previous studies have indicated that single relative telomere lengths are defined in the zygote. In order to explore the possibility that single telomere lengths segregate in families, we compared relative telomere lengths obtained from allelic chromosome extremities transmitted from parent to child, representing a total of 31 independent meiotic events. We find a significant positive correlation of 0.65 (P=0.0004) between these telomere lengths, whereas the correlation between the non-transmitted parental homologue and the transmitted homologue in the child is not statistically significant (r=0.16; P=0.195). This study indicates that, even though there is a telomerase-mediated maintenance/elongation of telomeres in germ cells, allele-specific relative telomere lengths are preserved in the next generation.
Collapse
Affiliation(s)
- Jesper Graakjaer
- Telomeres and Cancer Lab, UMR7147, CNRS-I, Curie-UPMC, Paris, France
| | | | | | | | | | | | | |
Collapse
|
16
|
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.
Collapse
Affiliation(s)
- H Riethman
- Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA.
| | | | | |
Collapse
|
17
|
Goldman F, Bouarich R, Kulkarni S, Freeman S, Du HY, Harrington L, Mason PJ, Londoño-Vallejo A, Bessler M. The effect of TERC haploinsufficiency on the inheritance of telomere length. Proc Natl Acad Sci U S A 2005; 102:17119-24. [PMID: 16284252 PMCID: PMC1287981 DOI: 10.1073/pnas.0505318102] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Telomeres protect chromosome ends from end-to-end fusion and degradation. Loss of telomere function causes cell-cycle arrest or cell death. Autosomal dominant dyskeratosis congenita (AD DC), a rare inherited bone marrow failure syndrome, is caused by mutations in TERC, the RNA component of telomerase. Here, we studied the telomere dynamics over three generations in a 32-member extended family with AD DC due to a TERC gene deletion. Our analysis shows that peripheral blood cells from family members haploinsufficient for TERC have very short telomeres. Telomeres are equally short in all individuals carrying the TERC gene deletion irrespective of their age. Chromosome-specific telomere analysis distinguishing the parental origin of telomeres showed that in gene deletion carriers, paternal and maternal telomeres are similarly short and similar in length to those of the affected parent. In children of affected parents who have normal TERC genes, parental telomeres are again similar in length, but two generations appear to be necessary to fully restore normal telomere length. These results are consistent with a model in which telomerase preferentially acts on the shortest telomeres. When TERC is limiting, this preference leads to the accelerated shortening of longer telomeres. The limited amount of active telomerase in TERC RNA haploinsufficiency may not be able to maintain the minimal length of the increasing number of short telomeres. Thus, the number of cells with excessively short telomeres and the degree of residual telomerase activity may determine the onset of disease in patients with AD DC.
Collapse
Affiliation(s)
- Fred Goldman
- Department of Pediatrics, University of Iowa Hospitals and Clinics, Iowa City, IA 52242, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Sanlaville D, Lapierre JM, Turleau C, Coquin A, Borck G, Colleaux L, Vekemans M, Romana SP. Molecular karyotyping in human constitutional cytogenetics. Eur J Med Genet 2005; 48:214-31. [PMID: 16179218 DOI: 10.1016/j.ejmg.2005.04.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Accepted: 04/08/2005] [Indexed: 01/22/2023]
Abstract
Using array CGH it is possible to detect very small genetic imbalances anywhere in the genome. Its usefulness has been well documented in cancer and more recently in constitutional disorders. In particular it has been used to detect interstitial and subtelomeric submicroscopic imbalances, to characterize their size at the molecular level and to define the breakpoints of chromosomal translocation. Here, we review the various applications of array CGH in constitutional cytogenetics. This technology remains expensive and the existence of numerous sequence polymorphisms makes its interpretation difficult. The challenge today is to transfer this technology in the clinical setting.
Collapse
Affiliation(s)
- Damien Sanlaville
- Service de cytogénétique, laboratoire de cytogénétique, hôpital Necker-Enfants Malades, 149, rue de Sèvres, 75015 Paris, France.
| | | | | | | | | | | | | | | |
Collapse
|
19
|
Hasenmaile S, Pawelec G. The concept of telomeric non-reciprocal recombination (TENOR) applied to human fibroblasts grown in serial cultures: concordance with genealogical data. Rejuvenation Res 2005; 8:154-71. [PMID: 16144470 DOI: 10.1089/rej.2005.8.154] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Since the discovery of the limited life span of human fibroblasts some 50 years ago, many genealogical studies have been undertaken to describe growth kinetics of fibroblasts in serial cultures by their individual division behavior. It is now accepted that proliferation capacities of human fibroblasts strongly depend on their telomere lengths and integrity. Telomeres shorten with each replication round, and there is a direct correlation between cell division capacity and telomere lengths; that is, the consumption of disposable telomeric DNA repeats during cell divisions progresses until critically short telomeres determining the replicative senescence of the cells are present. Recently, we have suggested that telomeres in fibroblasts can also become elongated during DNA replication by telomeric non-reciprocal recombination (TENOR). Here we discuss genealogical data collected over the last decades as well as more recent findings on the telomere-driven replicative senescence process, and we summarize both to give an integrated picture.
