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Cappelletti E, Piras FM, Sola L, Santagostino M, Petersen JL, Bellone RR, Finno CJ, Peng S, Kalbfleisch TS, Bailey E, Nergadze SG, Giulotto E. The localization of centromere protein A is conserved among tissues. Commun Biol 2023; 6:963. [PMID: 37735603 PMCID: PMC10514049 DOI: 10.1038/s42003-023-05335-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A. Although mammalian centromeres are typically associated with satellite DNA, we previously demonstrated that the centromere of horse chromosome 11 (ECA11) is completely devoid of satellite DNA. We also showed that the localization of its CENP-A binding domain is not fixed but slides within an about 500 kb region in different individuals, giving rise to positional alleles. These epialleles are inherited as Mendelian traits but their position can move in one generation. It is still unknown whether centromere sliding occurs during meiosis or during development. Here, we first improve the sequence of the ECA11 centromeric region in the EquCab3.0 assembly. Then, to test whether centromere sliding may occur during development, we map the CENP-A binding domains of ECA11 using ChIP-seq in five tissues of different embryonic origin from the four horses of the equine FAANG (Functional Annotation of ANimal Genomes) consortium. Our results demonstrate that the centromere is localized in the same region in all tissues, suggesting that the position of the centromeric domain is maintained during development.
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Affiliation(s)
| | - Francesca M Piras
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Ernest Bailey
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, USA
| | - Solomon G Nergadze
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy.
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2
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Cappelletti E, Piras FM, Sola L, Santagostino M, Abdelgadir WA, Raimondi E, Lescai F, Nergadze SG, Giulotto E. Robertsonian fusion and centromere repositioning contributed to the formation of satellite-free centromeres during the evolution of zebras. Mol Biol Evol 2022; 39:6650076. [PMID: 35881460 PMCID: PMC9356731 DOI: 10.1093/molbev/msac162] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Centromeres are epigenetically specified by the histone H3 variant CENP-A and typically associated to highly repetitive satellite DNA. We previously discovered natural satellite-free neocentromeres in Equus caballus and E. asinus. Here, through ChIP-seq with an anti-CENP-A antibody, we found an extraordinarily high number of centromeres lacking satellite DNA in the zebras E. burchelli (15 of 22) and E. grevyi (13 of 23), demonstrating that the absence of satellite DNA at the majority of centromeres is compatible with genome stability and species survival and challenging the role of satellite DNA in centromere function. Nine satellite-free centromeres are shared between the two species in agreement with their recent separation. We assembled all centromeric regions and improved the reference genome of E. burchelli. Sequence analysis of the CENP-A binding domains revealed that they are LINE-1 and AT-rich with four of them showing DNA amplification. In the two zebras, satellite-free centromeres emerged from centromere repositioning or following Robertsonian fusion. In five chromosomes, the centromeric function arose near the fusion points, which are located within regions marked by traces of ancestral pericentromeric sequences. Therefore, besides centromere repositioning, Robertsonian fusions are an important source of satellite-free centromeres during evolution. Finally, in one case, a satellite-free centromere was seeded on an inversion breakpoint. At eleven chromosomes, whose primary constrictions seemed to be associated to satellite repeats by cytogenetic analysis, satellite-free neocentromeres were instead located near the ancestral inactivated satellite-based centromeres, therefore, the centromeric function has shifted away from a satellite repeat containing locus to a satellite-free new position.
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Affiliation(s)
- Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorenzo Sola
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Wasma A Abdelgadir
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Francesco Lescai
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, 27100 Pavia, Italy
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3
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Peng S, Petersen JL, Bellone RR, Kalbfleisch T, Kingsley NB, Barber AM, Cappelletti E, Giulotto E, Finno CJ. Decoding the Equine Genome: Lessons from ENCODE. Genes (Basel) 2021; 12:genes12111707. [PMID: 34828313 PMCID: PMC8625040 DOI: 10.3390/genes12111707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/24/2021] [Accepted: 10/26/2021] [Indexed: 12/23/2022] Open
Abstract
The horse reference genome assemblies, EquCab2.0 and EquCab3.0, have enabled great advancements in the equine genomics field, from tools to novel discoveries. However, significant gaps of knowledge regarding genome function remain, hindering the study of complex traits in horses. In an effort to address these gaps and with inspiration from the Encyclopedia of DNA Elements (ENCODE) project, the equine Functional Annotation of Animal Genome (FAANG) initiative was proposed to bridge the gap between genome and gene expression, providing further insights into functional regulation within the horse genome. Three years after launching the initiative, the equine FAANG group has generated data from more than 400 experiments using over 50 tissues, targeting a variety of regulatory features of the equine genome. In this review, we examine how valuable lessons learned from the ENCODE project informed our decisions in the equine FAANG project. We report the current state of the equine FAANG project and discuss how FAANG can serve as a template for future expansion of functional annotation in the equine genome and be used as a reference for studies of complex traits in horse. A well-annotated reference functional atlas will also help advance equine genetics in the pan-genome and precision medicine era.
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Affiliation(s)
- Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Ted Kalbfleisch
- Department of Veterinary Science, Gluck Equine Research Center, University of Kentucky, Lexington, KY 40503, USA;
| | - N. B. Kingsley
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Alexa M. Barber
- Department of Animal Science, University of Nebraska, Lincoln, NE 68583-0908, USA; (J.L.P.); (A.M.B.)
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Elena Giulotto
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, 27100 Pavia, Italy; (E.C.); (E.G.)
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA 95616, USA; (S.P.); (R.R.B.); (N.B.K.)
- Correspondence:
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Donnelly CG, Bellone RR, Hales EN, Nguyen A, Katzman SA, Dujovne GA, Knickelbein KE, Avila F, Kalbfleisch TS, Giulotto E, Kingsley NB, Tanaka J, Esdaile E, Peng S, Dahlgren A, Fuller A, Mienaltowski MJ, Raudsepp T, Affolter VK, Petersen JL, Finno CJ. Generation of a Biobank From Two Adult Thoroughbred Stallions for the Functional Annotation of Animal Genomes Initiative. Front Genet 2021; 12:650305. [PMID: 33763124 PMCID: PMC7982670 DOI: 10.3389/fgene.2021.650305] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/15/2021] [Indexed: 12/27/2022] Open
Abstract
Following the successful creation of a biobank from two adult Thoroughbred mares, this study aimed to recapitulate sample collection in two adult Thoroughbred stallions as part of the Functional Annotation of the Animal Genome (FAANG) initiative. Both stallions underwent thorough physical, lameness, neurologic, and ophthalmic (including electroretinography) examinations prior to humane euthanasia. Epididymal sperm was recovered from both stallions immediately postmortem and cryopreserved. Aseptically collected full thickness skin biopsies were used to isolate, culture and cryopreserve dermal fibroblasts. Serum, plasma, cerebrospinal fluid, urine, and gastrointestinal content from various locations were collected and cryopreserved. Under guidance of a board-certified veterinary anatomic pathologist, 102 representative tissue samples were collected from both horses. Whole tissue samples were flash-frozen and prioritized tissues had nuclei isolated and cryopreserved. Spatially contemporaneous samples of each tissue were submitted for histologic examination. Antemortem and gross pathologic examination revealed mild abnormalities in both stallions. One stallion (ECA_UCD_AH3) had unilateral thoracic limb lameness and bilateral chorioretinal scars. The second stallion (ECA_UCD_AH4) had subtle symmetrical pelvic limb ataxia, symmetrical prostatomegally, and moderate gastrointestinal nematodiasis. DNA from each was whole-genome sequenced and genotyped using the GGP Equine 70K SNP array. The genomic resources and banked biological samples from these animals augments the existing resource available to the equine genomics community. Importantly we may now improve the resolution of tissue-specific gene regulation as affected by sex, as well as add sex-specific tissues and gametes.
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Affiliation(s)
- Callum G Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Rebecca R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Erin N Hales
- Morris Animal Foundation, Denver, CO, United States
| | - Annee Nguyen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Scott A Katzman
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ghislaine A Dujovne
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Kelly E Knickelbein
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Felipe Avila
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Ted S Kalbfleisch
- Gluck Equine Research Center, University of Kentucky, Lexington, KY, United States
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Nicole B Kingsley
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jocelyn Tanaka
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Elizabeth Esdaile
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Sichong Peng
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Anna Fuller
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Michael J Mienaltowski
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California, Davis, Davis, CA, United States
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, United States
| | - Verena K Affolter
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Jessica L Petersen
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
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5
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Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci 2020; 21:ijms21082838. [PMID: 32325780 PMCID: PMC7215372 DOI: 10.3390/ijms21082838] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 01/06/2023] Open
Abstract
Interstitial telomeric sequences (ITSs) are short stretches of telomeric-like repeats (TTAGGG)n at nonterminal chromosomal sites. We previously demonstrated that, in the genomes of primates and rodents, ITSs were inserted during the repair of DNA double-strand breaks. These conclusions were derived from sequence comparisons of ITS-containing loci and ITS-less orthologous loci in different species. To our knowledge, insertion polymorphism of ITSs, i.e., the presence of an ITS-containing allele and an ITS-less allele in the same species, has not been described. In this work, we carried out a genome-wide analysis of 2504 human genomic sequences retrieved from the 1000 Genomes Project and a PCR-based analysis of 209 human DNA samples. In spite of the large number of individual genomes analyzed we did not find any evidence of insertion polymorphism in the human population. On the contrary, the analysis of ITS loci in the genome of a single horse individual, the reference genome, allowed us to identify five heterozygous ITS loci, suggesting that insertion polymorphism of ITSs is an important source of genetic variability in this species. Finally, following a comparative sequence analysis of horse ITSs and of their orthologous empty loci in other Perissodactyla, we propose models for the mechanism of ITS insertion during the evolution of this order.
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6
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Roberti A, Bensi M, Mazzagatti A, Piras FM, Nergadze SG, Giulotto E, Raimondi E. Satellite DNA at the Centromere is Dispensable for Segregation Fidelity. Genes (Basel) 2019; 10:genes10060469. [PMID: 31226862 PMCID: PMC6627300 DOI: 10.3390/genes10060469] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 06/19/2019] [Indexed: 12/14/2022] Open
Abstract
The typical vertebrate centromeres contain long stretches of highly repeated DNA sequences (satellite DNA). We previously demonstrated that the karyotypes of the species belonging to the genus Equus are characterized by the presence of satellite-free and satellite-based centromeres and represent a unique biological model for the study of centromere organization and behavior. Using horse primary fibroblasts cultured in vitro, we compared the segregation fidelity of chromosome 11, whose centromere is satellite-free, with that of chromosome 13, which has similar size and a centromere containing long stretches of satellite DNA. The mitotic stability of the two chromosomes was compared under normal conditions and under mitotic stress induced by the spindle inhibitor, nocodazole. Two independent molecular-cytogenetic approaches were used—the interphase aneuploidy analysis and the cytokinesis-block micronucleus assay. Both assays were coupled to fluorescence in situ hybridization with chromosome specific probes in order to identify chromosome 11 and chromosome 13, respectively. In addition, we tested if the lack of centromeric satellite DNA affected chromatid cohesion under normal and stress conditions. We demonstrated that, in our system, the segregation fidelity of a chromosome is not influenced by the presence of long stretches of tandem repeats at its centromere. To our knowledge, the present study is the first analysis of the mitotic behavior of a natural satellite-free centromere.
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Affiliation(s)
- Annalisa Roberti
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Mirella Bensi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Alice Mazzagatti
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Francesca M Piras
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Solomon G Nergadze
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Elena Giulotto
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
| | - Elena Raimondi
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 1, 27100 Pavia, Italy.
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7
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Burns EN, Bordbari MH, Mienaltowski MJ, Affolter VK, Barro MV, Gianino F, Gianino G, Giulotto E, Kalbfleisch TS, Katzman SA, Lassaline M, Leeb T, Mack M, Müller EJ, MacLeod JN, Ming-Whitfield B, Alanis CR, Raudsepp T, Scott E, Vig S, Zhou H, Petersen JL, Bellone RR, Finno CJ. Generation of an equine biobank to be used for Functional Annotation of Animal Genomes project. Anim Genet 2018; 49:564-570. [PMID: 30311254 DOI: 10.1111/age.12717] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2018] [Indexed: 12/13/2022]
Abstract
The Functional Annotation of Animal Genomes (FAANG) project aims to identify genomic regulatory elements in both sexes across multiple stages of development in domesticated animals. This study represents the first stage of the FAANG project for the horse, Equus caballus. A biobank of 80 tissue samples, two cell lines and six body fluids was created from two adult Thoroughbred mares. Ante-mortem assessments included full physical examinations, lameness, ophthalmologic and neurologic evaluations. Complete blood counts and serum biochemistries were also performed. At necropsy, in addition to tissue samples, aliquots of serum, ethylenediaminetetraacetic acid (EDTA) plasma, heparinized plasma, cerebrospinal fluid, synovial fluid, urine and microbiome samples from all regions of the gastrointestinal and urogenital tracts were collected. Epidermal keratinocytes and dermal fibroblasts were cultured from skin samples. All tissues were grossly and histologically evaluated by a board-certified veterinary pathologist. The results of the clinical and pathological evaluations identified subclinical eosinophilic and lymphocytic infiltration throughout the length of the gastrointestinal tract as well as a mild clinical lameness in both animals. Each sample was cryo-preserved in multiple ways, and nuclei were extracted from selected tissues. These samples represent the first published systemically healthy equine-specific biobank with extensive clinical phenotyping ante- and post-mortem. The tissues in the biobank are intended for community-wide use in the functional annotation of the equine genome. The use of the biobank will improve the quality of the reference annotation and allow all equine researchers to elucidate unknown genomic and epigenomic causes of disease.
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Affiliation(s)
- E N Burns
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M H Bordbari
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M J Mienaltowski
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - V K Affolter
- Department of Pathology, Microbiology, and Immunology, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - M V Barro
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - F Gianino
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - G Gianino
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - E Giulotto
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, Pavia, I-27100, Italy
| | - T S Kalbfleisch
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Louisville, Louisville, KY, 40292, USA
| | - S A Katzman
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - M Lassaline
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95618, USA
| | - T Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - M Mack
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - E J Müller
- Department of Biomedical Research, Molecular Dermatology and Stem Cell Research, Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland.,Department of Dermatology, Inselspital, Bern University Hospital, University of Bern, Bern, 3001, Switzerland
| | - J N MacLeod
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY, 40546, USA
| | - B Ming-Whitfield
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - C R Alanis
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA
| | - E Scott
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - S Vig
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - H Zhou
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska - Lincoln, Lincoln, NE, 68583, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
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Bassi B, Dacarro G, Galinetto P, Giulotto E, Marchesi N, Pallavicini P, Pascale A, Perversi S, Taglietti A. Tailored coating of gold nanostars: rational approach to prototype of theranostic device based on SERS and photothermal effects at ultralow irradiance. Nanotechnology 2018; 29:235301. [PMID: 29547134 DOI: 10.1088/1361-6528/aab74f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The last decade has come across an increasing demand for theranostic biocompatible nanodevices possessing the double ability of diagnosis and therapy. In this work, we report the design, synthesis and step-by-step characterization of rationally coated gold nanostars (GNSs) for the SERS imaging and photothermal therapy of HeLa cancer cells. The nanodevices were realized by synthesizing GNSs with a seed growth approach, coating them with a controlled mixture of thiols composed of a Raman reporter and a polyethylene glycol with a terminal amino group, and then reacting these amino groups with folic acid (FA), in order to impart selectivity towards cancer cells which overexpress folate receptors on their membranes. After a complete characterization, we demonstrate that these FA-functionalized GNSs (FA-GNSs) are able to bind selectively to the membranes of HeLa cells, acting as SERS tags and allowing SERS imaging. Moreover, we demonstrate that once bound to HeLa cell membranes, FA-GNSs exhibit photothermal effect which can be exploited to kill the same cells in vitro using laser irradiation in the NIR at a very low and safe irradiance. We thus demonstrate that the FA-GNSs designed following the described approach are an efficient prototype of theranostic nanodevices.
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Affiliation(s)
- B Bassi
- Dipartimento di Chimica, Sezione di Chimica Generale, Università di Pavia, viale Taramelli, 12-27100 Pavia, Italy
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9
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Nergadze SG, Piras FM, Gamba R, Corbo M, Cerutti F, McCarter JGW, Cappelletti E, Gozzo F, Harman RM, Antczak DF, Miller D, Scharfe M, Pavesi G, Raimondi E, Sullivan KF, Giulotto E. Birth, evolution, and transmission of satellite-free mammalian centromeric domains. Genome Res 2018; 28:789-799. [PMID: 29712753 PMCID: PMC5991519 DOI: 10.1101/gr.231159.117] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 04/13/2018] [Indexed: 11/25/2022]
Abstract
Mammalian centromeres are associated with highly repetitive DNA (satellite DNA), which has so far hindered molecular analysis of this chromatin domain. Centromeres are epigenetically specified, and binding of the CENPA protein is their main determinant. In previous work, we described the first example of a natural satellite-free centromere on Equus caballus Chromosome 11. Here, we investigated the satellite-free centromeres of Equus asinus by using ChIP-seq with anti-CENPA antibodies. We identified an extraordinarily high number of centromeres lacking satellite DNA (16 of 31). All of them lay in LINE- and AT-rich regions. A subset of these centromeres is associated with DNA amplification. The location of CENPA binding domains can vary in different individuals, giving rise to epialleles. The analysis of epiallele transmission in hybrids (three mules and one hinny) showed that centromeric domains are inherited as Mendelian traits, but their position can slide in one generation. Conversely, centromere location is stable during mitotic propagation of cultured cells. Our results demonstrate that the presence of more than half of centromeres void of satellite DNA is compatible with genome stability and species survival. The presence of amplified DNA at some centromeres suggests that these arrays may represent an intermediate stage toward satellite DNA formation during evolution. The fact that CENPA binding domains can move within relatively restricted regions (a few hundred kilobases) suggests that the centromeric function is physically limited by epigenetic boundaries.
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Affiliation(s)
- Solomon G Nergadze
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Francesca M Piras
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Riccardo Gamba
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Marco Corbo
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Federico Cerutti
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Joseph G W McCarter
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Eleonora Cappelletti
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Francesco Gozzo
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Rebecca M Harman
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Donald Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14850, USA
| | - Maren Scharfe
- Genomanalytik (GMAK), Helmholtz Centre for Infection Research (HZI), 38124 Braunschweig, Germany
| | - Giulio Pavesi
- Department of Biosciences, University of Milano, 20122 Milano, Italy
| | - Elena Raimondi
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
| | - Kevin F Sullivan
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland, Galway, H91 TK33, Ireland
| | - Elena Giulotto
- Department of Biology and Biotechnology "Lazzaro Spallanzani," University of Pavia, 27100 Pavia, Italy
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10
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Vitelli V, Falvo P, G Nergadze S, Santagostino M, Khoriauli L, Pellanda P, Bertino G, Occhini A, Benazzo M, Morbini P, Paulli M, Porta C, Giulotto E. Telomeric Repeat-Containing RNAs (TERRA) Decrease in Squamous Cell Carcinoma of the Head and Neck Is Associated with Worsened Clinical Outcome. Int J Mol Sci 2018; 19:ijms19010274. [PMID: 29342094 PMCID: PMC5796220 DOI: 10.3390/ijms19010274] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 12/16/2022] Open
Abstract
Telomeres are transcribed into noncoding telomeric repeat-containing RNAs (TERRA), which are essential for telomere maintenance. Deregulation of TERRA transcription impairs telomere metabolism and a role in tumorigenesis has been proposed. Head and neck cancer (HNC) is one of the most frequent cancers worldwide, with head and neck squamous cell carcinoma (HNSCC) being the predominant type. Since HNSCC patients are characterized by altered telomere maintenance, a dysfunction in telomere transcription can be hypothesized. In this prospective study, we compared TERRA levels in the tumor and matched normal tissue from 23 HNSCC patients. We then classified patients in two categories according to the level of TERRA expression in the tumor compared to the normal tissue: (1) lower expression in the tumor, (2) higher or similar expression in tumor. A significant proportion of patients in the first group died of the disease within less than 34 months postsurgery, while the majority of patients in the second group were alive and disease-free. Our results highlight a striking correlation between TERRA expression and tumor aggressiveness in HNSCC suggesting that TERRA levels may be proposed as a novel molecular prognostic marker for HNSCC.