Collapse
Affiliation(s)
- Stefan Hasenmaile
- Tubingen Ageing and Tumour Immunology Group, Center for Medical Research, University of Tubingen Medical School, Tubingen, Germany.
| | | |
Collapse
|
20
|
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.
Collapse
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:
)
| |
Collapse
|
21
|
Yang TJ, Yu Y, Chang SB, de Jong H, Oh CS, Ahn SN, Fang E, Wing RA. Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:467-78. [PMID: 15965650 DOI: 10.1007/s00122-005-2034-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2005] [Accepted: 04/11/2005] [Indexed: 05/03/2023]
Abstract
Despite the collective efforts of the international community to sequence the complete rice genome, telomeric regions of most chromosome arms remain uncharacterized. In this report we present sequence data from subtelomere regions obtained by analyzing telomeric clones from two 8.8 x genome equivalent 10-kb libraries derived from partial restriction digestion with HaeIII or Sau3AI (OSJNPb HaeIII and OSJNPc Sau3AI). Seven telomere clones were identified and contain 25-100 copies of the telomere repeat (CCCTAAA)(n) on one end and unique sequences on the opposite end. Polymorphic sequence-tagged site markers from five clones and one additional PCR product were genetically mapped on the ends of chromosome arms 2S, 5L, 10S, 10L, 7L, and 7S. We found distinct chromosome-specific telomere-associated tandem repeats (TATR) on chromosome 7 (TATR7) and on the short arm of chromosome 10 (TATR10s) that showed no significant homology to any International Rice Genome Sequencing Project (IRGSP) genomic sequence. The TATR7, a degenerate tandem repeat which is interrupted by transposable elements, appeared on both ends of chromosome 7. The TATR10s was found to contain an inverted array of three tandem repeats displaying an interesting secondary folding pattern that resembles a telomere loop (t-loop) and which may be involved in a protective function against chromosomal end degradation.
Collapse
Affiliation(s)
- Tae-Jin Yang
- Brassica Genomics Team, National Institute of Agricultural Biotechnology, RDA, Suwon, 441-707, Korea
| | | | | | | | | | | | | | | |
Collapse
|
22
|
Paillisson A, Dadé S, Callebaut I, Bontoux M, Dalbiès-Tran R, Vaiman D, Monget P. Identification, characterization and metagenome analysis of oocyte-specific genes organized in clusters in the mouse genome. BMC Genomics 2005; 6:76. [PMID: 15907208 PMCID: PMC1166550 DOI: 10.1186/1471-2164-6-76] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2005] [Accepted: 05/20/2005] [Indexed: 01/18/2023] Open
Abstract
Background Genes specifically expressed in the oocyte play key roles in oogenesis, ovarian folliculogenesis, fertilization and/or early embryonic development. In an attempt to identify novel oocyte-specific genes in the mouse, we have used an in silico subtraction methodology, and we have focused our attention on genes that are organized in genomic clusters. Results In the present work, five clusters have been studied: a cluster of thirteen genes characterized by an F-box domain localized on chromosome 9, a cluster of six genes related to T-cell leukaemia/lymphoma protein 1 (Tcl1) on chromosome 12, a cluster composed of a SPErm-associated glutamate (E)-Rich (Speer) protein expressed in the oocyte in the vicinity of four unknown genes specifically expressed in the testis on chromosome 14, a cluster composed of the oocyte secreted protein-1 (Oosp-1) gene and two Oosp-related genes on chromosome 19, all three being characterized by a partial N-terminal zona pellucida-like domain, and another small cluster of two genes on chromosome 19 as well, composed of a TWIK-Related spinal cord K+ channel encoding-gene, and an unknown gene predicted in silico to be testis-specific. The specificity of expression was confirmed by RT-PCR and in situ hybridization for eight and five of them, respectively. Finally, we showed by comparing all of the isolated and clustered oocyte-specific genes identified so far in the mouse genome, that the oocyte-specific clusters are significantly closer to telomeres than isolated oocyte-specific genes are. Conclusion We have studied five clusters of genes specifically expressed in female, some of them being also expressed in male germ-cells. Moreover, contrarily to non-clustered oocyte-specific genes, those that are organized in clusters tend to map near chromosome ends, suggesting that this specific near-telomere position of oocyte-clusters in rodents could constitute an evolutionary advantage. Understanding the biological benefits of such an organization as well as the mechanisms leading to a specific oocyte expression in these clusters now requires further investigation.