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Affiliation(s)
- Valerio Vitelli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Paolo Falvo
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Solomon G Nergadze
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Marco Santagostino
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Lela Khoriauli
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Paola Pellanda
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
| | - Giulia Bertino
- Department of Otorhinolaryngology, IRCCS San Matteo University Hospital Foundation, 27100 Pavia, Italy.
| | - Antonio Occhini
- Department of Otorhinolaryngology, IRCCS San Matteo University Hospital Foundation, 27100 Pavia, Italy.
| | - Marco Benazzo
- Department of Otorhinolaryngology, IRCCS San Matteo University Hospital Foundation, 27100 Pavia, Italy.
| | - Patrizia Morbini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Marco Paulli
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy.
| | - Camillo Porta
- Division of Medical Oncology, IRCCS San Matteo University Hospital Foundation, 27100 Pavia, Italy.
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
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11
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Parolini M, Romano A, Costanzo A, Khoriauli L, Santagostino M, Nergadze SG, Canova L, Rubolini D, Giulotto E, Saino N. Telomere length is reflected by plumage coloration and predicts seasonal reproductive success in the barn swallow. Mol Ecol 2017; 26:6100-6109. [DOI: 10.1111/mec.14340] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/14/2017] [Accepted: 08/15/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Marco Parolini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - Andrea Romano
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - Alessandra Costanzo
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - Lela Khoriauli
- Department of Biology and Biotechnology University of Pavia Pavia Italy
| | | | | | - Luca Canova
- Department of Chemistry University of Pavia Pavia Italy
| | - Diego Rubolini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology University of Pavia Pavia Italy
| | - Nicola Saino
- Department of Environmental Science and Policy University of Milan Milan Italy
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12
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Parolini M, Khoriauli L, Possenti CD, Colombo G, Caprioli M, Santagostino M, Nergadze SG, Milzani A, Giulotto E, Saino N. Yolk vitamin E prevents oxidative damage in gull hatchlings. R Soc Open Sci 2017; 4:170098. [PMID: 28573018 PMCID: PMC5451819 DOI: 10.1098/rsos.170098] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
Oxidative stress experienced during early development can negatively affect diverse life-history traits, and organisms have evolved complex defence systems against its detrimental effects. Bird eggs contain maternally derived exogenous antioxidants that play a major role in embryo protection from oxidative damage, including the negative effects on telomere dynamics. In this study on the yellow-legged gull (Larus michahellis), we manipulated the concentration of vitamin E (VE) in the egg yolk and analysed the consequences on oxidative status markers and telomere length in the hatchlings. This study provides the first experimental evidence that, contrary to the expectation, a physiological increase in yolk VE concentration boosted total antioxidant capacity and reduced the concentration of pro-oxidant molecules in the plasma, but did not reduce telomere attrition or ameliorate oxidative damage to proteins and lipids in the early postnatal period.
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Affiliation(s)
- Marco Parolini
- Department of Environmental Science and Policy, via Celoria 26, I-20133 Milan, Italy
| | - Lela Khoriauli
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, I-27100 Pavia, Italy
| | | | - Graziano Colombo
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy, via Celoria 26, I-20133 Milan, Italy
| | - Marco Santagostino
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, I-27100 Pavia, Italy
| | - Solomon G. Nergadze
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, I-27100 Pavia, Italy
| | - Aldo Milzani
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Elena Giulotto
- Department of Biology and Biotechnology, University of Pavia, via Ferrata 1, I-27100 Pavia, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, via Celoria 26, I-20133 Milan, Italy
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13
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Abstract
Centromeres are highly distinctive genetic loci whose function is specified largely by epigenetic mechanisms. Understanding the role of DNA sequences in centromere function has been a daunting task due to the highly repetitive nature of centromeres in animal chromosomes. The discovery of a centromere devoid of satellite DNA in the domestic horse consolidated observations on the epigenetic nature of centromere identity, showing that entirely natural chromosomes could function without satellite DNA cues. Horses belong to the genus Equus which exhibits a very high degree of evolutionary plasticity in centromere position and DNA sequence composition. Examination of horses has revealed that the position of the satellite-free centromere is variable among individuals. Analysis of centromere location and composition in other Equus species, including domestic donkey and zebras, confirms that the satellite-less configuration of centromeres is common in this group which has undergone particularly rapid karyotype evolution. These features have established the equids as a new mammalian system in which to investigate the molecular organization, dynamics and evolutionary behaviour of centromeres.
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Affiliation(s)
- Elena Giulotto
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy
| | - Kevin F Sullivan
- National University of Ireland Galway, University Road, Galway, Ireland
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14
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Costanzo A, Parolini M, Bazzi G, Khoriauli L, Santagostino M, Possenti CD, Romano A, Nergadze SG, Rubolini D, Giulotto E, Saino N. Brood size, telomere length, and parent-offspring color signaling in barn swallows. Behav Ecol 2016. [DOI: 10.1093/beheco/arw147] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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15
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Cerutti F, Gamba R, Mazzagatti A, Piras FM, Cappelletti E, Belloni E, Nergadze SG, Raimondi E, Giulotto E. The major horse satellite DNA family is associated with centromere competence. Mol Cytogenet 2016; 9:35. [PMID: 27123044 PMCID: PMC4847189 DOI: 10.1186/s13039-016-0242-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 04/01/2016] [Indexed: 01/08/2023] Open
Abstract
Background The centromere is the specialized locus required for correct chromosome segregation during cell division. The DNA of most eukaryotic centromeres is composed of extended arrays of tandem repeats (satellite DNA). In the horse, we previously showed that, although the centromere of chromosome 11 is completely devoid of tandem repeat arrays, all other centromeres are characterized by the presence of satellite DNA. We isolated three horse satellite DNA sequences (37cen, 2P1 and EC137) and described their chromosomal localization in four species of the genus Equus. Results In the work presented here, using the ChIP-seq methodology, we showed that, in the horse, the 37cen satellite binds CENP-A, the centromere-specific histone-H3 variant. The 37cen sequence bound by CENP-A is GC-rich with 221 bp units organized in a head-to-tail fashion. The physical interaction of CENP-A with 37cen was confirmed through slot blot experiments. Immuno-FISH on stretched chromosomes and chromatin fibres demonstrated that the extension of satellite DNA stretches is variable and is not related to the organization of CENP-A binding domains. Finally, we proved that the centromeric satellite 37cen is transcriptionally active. Conclusions Our data offer new insights into the organization of horse centromeres. Although three different satellite DNA families are cytogenetically located at centromeres, only the 37cen family is associated to the centromeric function. Moreover, similarly to other species, CENP-A binding domains are variable in size. The transcriptional competence of the 37cen satellite that we observed adds new evidence to the hypothesis that centromeric transcripts may be required for centromere function. Electronic supplementary material The online version of this article (doi:10.1186/s13039-016-0242-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Federico Cerutti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Riccardo Gamba
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Alice Mazzagatti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Francesca M Piras
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Eleonora Cappelletti
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Elisa Belloni
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Solomon G Nergadze
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
| | - Elena Giulotto
- Dipartimento di Biologia e Biotecnologie, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
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16
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Santagostino M, Khoriauli L, Gamba R, Bonuglia M, Klipstein O, Piras FM, Vella F, Russo A, Badiale C, Mazzagatti A, Raimondi E, Nergadze SG, Giulotto E. Genome-wide evolutionary and functional analysis of the Equine Repetitive Element 1: an insertion in the myostatin promoter affects gene expression. BMC Genet 2015; 16:126. [PMID: 26503543 PMCID: PMC4623272 DOI: 10.1186/s12863-015-0281-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/13/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND In mammals, an important source of genomic variation is insertion polymorphism of retrotransposons. These may acquire a functional role when inserted inside genes or in their proximity. The aim of this work was to carry out a genome wide analysis of ERE1 retrotransposons in the horse and to analyze insertion polymorphism in relation to evolution and function. The effect of an ERE1 insertion in the promoter of the myostatin gene, which is involved in muscle development, was also investigated. RESULTS In the horse population, the fraction of ERE1 polymorphic loci is related to the degree of similarity to their consensus sequence. Through the analysis of ERE1 conservation in seven equid species, we established that the level of identity to their consensus is indicative of evolutionary age of insertion. The position of ERE1s relative to genes suggests that some elements have acquired a functional role. Reporter gene assays showed that the ERE1 insertion within the horse myostatin promoter affects gene expression. The frequency of this variant promoter correlates with sport aptitude and racing performance. CONCLUSIONS Sequence conservation and insertion polymorphism of ERE1 elements are related to the time of their appearance in the horse lineage, therefore, ERE1s are a useful tool for evolutionary and population studies. Our results suggest that the ERE1 insertion at the myostatin locus has been unwittingly selected by breeders to obtain horses with specific racing abilities. Although a complex combination of environmental and genetic factors contributes to athletic performance, breeding schemes may take into account ERE1 insertion polymorphism at the myostatin promoter.
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Affiliation(s)
- Marco Santagostino
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Lela Khoriauli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Riccardo Gamba
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Margherita Bonuglia
- Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy.
| | - Ori Klipstein
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Francesca M Piras
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Francesco Vella
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Alessandra Russo
- Laboratorio di Genetica Forense Veterinaria, UNIRELAB srl, Via A. Gramsci 70, 20019, Settimo Milanese (MI), Italy.
| | - Claudia Badiale
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Alice Mazzagatti
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Raimondi
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Solomon G Nergadze
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
| | - Elena Giulotto
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia, Via Ferrata 1, 27100, Pavia, Italy.
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17
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Abstract
The insertion of mitochondrial DNA in the nuclear genome generates numts, nuclear sequences of mitochondrial origin. In the horse reference genome, we identified 82 numts and showed that the entire horse mitochondrial DNA is represented as numts without gross bias. Numts were inserted in the horse nuclear genome at random sites and were probably generated during the repair of DNA double-strand breaks. We then analysed 12 numt loci in 20 unrelated horses and found that null alleles, lacking the mitochondrial DNA insertion, were present at six of these loci. At some loci, the null allele is prevalent in the sample analysed, suggesting that, in the horse population, the number of numt loci may be higher than 82 present in the reference genome. Contrary to humans, the insertion polymorphism of numts is extremely frequent in the horse population, supporting the hypothesis that the genome of this species is in a rapidly evolving state.
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Affiliation(s)
- S G Nergadze
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy
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18
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Purgato S, Belloni E, Piras FM, Zoli M, Badiale C, Cerutti F, Mazzagatti A, Perini G, Della Valle G, Nergadze SG, Sullivan KF, Raimondi E, Rocchi M, Giulotto E. Centromere sliding on a mammalian chromosome. Chromosoma 2014; 124:277-87. [PMID: 25413176 PMCID: PMC4446527 DOI: 10.1007/s00412-014-0493-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 11/25/2022]
Abstract
The centromere directs the segregation of chromosomes during mitosis and meiosis. It is a distinct genetic locus whose identity is established through epigenetic mechanisms that depend on the deposition of centromere-specific centromere protein A (CENP-A) nucleosomes. This important chromatin domain has so far escaped comprehensive molecular analysis due to its typical association with highly repetitive satellite DNA. In previous work, we discovered that the centromere of horse chromosome 11 is completely devoid of satellite DNA; this peculiar feature makes it a unique model to dissect the molecular architecture of mammalian centromeres. Here, we exploited this native satellite-free centromere to determine the precise localization of its functional domains in five individuals: We hybridized DNA purified from chromatin immunoprecipitated with an anti CENP-A antibody to a high resolution array (ChIP-on-chip) of the region containing the primary constriction of horse chromosome 11. Strikingly, each individual exhibited a different arrangement of CENP-A binding domains. We then analysed the organization of each domain using a single nucleotide polymorphism (SNP)-based approach and single molecule analysis on chromatin fibres. Examination of the ten instances of chromosome 11 in the five individuals revealed seven distinct ‘positional alleles’, each one extending for about 80–160 kb, were found across a region of about 500 kb. Our results demonstrate that CENP-A binding domains are autonomous relative to the underlying DNA sequence and are characterized by positional instability causing the sliding of centromere position. We propose that this dynamic behaviour may be common in mammalian centromeres and may determine the establishment of epigenetic alleles.
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Affiliation(s)
- Stefania Purgato
- Dipartimento di Farmacia e Biotecnologie (FABIT), Università di Bologna, Bologna, Italy
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19
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Nergadze SG, Belloni E, Piras FM, Khoriauli L, Mazzagatti A, Vella F, Bensi M, Vitelli V, Giulotto E, Raimondi E. Discovery and comparative analysis of a novel satellite, EC137, in horses and other equids. Cytogenet Genome Res 2014; 144:114-23. [PMID: 25342230 DOI: 10.1159/000368138] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 11/19/2022] Open
Abstract
Centromeres are the sites of kinetochore assembly and spindle fiber attachment and consist of protein-DNA complexes in which the DNA component is typically characterized by the presence of extended arrays of tandem repeats called satellite DNA. Here, we describe the isolation and characterization of a 137-bp-long new satellite DNA sequence from the horse genome (EC137), which is also present, even if less abundant, in the domestic donkey, the Grevy's zebra and the Burchelli's zebra. We investigated the chromosomal distribution of the EC137 sequence in these 4 species. Moreover, we analyzed its architectural organization by high-resolution FISH. The position of this sequence with respect to the primary constriction and in relation to the 2 major horse satellite tandem repeats (37 cen and 2PI) on horse chromosomes suggests that the new centromeric equine satellite is an accessory DNA element, presumably contributing to the organization of pericentromeric chromatin. FISH on combed DNA fibers reveals that the EC137 satellite is organized in relatively short stretches (2-8 kb) which are strictly intermingled within 37 cen or 2PI arrays. This arrangement suggests that interchanges between satellite families are a frequent occurrence in the horse genome.
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Affiliation(s)
- Solomon G Nergadze
- Department of Biology and Biotechnology 'L. Spallanzani', University of Pavia, Pavia, Italy
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20
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Reig-Viader R, Vila-Cejudo M, Vitelli V, Buscà R, Sabaté M, Giulotto E, Caldés MG, Ruiz-Herrera A. Telomeric Repeat-Containing RNA (TERRA) and Telomerase Are Components of Telomeres During Mammalian Gametogenesis1. Biol Reprod 2014; 90:103. [DOI: 10.1095/biolreprod.113.116954] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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21
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Vitelli V, Falvo P, Khoriauli L, Smirnova A, Gamba R, Santagostino M, Nergadze SG, Giulotto E. More on the Lack of Correlation between Terra Expression and Telomere Length. Front Oncol 2013; 3:245. [PMID: 24066279 PMCID: PMC3776138 DOI: 10.3389/fonc.2013.00245] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022] Open
Affiliation(s)
- Valerio Vitelli
- Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani," Università degli Studi di Pavia , Pavia, Italy
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Smirnova A, Gamba R, Khoriauli L, Vitelli V, Nergadze SG, Giulotto E. TERRA Expression Levels Do Not Correlate with Telomere Length and Radiation Sensitivity in Human Cancer Cell Lines. Front Oncol 2013; 3:115. [PMID: 23717814 PMCID: PMC3650684 DOI: 10.3389/fonc.2013.00115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 04/25/2013] [Indexed: 11/13/2022] Open
Abstract
Mammalian telomeres are transcribed into long non-coding telomeric repeat-containing RNA (TERRA) molecules that seem to play a role in the maintenance of telomere stability. In human cells, CpG-island promoters drive TERRA transcription and are regulated by methylation. It was suggested that the amount of TERRA may be related to telomere length. To test this hypothesis we measured telomere length and TERRA levels in single clones isolated from five human cell lines: HeLa (cervical carcinoma), BRC-230 (breast cancer), AKG and GK2 (gastric cancers), and GM847 (SV40 immortalized skin fibroblasts). However, these two parameters did not correlate with each other. Moreover, cell survival to γ-rays did not show a significant variation among the clones, suggesting that, in this cellular system, the intra-population variability in telomere length and TERRA levels does not influence sensitivity to ionizing radiation. This conclusion was supported by the observation that in a cell line in which telomeres were greatly elongated by the ectopic expression of telomerase, TERRA expression levels and radiation sensitivity were similar to the parental HeLa cell line.
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Affiliation(s)
- Alexandra Smirnova
- Laboratorio di Biologia Molecolare e Cellulare, Dipartimento di Biologia e Biotecnologie "Lazzaro Spallanzani", Università di Pavia Pavia, Italy
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Chiodi I, Belgiovine C, Zongaro S, Ricotti R, Horard B, Lossani A, Focher F, Gilson E, Giulotto E, Mondello C. Super-telomeres in transformed human fibroblasts. Biochim Biophys Acta 2013; 1833:1885-93. [PMID: 23570868 DOI: 10.1016/j.bbamcr.2013.03.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/22/2013] [Accepted: 03/29/2013] [Indexed: 01/13/2023]
Abstract
Telomere length maintenance is critical for organisms' long-term survival and cancer cell proliferation. Telomeres are kept within species-specific length ranges by the interplay between telomerase activity and telomeric chromatin organization. In this paper, we exploited telomerase immortalized human fibroblasts (cen3tel) that gradually underwent neoplastic transformation during culture propagation to study telomere composition and length regulation during the transformation process. Just after telomerase catalytic subunit (hTERT) expression, cen3tel telomeres shortened despite the presence of telomerase activity. At a later stage and concomitantly with transformation, cells started elongating telomeres, which reached a mean length greater than 100kb in about 900 population doublings. Super-telomeres were stable and compatible with cell growth and tumorigenesis. Telomere extension was associated with increasing levels of telomerase activity that were linked to the deregulation of endogenous telomerase RNA (hTERC) and exogenous telomerase reverse transcriptase (hTERT) expression. Notably, the increase in hTERC levels paralleled the increase in telomerase activity, suggesting that this subunit plays a role in regulating enzyme activity. Telomeres ranging in length between 10 and more than 100kb were maintained in an extendible state although TRF1 and TRF2 binding increased with telomere length. Super-telomeres neither influenced subtelomeric region global methylation nor the expression of the subtelomeric gene FRG1, attesting the lack of a clear-cut relationship between telomere length, subtelomeric DNA methylation and expression in human cells. The cellular levels of the telomeric proteins hTERT, TRF1, TRF2 and Hsp90 rose with transformation and were independent of telomere length, pointing to a role of these proteins in tumorigenesis.
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Reig-Viader R, Brieno-Enriquez MA, Khouriauli L, Toran N, Cabero L, Giulotto E, Garcia-Caldes M, Ruiz-Herrera A. Telomeric repeat-containing RNA and telomerase in human fetal oocytes. Hum Reprod 2012; 28:414-22. [DOI: 10.1093/humrep/des363] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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25
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Vidale P, Piras FM, Nergadze SG, Bertoni L, Verini-Supplizi A, Adelson D, Guérin G, Giulotto E. Chromosomal assignment of six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) in four species of the genus Equus. Anim Biotechnol 2011; 22:119-23. [PMID: 21774619 DOI: 10.1080/10495398.2011.575300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We mapped six genes (EIF4G3, HSP90, RBBP6, IL8, TERT, and TERC) on the chromosomes of Equus caballus, Equus asinus, Equus grevyi, and Equus burchelli by fluorescence in situ hybridization. Our results add six type I markers to the cytogenetic map of these species and provide new information on the comparative genomics of the genus Equus.