Collapse
Affiliation(s)
- Amélie Paillisson
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France
| | - Sébastien Dadé
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France
| | - Isabelle Callebaut
- Département de Biologie Structurale, LMCP, CNRS, UMR 7590, Universités Paris6 et Paris 7, case 115, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Martine Bontoux
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France
| | - Rozenn Dalbiès-Tran
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France
| | - Daniel Vaiman
- U709 – INSERM, Pavillon Baudelocque, Hôpital Cochin, 123, Boulevard de Port-Royal, 75014 Paris, and INRA, Département de Génétique animale
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, UMR 6175 INRA-CNRS-Université François Rabelais de Tours-Haras Nationaux, 37380 Nouzilly, France
| |
Collapse
|
23
|
Font-Montgomery E, Weaver DD, Walsh L, Christensen C, Thurston VC. Clinical and cytogenetic manifestations of subtelomeric aberrations: Report of six cases. ACTA ACUST UNITED AC 2005; 70:408-15. [PMID: 15211711 DOI: 10.1002/bdra.20036] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
BACKGROUND Fluorescent subtelomeric probes for the 41 different subtelomeric regions (the p arms of the acrocentric chromosomes were excluded) have been developed over the last 10 years. These probes can detect deletions, duplications, and translocations in the gene-rich subtelomeric regions of human chromosomes, regions where crossing over frequently occurs and where a high number of abnormalities have been found. Recently, commercially produced probes have become available, which has led to the detection of subtelomeric abnormalities in 7.4% of patients with moderate to severe mental retardation (Knight et al., 1999). CASES We evaluated 43 dysmorphic children with developmental delay and/or mental retardation of unknown etiology and/or autism who were previously assessed for chromosome abnormalities, metabolic disorders, or recognizable dysmorphic syndromes, all of which were ruled out. Of the 43 children tested, 6 (14%) were found to have subtelomeric aberrations. CONCLUSIONS We recommend that patients with dysmorphic features and mental retardation of unknown etiology who also have a normal standard chromosome analysis should have subtelomeric FISH testing performed earlier in their clinical workup.
Collapse
Affiliation(s)
- Esperanza Font-Montgomery
- Department of Medical and Molecular Genetics, School of Medicine, Indiana University, Indianapolis, Indiana 46202-5251, USA.
| | | | | | | | | |
Collapse
|
24
|
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.
Collapse
|
25
|
Li J, Jiang T, Mao JH, Balmain A, Peterson L, Harris C, Rao PH, Havlak P, Gibbs R, Cai WW. Genomic segmental polymorphisms in inbred mouse strains. Nat Genet 2004; 36:952-4. [PMID: 15322544 DOI: 10.1038/ng1417] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2004] [Accepted: 08/03/2004] [Indexed: 11/08/2022]
Abstract
By analyzing genomic copy-number differences using high-resolution mouse whole-genome BAC arrays, we uncover substantial differences in regional DNA content between inbred strains of mice. The identification of these apparently common segmental polymorphisms suggests that these differences can contribute to genetic variability and pathologic susceptibility.
Collapse
Affiliation(s)
- Jiangzhen Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Graakjaer J, Pascoe L, Der-Sarkissian H, Thomas G, Kolvraa S, Christensen K, Londoño-Vallejo JA. The relative lengths of individual telomeres are defined in the zygote and strictly maintained during life. Aging Cell 2004; 3:97-102. [PMID: 15153177 DOI: 10.1111/j.1474-9728.2004.00093.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Previous studies have indicated that average telomere length is partly inherited (Slagboom et al., 1994; Rufer et al., 1999) and that there is an inherited telomere pattern in each cell (Graakjaer et al., 2003); (Londoño-Vallejo et al., 2001). In this study, we quantify the importance of the initially inherited telomere lengths within cells, in relation to other factors that influence telomere length during life. We have estimated the inheritance by measuring telomere length in monozygotic (MZ) twins using Q-FISH with a telomere specific peptide nucleic acid (PNA)-probe. Homologous chromosomes were identified using subtelomeric polymorphic markers. We found that identical homologous telomeres from two aged MZ twins show significantly less differences in relative telomere length than when comparing the two homologues within one individual. This result means that towards the end of life, individual telomeres retain the characteristic relative length they had at the outset of life and that any length alteration during the lifespan impacts equally on genetically identical homologues. As the result applies across independent individuals, we conclude that, at least in lymphocytes, epigenetic/environmental effects on relative telomere length are relatively minor during life.