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Affiliation(s)
- Pamela Vidale
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, Pavia, Italy
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Engman M, Bystrom B, Varghese S, Lalitkumar PGL, Gemzell-Danielsson K, Romeu C, Urries A, Lierta M, Sanchez Rubio J, Sanz B, Perez I, Casis L, Salerno A, Nazzaro A, Di Iorio L, Bonassisa P, Van Os L, Vink-Ranti CQJ, de Haan-Cramer JH, Rijnders PM, Jansen CAM, Nazzaro A, Salerno A, Marino S, Granato C, Pastore E, Brandes M, Hamilton CJCM, de Bruin JP, Bots RSGM, Nelen WLDM, Kremer JAM, Szkodziak P, Wozniak S, Czuczwar P, Paszkowski T, Wozniak S, Szkodziak P, Czuczwar P, Paszkowski T, Agirregoitia N, Peralta L, Mendoza R, Exposito A, Matorras R, Agirregoitia E, Chuderland D, Ben-Ami I, Kaplan-Kraicer R, Grossman H, Satchi- Fainaro R, Eldar-Boock A, Ron-El R, Shalgi R, Custers IM, Scholten I, Moolenaar LM, Flierman PA, Dessel TJHM, Gerards MH, Cox T, Janssen CAH, van der Veen F, Mol BWJ, Wathlet S, Adriaenssens T, Verheyen G, Coucke W, Smitz J, Feliciani E, Ferraretti AP, Paesano C, Pellizzaro E, Magli MC, Gianaroli L, Hernandez J, Rodriguez-Fuentes A, Garcia-Guzman R, Palumbo A, Radunovic N, Tosic T, Djukic S, Lockwood JC, Adriaenssens T, Wathlet S, Van Landuyt L, Verheyen G, Coucke W, Smitz J, Karayalcin R, Ozcan SARP, Ozyer S, Gurlek B, Kale I, Moraloglu O, Batioglu S, Chaudhury K, Narendra Babu K, Mamata Joshi V, Srivastava S, Chakravarty BN, Viardot-Foucault V, Prasath EB, Tai BC, Chan JKY, Loh SF, Cordeiro I, Leal F, Soares AP, Nunes J, Sousa S, Aguiar A, Carvalho M, Calhaz-Jorge C, Karkanaki A, Piouk A, Katsikis I, Mousatat T, Koiou E, Daskalopoulos GN, Panidis D, Tolikas A, Tsakos E, Gerou S, Prapas Y, Loufopoulos A, Abanto E, Barrenetxea G, Agirregoikoa J, Anarte C, De Pablo JL, Burgos J, Komarovsky D, Friedler S, Gidoni Y, Ben-ami I, Strassburger D, Bern O, Kasterstein E E, Komsky A, Maslansky B, Ron-El R, Raziel A, Fuentes A, Argandona F, Gabler F, Galleguillos A, Torres A, Palomino WA, Gonzalez-Fernandez R, Pena O, Hernandez J, Palumbo A, Avila J, Talebi Chahvar S, Biondini V, Battistoni S, Giannubilo S, Tranquilli AL, Stensen MH, Tanbo T, Storeng R, Abyholm T, Fedorcsak P, Johnson SR, Foster L, Ellis J, Choi JR, Joo JK, Son JB, Lee KS, Helmgaard L, Klein BM, Arce JC, Sanhueza P, Donoso P, Salinas R, Enriquez R, Saez V, Carrasco I, Rios M, Gonzalez P, Macklon N, Guo M, Richardson M, Wilson P, Chian RC, Eapen A, Hrehorcak M, Campbell S, Nargund G, Oron G, Fisch B, Ao A, Freidman O, Zhang XY, Ben-Haroush A, Abir R, Hantisteanu S, Ellenbogen A, Hallak M, Michaeli M, Fainaru O, Maman E, Yong G, Kedem A, Yeruahlmi G, Konopnicki S, Cohen B, Dor J, Hourvitz A, Moshin V, Croitor M, Hotineanu A, Ciorap Z, Rasohin E, Aleyasin A, Agha Hosseini M, Mahdavi A, Safdarian L, Fallahi P, Mohajeri MR, Abbasi M, Esfahani F, Elnashar A, Badawy A, Totongy M, Mohamed H, Mustafa F, Seidman DS, Tadir Y, Goldchmit C, Gilboa Y, Siton A, Mashiach R, Rabinovici J, Yerushalmi GM, Inoue O, Kuji N, Fukunaga T, Ogawa S, Sugawara K, Yamada M, Hamatani T, Hanabusa H, Yoshimura Y, Kato S, Casarini L, La Marca A, Lispi M, Longobardi S, Pignatti E, Simoni M, Halpern G, Braga DPAF, Figueira RCS, Setti AS, Iaconelli Jr. A, Borges Jr. E, Vingris L, Setti AS, Braga DPAF, Figueira RCS, Iaconelli Jr. A, Pasqualotto FF, Borges Jr. E, Collado-Fernandez E, Harris SE, Cotterill M, Elder K, Picton HM, Serra V, Garrido N, Casanova C, Lara C, Remohi J, Bellver J, Steiner HP, Kim CH, You RM, Nah HY, Kang HJ, Kim S, Chae HD, Kang BM, Reig Viader R, Brieno Enriquez MA, Toran N, Cabero L, Giulotto E, Garcia Caldes M, Ruiz-Herrera A, Brieno-Enriquez M, Reig-Viader R, Toran N, Cabero L, Martinez F, Garcia-Caldes M, Velthut A, Zilmer M, Zilmer K, Haller T. Kaart E, Karro H, Salumets A, Bromfield JJ, Sheldon IM, Rezacova J, Madar J, Cuchalova L, Fiserova A, Shao R, Billig H. POSTER VIEWING SESSION - FEMALE (IN) FERTILITY. Hum Reprod 2011. [DOI: 10.1093/humrep/26.s1.82] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Raimondi E, Piras FM, Nergadze SG, Di Meo GP, Ruiz-Herrera A, Ponsà M, Ianuzzi L, Giulotto E. Polymorphic organization of constitutive heterochromatin in Equus asinus (2n = 62) chromosome 1. Hereditas 2011; 148:110-3. [PMID: 21756256 DOI: 10.1111/j.1601-5223.2011.02218.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In the karyotype of Equus asinus (domestic donkey, 2n = 62), non-centromeric heterochromatic bands have been described in subcentromeric and telomeric positions. In particular, chromosome 1 is characterised by heterochromatic bands in the proximal region of the long arm and in the short arm; it has been shown that these regions are polymorphic in size. Here we investigated the variation in the intensity and distribution of fluorescence signals observed on donkey chromosome 1 after in situ hybridization with two DNA probes containing fragments from the two major equine satellite DNA families. Our results show that, in Equus asinus chromosome 1, the amount and distribution of large clusters of satellite DNA can define at least nine polymorphic variants of the constitutive heterochromatin that cannot be detected by C-banding alone.
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Affiliation(s)
- Elena Raimondi
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, Pavia, Italy
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Ruiz-Herrera A, Smirnova A, Khoriauli L, Nergadze SG, Mondello C, Giulotto E. Gene amplification in human cells knocked down for RAD54. Genome Integr 2011; 2:5. [PMID: 21418575 PMCID: PMC3074559 DOI: 10.1186/2041-9414-2-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 03/18/2011] [Indexed: 12/18/2022] Open
Abstract
Background In mammalian cells gene amplification is a common manifestation of genome instability promoted by DNA double-strand breaks (DSBs). The repair of DSBs mainly occurs through two mechanisms: non-homologous end-joining (NHEJ) and homologous recombination (HR). We previously showed that defects in the repair of DSBs via NHEJ could increase the frequency of gene amplification. In this paper we explored whether a single or a combined defect in DSBs repair pathways can affect gene amplification. Results We constructed human cell lines in which the expression of RAD54 and/or DNA-PKcs was constitutively knocked-down by RNA interference. We analyzed their radiosensitivity and their capacity to generate amplified DNA. Our results showed that both RAD54 and DNA-PKcs deficient cells are hypersensitive to γ-irradiation and generate methotrexate resistant colonies at a higher frequency compared to the proficient cell lines. In addition, the analysis of the cytogenetic organization of the amplicons revealed that isochromosome formation is a prevalent mechanism responsible for copy number increase in RAD54 defective cells. Conclusions Defects in the DSBs repair mechanisms can influence the organization of amplified DNA. The high frequency of isochromosome formation in cells deficient for RAD54 suggests that homologous recombination proteins might play a role in preventing rearrangements at the centromeres.
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Affiliation(s)
- Aurora Ruiz-Herrera
- Dipartimento di Genetica e Microbiologia "Adriano Buzzati-Traverso", Università di Pavia, Via Ferrata 1, 27100 Pavia, Italy.
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Farnung BO, Giulotto E, Azzalin CM. Promoting transcription of chromosome ends. Transcription 2010; 1:140-143. [PMID: 21326888 DOI: 10.4161/trns.1.3.13191] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2010] [Revised: 07/23/2010] [Accepted: 07/27/2010] [Indexed: 12/19/2022] Open
Abstract
We recently identified CpG island promoters driving transcription of human telomeric repeat-containing RNA (TERRA). This discovery has shaped a new concept in telomere biology, where TERRA promoters and downstream telomeric sequences constitute autonomous genic units.
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Affiliation(s)
- Benjamin O Farnung
- Institute of Biochemistry; Eidgenössische Technische Hochschule Zürich (ETHZ); Zürich, Switzerland
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30
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Piras FM, Nergadze SG, Magnani E, Bertoni L, Attolini C, Khoriauli L, Raimondi E, Giulotto E. Uncoupling of satellite DNA and centromeric function in the genus Equus. PLoS Genet 2010; 6:e1000845. [PMID: 20169180 PMCID: PMC2820525 DOI: 10.1371/journal.pgen.1000845] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 01/12/2010] [Indexed: 12/21/2022] Open
Abstract
In a previous study, we showed that centromere repositioning, that is the shift along the chromosome of the centromeric function without DNA sequence rearrangement, has occurred frequently during the evolution of the genus Equus. In this work, the analysis of the chromosomal distribution of satellite tandem repeats in Equus caballus, E. asinus, E. grevyi, and E. burchelli highlighted two atypical features: 1) several centromeres, including the previously described evolutionary new centromeres (ENCs), seem to be devoid of satellite DNA, and 2) satellite repeats are often present at non-centromeric termini, probably corresponding to relics of ancestral now inactive centromeres. Immuno-FISH experiments using satellite DNA and antibodies against the kinetochore protein CENP-A demonstrated that satellite-less primary constrictions are actually endowed with centromeric function. The phylogenetic reconstruction of centromere repositioning events demonstrates that the acquisition of satellite DNA occurs after the formation of the centromere during evolution and that centromeres can function over millions of years and many generations without detectable satellite DNA. The rapidly evolving Equus species gave us the opportunity to identify different intermediate steps along the full maturation of ENCs. Centromeres are the functional elements controlling chromosome segregation during cell division. Vertebrate centromeres, which typically contain large amounts of tandem repeats (satellite DNA), are highly conserved for function but not for DNA sequence, suggesting that centromeric function is mainly determined by epigenetic factors. Evolutionary centromere repositioning is the shift of a centromere to a new position in the absence of structural chromosome rearrangements. In previous work, we demonstrated that centromere repositioning was exceptionally frequent during the evolution of the genus Equus (horses, asses, and zebras). In the present paper, we show that several Equus centromeres, including all the previously described evolutionary new centromeres, are apparently satellite-free, supporting the idea that large blocks of repeats are not necessarily required for the stability of centromeres. Our results suggest that centromere repositioning might be a two-step event: first, a neocentromere arises in a satellite-less region; satellite repeats may then colonize this repositioned centromere at a later stage, giving rise to a “mature” centromere. The rapidly evolving Equus species gave us the opportunity to catch snapshots of several evolutionary novel centromeres in different stages during their maturation.
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Affiliation(s)
- Francesca M. Piras
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Solomon G. Nergadze
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Elisa Magnani
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Livia Bertoni
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Carmen Attolini
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Lela Khoriauli
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Elena Raimondi
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
| | - Elena Giulotto
- Dipartimento di Genetica e Microbiologia “Adriano Buzzati-Traverso”, Università di Pavia, Pavia, Italy
- * E-mail:
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Mondello C, Smirnova A, Giulotto E. Gene amplification, radiation sensitivity and DNA double-strand breaks. Mutat Res 2010; 704:29-37. [PMID: 20093194 DOI: 10.1016/j.mrrev.2010.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/21/2009] [Accepted: 01/11/2010] [Indexed: 11/25/2022]
Abstract
DNA double-strand breaks (DSBs) are one of the main types of damage induced by ionizing radiations. Free DNA ends that are not correctly repaired can be engaged in pathways triggering gene amplification. Following gene amplification the copy number of a portion of the genome is increased, leading to an enhanced expression of the genes located in the amplified region. Gene amplification plays an important role in cancer, being one of the mechanisms of oncogene activation; in addition, it can confer resistance to chemotherapeutic agents, through the increase in the copy number of genes coding for drug targets. The presence of gene amplification can have a prognostic and a diagnostic value and can help in orienting therapy in specific tumour types. The amplified DNA is primarily produced through recombination-based pathways and can be located either within chromosomes or on extra-chromosomal acentric elements. Studies on the organization of the amplified DNA in tumour cells and in cultured drug resistant cells have suggested that a single DSB can trigger a cascade of events leading to a large number of copies of a region of the genome. In addition, it has been shown that amplified DNA is unstable, further increasing the long-term effect of the initial event. Gene amplification is a peculiar feature of transformed cells and the ability to amplify is strongly influenced by the cellular genetic background. Genes involved in DNA damage response and in DNA damage repair can play a role in controlling the amplification process, in particular, it has been shown that defects in DSB repair functions can increase the frequency of gene amplification. In this review, we will discuss the biological significance of gene amplification, together with the role of DNA DSBs and DSB repair genes in the generation of amplified DNA.
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Affiliation(s)
- Chiara Mondello
- Istituto di Genetica Molecolare, CNR, Via Abbiategrasso 207, 27100 Pavia, Italy
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Piras FM, Nergadze SG, Poletto V, Cerutti F, Ryder OA, Leeb T, Raimondi E, Giulotto E. Phylogeny of horse chromosome 5q in the genus Equus and centromere repositioning. Cytogenet Genome Res 2009; 126:165-72. [PMID: 20016166 DOI: 10.1159/000245916] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2009] [Indexed: 11/19/2022] Open
Abstract
Horses, asses and zebras belong to the genus Equus and are the only extant species of the family Equidae in the order Perissodactyla. In a previous work we demonstrated that a key factor in the rapid karyotypic evolution of this genus was evolutionary centromere repositioning, that is, the shift of the centromeric function to a new position without alteration of the order of markers along the chromosome. In search of previously undiscovered evolutionarily new centromeres, we traced the phylogeny of horse chromosome 5, analyzing the order of BAC markers, derived from a horse genomic library, in 7 Equus species (E. caballus, E. hemionus onager, E. kiang, E. asinus, E. grevyi, E. burchelli and E. zebra hartmannae). This analysis showed that repositioned centromeres are present in E. asinus (domestic donkey, EAS) chromosome 16 and in E. burchelli (Burchell's zebra, EBU) chromosome 17, confirming that centromere repositioning is a strikingly frequent phenomenon in this genus. The observation that the neocentromeres in EAS16 and EBU17 are in the same chromosomal position suggests that they may derive from the same event and therefore, E. asinus and E. burchelli may be more closely related than previously proposed; alternatively, 2 centromere repositioning events, involving the same chromosomal region, may have occurred independently in different lineages, pointing to the possible existence of hot spots for neocentromere formation. Our comparative analysis also showed that, while E. caballus chromosome 5 seems to represent the ancestral configuration, centric fission followed by independent fusion events gave rise to 3 different submetacentric chromosomes in other Equus lineages.
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Affiliation(s)
- F M Piras
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, Pavia, Italy
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Wade CM, Giulotto E, Sigurdsson S, Zoli M, Gnerre S, Imsland F, Lear TL, Adelson DL, Bailey E, Bellone RR, Blöcker H, Distl O, Edgar RC, Garber M, Leeb T, Mauceli E, MacLeod JN, Penedo MCT, Raison JM, Sharpe T, Vogel J, Andersson L, Antczak DF, Biagi T, Binns MM, Chowdhary BP, Coleman SJ, Della Valle G, Fryc S, Guérin G, Hasegawa T, Hill EW, Jurka J, Kiialainen A, Lindgren G, Liu J, Magnani E, Mickelson JR, Murray J, Nergadze SG, Onofrio R, Pedroni S, Piras MF, Raudsepp T, Rocchi M, Røed KH, Ryder OA, Searle S, Skow L, Swinburne JE, Syvänen AC, Tozaki T, Valberg SJ, Vaudin M, White JR, Zody MC, Lander ES, Lindblad-Toh K. Genome sequence, comparative analysis, and population genetics of the domestic horse. Science 2009; 326:865-7. [PMID: 19892987 DOI: 10.1126/science.1178158] [Citation(s) in RCA: 555] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We report a high-quality draft sequence of the genome of the horse (Equus caballus). The genome is relatively repetitive but has little segmental duplication. Chromosomes appear to have undergone few historical rearrangements: 53% of equine chromosomes show conserved synteny to a single human chromosome. Equine chromosome 11 is shown to have an evolutionary new centromere devoid of centromeric satellite DNA, suggesting that centromeric function may arise before satellite repeat accumulation. Linkage disequilibrium, showing the influences of early domestication of large herds of female horses, is intermediate in length between dog and human, and there is long-range haplotype sharing among breeds.
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Affiliation(s)
- C M Wade
- Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA.
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Nergadze SG, Farnung BO, Wischnewski H, Khoriauli L, Vitelli V, Chawla R, Giulotto E, Azzalin CM. CpG-island promoters drive transcription of human telomeres. RNA 2009; 15:2186-94. [PMID: 19850908 PMCID: PMC2779677 DOI: 10.1261/rna.1748309] [Citation(s) in RCA: 177] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 09/03/2009] [Indexed: 05/22/2023]
Abstract
The longstanding dogma that telomeres, the heterochromatic extremities of linear eukaryotic chromosomes, are transcriptionally silent was overturned by the discovery that DNA-dependent RNA polymerase II (RNAPII) transcribes telomeric DNA into telomeric repeat-containing RNA (TERRA). Here, we show that CpG dinucleotide-rich DNA islands, shared among multiple human chromosome ends, promote transcription of TERRA molecules. TERRA promoters sustain cellular expression of reporter genes, are located immediately upstream of TERRA transcription start sites, and are bound by active RNAPII in vivo. Finally, the identified promoter CpG dinucleotides are methylated in vivo, and cytosine methylation negatively regulates TERRA abundance. The existence of subtelomeric promoters, driving TERRA transcription from independent chromosome ends, supports the idea that TERRA exerts fundamental functions in the context of telomere biology.
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Affiliation(s)
- Solomon G Nergadze
- Dipartimento di Genetica e Microbiologia Adriano Buzzati-Traverso, Università di Pavia, 2700 Pavia, Italy
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Giulotto E. Neocentromere formation and evolution in the genus Equus. N Biotechnol 2009. [DOI: 10.1016/j.nbt.2009.06.842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Ruiz-Herrera A, Nergadze SG, Santagostino M, Giulotto E. Telomeric repeats far from the ends: mechanisms of origin and role in evolution. Cytogenet Genome Res 2009; 122:219-28. [PMID: 19188690 DOI: 10.1159/000167807] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2008] [Indexed: 11/19/2022] Open
Abstract
In addition to their location at terminal positions, telomeric-like repeats are also present at internal sites of the chromosomes (intrachromosomal or interstitial telomeric sequences, ITSs). According to their sequence organization and genomic location, two different kinds of ITSs can be identified: (1) heterochromatic ITSs (het-ITSs), large (up to hundreds of kb) stretches of telomeric-like DNA localized mainly at centromeres, and (2) short ITSs (s-ITSs), short stretches of telomeric hexamers distributed at internal sites of the chromosomes. Het-ITSs have been only described in some vertebrate species and they probably represent the remnants of evolutionary chromosomal rearrangements. On the contrary, s-ITSs are probably present in all mammalian genomes although they have been described in detail only in some completely sequenced genomes. Sequence database analysis revealed the presence of 83, 79, 244 and 250 such s-ITSs in the human, chimpanzee, mouse and rat genomes, respectively. Analysis of the flanking sequences suggested that s-ITSs were inserted during the repair of DNA double-strand breaks that occurred in the course of evolution. An extensive comparative analysis of the s-ITS loci and their orthologous 'empty' loci confirmed this hypothesis and suggested that the repair event involved the direct action of telomerase. Whereas het-ITSs seem to be intrinsically prone to breakage, the instability of s-ITSs is more controversial. This observation is consistent with the hypothesis that s-ITSs are probably not themselves prone to breakage but represent 'scars' of ancient breakage that may have occurred within fragile regions. This study will review the current knowledge on these two types of ITS, their molecular organization, how they arose during evolution, their implications for chromosomal instability and their potential applications as phylogenetic/forensic markers.