Collapse
Affiliation(s)
- Jesper Graakjaer
- Institute for Human Genetics, University of Aarhus, Aarhus, Denmark
| | | | | | | | | | | | | |
Collapse
|
27
|
der-Sarkissian H, Bacchetti S, Cazes L, Londoño-Vallejo JA. The shortest telomeres drive karyotype evolution in transformed cells. Oncogene 2004; 23:1221-8. [PMID: 14716292 DOI: 10.1038/sj.onc.1207152] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Maintenance of telomeres is essential for chromosome stability. In the absence of telomerase, telomeres shorten with cell division until they approach a stability threshold, at which point cells enter senescence. When senescence-signaling pathways are inactive, further telomere shortening leads to chromosome instability characterized by telomeric fusions and breakage-fusion-bridge (BFB) cycles. Since the distribution of telomere lengths among chromosome extremities is heterogeneous, we wondered about the impact of such variability on the stability of particular chromosome arms. We correlated the initial length of individual telomeres in telomerase-negative-transformed cells with the stability of the corresponding chromosome arms during the precrisis period. We show that arms carrying the shortest telomeres are the first to become unstable and this instability affects the chromosome homologues with shorter telomeres almost exclusively. The analysis of several postcrisis cell populations, which had stabilized their telomeres by re-expressing telomerase, showed that the karyotypic outcome is strongly influenced by the initial telomere length heterogeneity. The timing of telomerase re-expression also seems to play a role in limiting the extent of karyotypic changes, probably by reducing the frequency of telomeric fusions and hence BFB. Since the distribution of telomere lengths within somatic cells is proper to every individual, our results predict that the risk for a particular chromosome arm of becoming unstable early in tumorigenesis will differ between individuals and contribute directly to the heterogeneity of chromosome aberrations found in tumors.
Collapse
Affiliation(s)
- Héra der-Sarkissian
- Centre d'Etude du Polymorphisme Humain, 27 rue Julliette Dodu, Paris 75010, France
| | | | | | | |
Collapse
|
28
|
Vissers LELM, de Vries BBA, Osoegawa K, Janssen IM, Feuth T, Choy CO, Straatman H, van der Vliet W, Huys EHLPG, van Rijk A, Smeets D, van Ravenswaaij-Arts CMA, Knoers NV, van der Burgt I, de Jong PJ, Brunner HG, van Kessel AG, Schoenmakers EFPM, Veltman JA. Array-based comparative genomic hybridization for the genomewide detection of submicroscopic chromosomal abnormalities. Am J Hum Genet 2003; 73:1261-70. [PMID: 14628292 PMCID: PMC1180392 DOI: 10.1086/379977] [Citation(s) in RCA: 349] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2003] [Accepted: 09/12/2003] [Indexed: 12/20/2022] Open
Abstract
Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using approximately 3,500 flourescent in situ hybridization-verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome.
Collapse
Affiliation(s)
- Lisenka E L M Vissers
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Nguyen TX, Cole AM, Lehrer RI. Evolution of primate theta-defensins: a serpentine path to a sweet tooth. Peptides 2003; 24:1647-54. [PMID: 15019196 DOI: 10.1016/j.peptides.2003.07.023] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2003] [Accepted: 07/04/2003] [Indexed: 12/13/2022]
Abstract
Retrocyclins (ancestral human theta-defensins) are cyclic antimicrobial octadecapeptides that interfere with viral uptake and protect human cells from infection by T- and M-tropic strains of HIV-1 in vitro. As are other theta-defensins, retrocyclins are lectins that bind gp120, CD4, and galactosylceramide-all of which are implicated in HIV-1 uptake. Although theta-defensin mRNA transcripts are present in human bone marrow, spleen, thymus, testis, and skeletal muscle, a premature stop codon aborts their translation. We found six theta-defensin (DEFT) genes in the human genome; five on chromosome 8p23 and one on chromosome 1. All six of these pseudogenes, as well as their homologues in chimpanzees and gorillas, contained the same premature stop codon mutation. Whereas we found intact DEFT genes in DNA from several Old World Monkeys, Hylobates syndactylus (a lesser ape) and orangutans, no homologues were present in DNA from six New World Monkeys and five prosimians. We conclude that DEFT genes and theta-defensins arose in Old World Monkeys by mutation of a pre-existing alpha-defensin gene. Although intact DEFT genes survive in some nonhuman primates, our hominid ancestors lost their ability to produce theta-defensins after the orangutan and hominid lineages diverged. It is possible (but may be difficult to prove) that this mutation rendered our species more susceptible to infection by HIV-1.
Collapse
Affiliation(s)
- Tung X Nguyen
- Department of Medicine, UCLA Center for the Health Sciences, Room CHS 37-062, 10833 LeConte Avenue, Los Angeles, CA 90095, USA
| | | | | |
Collapse
|