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Affiliation(s)
- A Ruiz-Herrera
- Dipartimento di Genetica e Microbiologia, Adriano Buzzati-Traverso, Università di Pavia, Pavia, Italy
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Zongaro S, Verri A, Giulotto E, Mondello C. Telomere length and radiosensitivity in human fibroblast clones immortalized by ectopic telomerase expression. Oncol Rep 2008; 19:1605-1609. [PMID: 18497972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023] Open
Abstract
Telomeres, the ends of eukaryotic chromosomes, have a variable length among individuals and cell types. While studies in telomerase-deficient mice and cells showed an inverse correlation between telomere length and radiosensitivity, it is less clear whether this remains true in telomerase-proficient cells. To gain insight into this topic, we studied radiosensitivity in three telomerase immortalized fibroblast clones derived from the same cell line and characterized by different telomere length. In two clones, cen3tel4 and cen3tel5, the mean terminal restriction fragment length was approximately 13 and 10 kb, respectively and in the third clone, cen3pci16, it was approximately 4 kb, which is lower than in senescent fibroblasts. To test radiosensitivity, we determined survival to gamma-rays and the induction of chromosomal aberrations after irradiation. Neither the LD50, the gamma-ray dose that reduces survival to 50%, nor the frequency of aberrations detected in the three cell lines showed an inverse correlation with telomere length. In particular, the cen3pci16 cells, which have very short telomeres, did not show a higher sensitivity to irradiation or a greater frequency of chromosomal abnormalities compared to the other two cell lines. Our results suggest that, in the presence of telomerase activity, short telomeres are stabilized and do not cause an increase in radiosensitivity.
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Mondello C, Giulotto E, Verri A, Zongaro S. Telomere length and radiosensitivity in human fibroblast clones immortalized by ectopic telomerase expression. Oncol Rep 2008. [DOI: 10.3892/or.19.6.1605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Nergadze SG, Santagostino MA, Salzano A, Mondello C, Giulotto E. Contribution of telomerase RNA retrotranscription to DNA double-strand break repair during mammalian genome evolution. Genome Biol 2008; 8:R260. [PMID: 18067655 PMCID: PMC2246262 DOI: 10.1186/gb-2007-8-12-r260] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Revised: 11/28/2007] [Accepted: 12/07/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In vertebrates, tandem arrays of TTAGGG hexamers are present at both telomeres and intrachromosomal sites (interstitial telomeric sequences (ITSs)). We previously showed that, in primates, ITSs were inserted during the repair of DNA double-strand breaks and proposed that they could arise from either the capture of telomeric fragments or the action of telomerase. RESULTS An extensive comparative analysis of two primate (Homo sapiens and Pan troglodytes) and two rodent (Mus musculus and Rattus norvegicus) genomes allowed us to describe organization and insertion mechanisms of all the informative ITSs present in the four species. Two novel observations support the hypothesis of telomerase involvement in ITS insertion: in a highly significant fraction of informative loci, the ITSs were introduced at break sites where a few nucleotides homologous to the telomeric hexamer were exposed; in the rodent genomes, complex ITS loci are present in which a retrotranscribed fragment of the telomerase RNA, far away from the canonical template, was inserted together with the telomeric repeats. Moreover, mutational analysis of the TTAGGG arrays in the different species suggests that they were inserted as exact telomeric hexamers, further supporting the participation of telomerase in ITS formation. CONCLUSION These results strongly suggest that telomerase was utilized, in some instances, for the repair of DNA double-strand breaks occurring in the genomes of rodents and primates during evolution. The presence, in the rodent genomes, of sequences retrotranscribed from the telomerase RNA strengthens the hypothesis of the origin of telomerase from an ancient retrotransposon.
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Affiliation(s)
- Solomon G Nergadze
- Dipartimento di Genetica e Microbiologia 'Adriano Buzzati-Traverso', Università degli Studi di Pavia, Via Ferrata, 27100 Pavia, Italy
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Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends. Science 2007; 318:798-801. [PMID: 17916692 DOI: 10.1126/science.1147182] [Citation(s) in RCA: 939] [Impact Index Per Article: 55.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Telomeres, the DNA-protein complexes located at the end of linear eukaryotic chromosomes, are essential for chromosome stability. Until now, telomeres have been considered to be transcriptionally silent. We demonstrate that mammalian telomeres are transcribed into telomeric repeat-containing RNA (TERRA). TERRA molecules are heterogeneous in length, are transcribed from several subtelomeric loci toward chromosome ends, and localize to telomeres. We also show that suppressors with morphogenetic defects in genitalia (SMG) proteins, which are effectors of nonsense-mediated messenger RNA decay, are enriched at telomeres in vivo, negatively regulate TERRA association with chromatin, and protect chromosome ends from telomere loss. Thus, telomeres are actively transcribed into TERRA, and SMG factors represent a molecular link between TERRA regulation and the maintenance of telomere integrity.
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Affiliation(s)
- Claus M Azzalin
- Swiss Institute for Experimental Cancer Research (ISREC), CH-1066 Epalinges, Switzerland
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41
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Herszberg B, Mata X, Giulotto E, Decaunes P, Piras FM, Chowdhary BP, Chaffaux S, Guérin G. Characterization of the equine glycogen debranching enzyme gene (AGL): Genomic and cDNA structure, localization, polymorphism and expression. Gene 2007; 404:1-9. [PMID: 17905541 DOI: 10.1016/j.gene.2007.07.034] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2007] [Revised: 07/20/2007] [Accepted: 07/24/2007] [Indexed: 10/22/2022]
Abstract
Glycogen debranching enzyme (AGL) is a multifunctional enzyme acting in the glycogen degradation pathway. In humans, the AGL activity deficiency causes a type III glycogen storage disease (Cori-Forbes disease). One particularity of AGL gene expression lies in the multiple alternative splicing in its 5' region. The AGL gene was localized on ECA5q14-q15. The sequence of the equine cDNA was determined to be 7.5 kb in length with an open reading frame of 4602 bp. The gene is 69 kb long and contains 35 exons. The equine AGL gene has an ubiquitous expression and presents five tissue-dependent cDNA variants arising from alternative splicing of the first exons. The equine skeletal muscle and heart contain four out of six variants previously described in humans and the equine liver express three of these four human variants. We identified a new alternative splicing variant expressed in equine skeletal and heart muscles. All these mRNA variants most probably encode only two different protein isoforms of 1533 and 1377 amino-acids. Four SNPs were detected in the mRNA. The equine in silico promoter sequence reveals a structure similar to those of other mammalian species. The disposition of the transcription factor biding sites does not correlate to the transcription start sites of tissue-specific variants.
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Affiliation(s)
- Bérénice Herszberg
- Institut National de la Recherche Agronomique, UR339, Centre de Recherches de Jouy, Laboratoire de Génétique biochimique et de Cytogénétique, 78350 Jouy-en-Josas, France
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Prause A, Guionaud CT, Klukowska-Rötzler J, Giulotto E, Magnani E, Chowdhary BP, Philipp U, Leeb T, Mevissen M. Chromosomal assignment of five equine HTR genes by FISH and RH mapping. Anim Genet 2007; 38:83-4. [PMID: 17257197 DOI: 10.1111/j.1365-2052.2006.01546.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- A Prause
- Division of Veterinary Pharmacology and Toxicology, University of Berne, PO box 8466, 3001 Berne, Switzerland
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Rebuzzini P, Martinelli P, Blasco M, Giulotto E, Mondello C. Inhibition of gene amplification in telomerase deficient immortalized mouse embryonic fibroblasts. Carcinogenesis 2006; 28:553-9. [PMID: 16973670 DOI: 10.1093/carcin/bgl158] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mutations in genes important for the preservation of genome stability can increase the frequency of gene amplification, a process relevant to tumor development. To investigate whether telomerase, the enzyme deputed to telomere maintenance, also plays a role in gene amplification, we studied the amplification of the carbamyl-P-synthetase, aspartate transcarbamilase, dihydro-orotase (CAD) gene in immortalized embryonic fibroblasts derived from telomerase knockout mice (mTERC(-/-)) of the first and of the sixth generation. As expected, in 9 out of 10 N-(phosphonacetyl)-L-aspartate (PALA) resistant clones derived from wild-type cells, CAD was amplified; in contrast, in none of the 30 PALA resistant clones isolated from the three mTERC(-/-) cell lines we could detect CAD amplification, indicating that, in the absence of telomerase activity, gene amplification is inhibited. The causal relationship between mTERC deficiency and lack of gene amplification was demonstrated by the restoration of CAD gene amplification in two of the three deficient cell lines transfected with mTERC. The lack of amplification in mTERC deficient cells could be related to a defect in the stabilization of the ends of the amplified chromosomes in the absence of telomerase, to a more general effect of telomerase in the regulation of gene expression, including genes involved in amplification, or to a possible interaction of the telomerase RNA with proteins involved in gene amplification.
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Affiliation(s)
- Paola Rebuzzini
- Istituto di Genetica Molecolare, CNR Via Abbiategrasso 207, 27100 Pavia, Italy
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Carbone L, Nergadze SG, Magnani E, Misceo D, Francesca Cardone M, Roberto R, Bertoni L, Attolini C, Francesca Piras M, de Jong P, Raudsepp T, Chowdhary BP, Guérin G, Archidiacono N, Rocchi M, Giulotto E. Evolutionary movement of centromeres in horse, donkey, and zebra. Genomics 2006; 87:777-82. [PMID: 16413164 DOI: 10.1016/j.ygeno.2005.11.012] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2005] [Revised: 11/22/2005] [Accepted: 11/22/2005] [Indexed: 10/25/2022]
Abstract
Centromere repositioning (CR) is a recently discovered biological phenomenon consisting of the emergence of a new centromere along a chromosome and the inactivation of the old one. After a CR, the primary constriction and the centromeric function are localized in a new position while the order of physical markers on the chromosome remains unchanged. These events profoundly affect chromosomal architecture. Since horses, asses, and zebras, whose evolutionary divergence is relatively recent, show remarkable morphological similarity and capacity to interbreed despite their chromosomes differing considerably, we investigated the role of CR in the karyotype evolution of the genus Equus. Using appropriate panels of BAC clones in FISH experiments, we compared the centromere position and marker order arrangement among orthologous chromosomes of Burchelli's zebra (Equus burchelli), donkey (Equus asinus), and horse (Equus caballus). Surprisingly, at least eight CRs took place during the evolution of this genus. Even more surprisingly, five cases of CR have occurred in the donkey after its divergence from zebra, that is, in a very short evolutionary time (approximately 1 million years). These findings suggest that in some species the CR phenomenon could have played an important role in karyotype shaping, with potential consequences on population dynamics and speciation.
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Affiliation(s)
- Lucia Carbone
- Department of Genetics and Microbiology, University of Bari, Via Amendola 165/A, 70126 Bari, Italy
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Camats N, Ruiz-Herrera A, Parrilla JJ, Acien M, Payá P, Giulotto E, Egozcue J, García F, Garcia M. Genomic instability in rat: breakpoints induced by ionising radiation and interstitial telomeric-like sequences. Mutat Res 2006; 595:156-66. [PMID: 16413932 DOI: 10.1016/j.mrfmmm.2005.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 10/27/2005] [Accepted: 11/18/2005] [Indexed: 11/16/2022]
Abstract
The Norwegian rat (Rattus norvegicus) is the most widely studied experimental species in biomedical research although little is known about its chromosomal structure. The characterisation of possible unstable regions of the karyotype of this species would contribute to the better understanding of its genomic architecture. The cytogenetic effects of ionising radiation have been widely used for the study of genomic instability, and the importance of interstitial telomeric-like sequences (ITSs) in instability of the genome has also been reported in previous studies in vertebrates. In order to describe the unstable chromosomal regions of R. norvegicus, the distribution of breakpoints induced by X-irradiation and ITSs in its karyotype were analysed in this work. For the X-irradiation analysis, 52 foetuses (from 14 irradiated rats) were studied, 4803 metaphases were analysed, and a total of 456 breakpoints induced by X-rays were detected, located in 114 chromosomal bands, with 25 of them significantly affected by X-irradiation (hot spots). For the analysis of ITSs, three foetuses (from three rats) were studied, 305 metaphases were analysed and 121 ITSs were detected, widely distributed in the karyotype of this species. Seventy-six percent of all hot spots analysed in this study were co-localised with ITSs.
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Affiliation(s)
- Núiria Camats
- Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
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46
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Nergadze SG, Magnani E, Attolini C, Bertoni L, Adelson DL, Cappelli K, Verini Supplizi A, Giulotto E. Assignment of the Equus caballus interleukin 8 gene (IL8) to chromosome 3q14.2-->q14.3 by in situ hybridization. Cytogenet Genome Res 2006; 112:341B. [PMID: 16484794 DOI: 10.1159/000089892] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Accepted: 10/10/2005] [Indexed: 11/19/2022] Open
Affiliation(s)
- S G Nergadze
- Dipartimento di Genetica e Microbiologia, Università di Pavia, Pavia, Italy
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47
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Zongaro S, de Stanchina E, Colombo T, D'Incalci M, Giulotto E, Mondello C. Stepwise neoplastic transformation of a telomerase immortalized fibroblast cell line. Cancer Res 2006; 65:11411-8. [PMID: 16357149 DOI: 10.1158/0008-5472.can-05-1140] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We have described recently a human fibroblast cell line immortalized through ectopic telomerase expression (cen3tel), in which the extension of the life span was associated with the appearance of chromosomal aberrations and with the ability to grow in the absence of solid support. As reported in this article, on further propagation in culture, cen3tel cells became neoplastically transformed, being able to form tumors in nude mice. The analysis of the cells, during the gradual transition toward the tumorigenic phenotype, allowed us to trace cellular and molecular changes associated with different phases of transformation. At the stage in which they were able to grow in agar, cen3tel cells had lost contact growth inhibition but still retained the requirement of serum to proliferate and were not tumorigenic in immunocompromised mice. Moreover, they showed a down-regulation of the INK4A locus and were resistant to oncogenic Ras-induced senescence but still retained a functional p53. Subsequently, cen3tel cells became tumorigenic, lost p53 function because of a mutation in the DNA-binding motif, and overexpressed c-myc. Interestingly, tumorigenic cells did not carry activating mutations either in the ras proto-oncogenes (H-ras, N-ras, and K-ras) or in B-raf. Cen3tel cells gradually became hyperdiploid but did not display centrosome abnormalities. To our knowledge, cen3tel is the first telomerase immortalized fibroblast line, which became neoplastically transformed. In this system, we could associate a down-regulation of the INK4A locus with anchorage-independent growth and with resistance to Ras-induced senescence and link p53 mutations and c-myc overexpression with tumorigenicity.
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Affiliation(s)
- Samantha Zongaro
- Istituto di Genetica Molecolare, Consiglio Nazionale della Ricerche, Pavia, Italy
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48
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Rebuzzini P, Khoriauli L, Azzalin CM, Magnani E, Mondello C, Giulotto E. New mammalian cellular systems to study mutations introduced at the break site by non-homologous end-joining. DNA Repair (Amst) 2005; 4:546-55. [PMID: 15811627 DOI: 10.1016/j.dnarep.2004.12.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2004] [Accepted: 12/27/2004] [Indexed: 01/03/2023]
Abstract
The non-homologous end-joining (NHEJ) pathway is a mechanism to repair DNA double strand breaks, which can introduce mutations at repair sites. We constructed new cellular systems to specifically analyze sequence modifications occurring at the repair site. In particular, we looked for the presence of telomeric repeats at the repair junctions, since our previous work indicated that telomeric sequences could be inserted at break sites in germ-line cells during primate evolution. To induce specific DNA breaks, we used the I-SceI system of Saccharomyces cerevisiae or digestion with restriction enzymes. We isolated human and hamster cell lines containing the I-SceI target site integrated in a single chromosomal locus and we exposed the cells to a continuous expression of the I-SceI endonuclease gene. Additionally, we isolated human cell lines that expressed constitutively the I-SceI endonuclease and we introduced the target site on an episomal plasmid stably transfected into the cells. These strategies allowed us to recover repair junctions in which the I-SceI target site was modified at high frequency (100% in hamster cells and about 70% in human cells). Finally, we analyzed junctions produced on an episomal plasmid linearized by restriction enzymes. In all the systems studied, sequence analysis of individual repair junctions showed that deletions were the most frequent modifications, being present in more than 80% of the junctions. On the episomal plasmids, the average deletion length was greater than at intrachromosomal sites. Insertions of nucleotides or deletions associated with insertions were rare events. Junction organization suggested different mechanisms of formation. To check for the insertion of telomeric sequences, we screened plasmid libraries representing about 3.5 x 10(5) junctions with a telomeric repeat probe. No positive clones were detected, suggesting that the addition of telomeric sequences during double strand break repair in somatic cells in culture is either a very rare event or does not occur at all.
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Affiliation(s)
- Paola Rebuzzini
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche, via Abbiategrasso 207, 27100 Pavia, Italy
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Ruiz-Herrera A, García F, Giulotto E, Attolini C, Egozcue J, Ponsà M, Garcia M. Evolutionary breakpoints are co-localized with fragile sites and intrachromosomal telomeric sequences in primates. Cytogenet Genome Res 2005; 108:234-47. [PMID: 15545736 DOI: 10.1159/000080822] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2003] [Accepted: 12/22/2003] [Indexed: 01/22/2023] Open
Abstract
The concentration of evolutionary breakpoints in primate karyotypes in some particular regions or chromosome bands suggests that these chromosome regions are more prone to breakage. This is the first extensive comparative study which investigates a possible relationship of two genetic markers (intrachromosomal telomeric sequences [TTAGGG]n, [ITSs] and fragile sites [FSs]), which are implicated in the evolutionary process as well as in chromosome rearrangements. For this purpose, we have analyzed: (a) the cytogenetic expression of aphidicolin-induced FSs in Cebus apella and Cebus nigrivittatus (F. Cebidae, Platyrrhini) and Mandrillus sphinx (F. Cercopithecidae, Catarrhini), and (b) the intrachromosomal position of telomeric-like sequences by FISH with a synthetic (TTAGGG)n probe in C. apella chromosomes. The multinomial FSM statistical model allowed us to determinate 53 FSs in C. apella, 16 FSs in C. nigrivittatus and 50 FSs in M. sphinx. As expected, all telomeres hybridized with the probe, and 55 intrachromosomal loci were also detected in the Cebus apella karyotype. The chi(2) test indicates that the coincidence of the location of Cebus and Mandrillus FSs with the location of human FSs is significant (P < 0.005). Based on a comparative cytogenetic study among different primate species we have identified (or described) the chromosome bands in the karyotypes of Papionini and Cebus species implicated in evolutionary reorganizations. More than 80% of these evolutionary breakpoints are located in chromosome bands that express FSs and/or contain ITSs.
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Affiliation(s)
- A Ruiz-Herrera
- Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Spain
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Nergadze SG, Rocchi M, Azzalin CM, Mondello C, Giulotto E. Insertion of telomeric repeats at intrachromosomal break sites during primate evolution. Genome Res 2004; 14:1704-10. [PMID: 15310657 PMCID: PMC515315 DOI: 10.1101/gr.2778904] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Short blocks of telomeric-like DNA (Interstitial Telomeric Sequences, ITSs) are found far from chromosome ends. We addressed the question as to how such sequences arise by comparing the loci of 10 human ITSs with their genomic orthologs in 12 primate species. The ITSs did not derive from expansion of pre-existing TTAGGG units, as described for other microsatellites, but appeared suddenly during evolution. Nine insertion events were dated along the primate evolutionary tree, the dates ranging between 40 and 6 million years ago. Sequence comparisons suggest that in each case the block of (TTAGGG)n DNA arose as a result of double-strand break repair. In fact, ancestral sequences were either interrupted precisely by the tract of telomeric-like repeats or showed the typical modifications observed at double-strand break repair sites such as short deletions, addition of random sequences, or duplications. Similar conclusions were drawn from the analysis of a chimpanzee-specific ITS. We propose that telomeric sequences were inserted by the capture of a telomeric DNA fragment at the break site or by the telomerase enzyme. Our conclusions indicate that human ITSs are relics of ancient breakage rather than fragile sites themselves, as previously suggested.
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Affiliation(s)
- Solomon G Nergadze
- Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, 27100 Pavia, Italy
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