FREE SHIPPING over $40
OVER 9000 FIVE-STAR REVIEWS
5% OFF ALL SUBSCRIPTIONS
100% HAPPINESS GUARANTEE
Analyze Diet
0
Home / Equine Research Bank / Int J Mol Sci / Insertion of Telomeric Repeats in the Human and Horse Genome...
International journal of molecular sciences2020; 21(8); 2838; doi: 10.3390/ijms21082838

Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective.

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.
Get Full Text
Publication Date: 2020-04-18 PubMed ID: 32325780PubMed Central: PMC7215372DOI: 10.3390/ijms21082838Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
LinkedInCopy
  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research examines the existence of Interstitial Telomeric Sequences (ITSs), specific DNA sequences, in human and horse genomes. The study didn’t find any variability of these sequences is in the human population, but it did identify such variation in horses which could have important genetic implications.

Understanding the Basics

  • The article focuses on short portions of DNA known as Interstitial Telomeric Sequences. These are sequences similar to telomeres, the protective end caps of our chromosomes, but are located at non-terminal chromosomal locations, or within chromosomes.
  • Previous studies highlighted how this sequence emerged during repair of DNA double-strand breaks in primates and rodents – this type of DNA damage can lead to genetic disorders or cancer if not properly repaired.

The Human Genome Analysis

  • The researchers used genomic data from 2504 humans from the 1000 Genomes Project, a global initiative to create a detailed catalogue of human genetic variation.
  • They searched for evidence of ITS insertion polymorphism – variation due to the presence of an ITS in some instances (ITS-containing) and its absence in others (ITS-less) within the same species.
  • To their knowledge, no such variability has been described earlier, and their research further confirmed this – they found no evidence of ITS insertion polymorphism in the human genome.

Horse Genome Analysis and Comparative Modeling

  • Analysis of the horse genome, on the other hand, revealed five instances of ITS insertion polymorphism.
  • This is significant as it suggests that ITS insertion could be an important source of genetic variability or diversity in horses. Genetic diversity is crucial for species adaptation and evolution.
  • The researchers also compared these horse ITS sequences with their counterparts in other members of the horse family (Perissodactyla), proposing models for how these ITS sequences may have been inserted throughout the evolution of this family.

In summary, this study contributes toward understanding how these unique DNA sequences play a role in species’ genetic variability, potentially influencing how they evolve and adapt.

Cite This Article

APA
Santagostino M, Piras FM, Cappelletti E, Del Giudice S, Semino O, Nergadze SG, Giulotto E. (2020). Insertion of Telomeric Repeats in the Human and Horse Genomes: An Evolutionary Perspective. Int J Mol Sci, 21(8), 2838. https://doi.org/10.3390/ijms21082838

Publication

International journal of molecular sciences
ISSN: 1422-0067
NlmUniqueID: 101092791
Country: Switzerland
Language: English
Volume: 21
Issue: 8
PII: 2838

Researcher Affiliations

Santagostino, Marco
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Piras, Francesca M
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Cappelletti, Eleonora
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Del Giudice, Simone
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Semino, Ornella
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Nergadze, Solomon G
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.
Giulotto, Elena
  • Department of Biology and Biotechnology, University of Pavia, 27100 Pavia, Italy.

MeSH Terms

  • Alleles
  • Animals
  • Cells, Cultured
  • Chromosomes / genetics
  • Evolution, Molecular
  • Fibroblasts / cytology
  • Fibroblasts / metabolism
  • Genome, Human
  • Genome-Wide Association Study
  • Heterozygote
  • Horses / genetics
  • Humans
  • In Situ Hybridization, Fluorescence
  • Polymorphism, Genetic
  • Repetitive Sequences, Nucleic Acid / genetics
  • Telomere / genetics

Conflict of Interest Statement

The authors declare no conflict of interest.

References

This article includes 89 references
  1. Shay JW, Wright WE. Telomeres and telomerase: three decades of progress.. Nat Rev Genet 2019 May;20(5):299-309.
    doi: 10.1038/s41576-019-0099-1pubmed: 30760854google scholar: lookup
  2. de Lange T. Shelterin-Mediated Telomere Protection.. Annu Rev Genet 2018 Nov 23;52:223-247.
    doi: 10.1146/annurev-genet-032918-021921pubmed: 30208292google scholar: lookup
  3. Campisi J. Cellular senescence as a tumor-suppressor mechanism.. Trends Cell Biol 2001 Nov;11(11):S27-31.
    doi: 10.1016/S0962-8924(01)02151-1pubmed: 11684439google scholar: lookup
  4. Deng Y, Chan SS, Chang S. Telomere dysfunction and tumour suppression: the senescence connection.. Nat Rev Cancer 2008 Jun;8(6):450-8.
    doi: 10.1038/nrc2393pmc: PMC3688269pubmed: 18500246google scholar: lookup
  5. McHugh D, Gil J. Senescence and aging: Causes, consequences, and therapeutic avenues.. J Cell Biol 2018 Jan 2;217(1):65-77.
    doi: 10.1083/jcb.201708092pmc: PMC5748990pubmed: 29114066google scholar: lookup
  6. Shay JW. Telomeres and aging.. Curr Opin Cell Biol 2018 Jun;52:1-7.
    doi: 10.1016/j.ceb.2017.12.001pubmed: 29253739google scholar: lookup
  7. Azzalin CM, Reichenbach P, Khoriauli L, Giulotto E, Lingner J. Telomeric repeat containing RNA and RNA surveillance factors at mammalian chromosome ends.. Science 2007 Nov 2;318(5851):798-801.
    doi: 10.1126/science.1147182pubmed: 17916692google scholar: lookup
  8. Bettin N, Oss Pegorar C, Cusanelli E. The Emerging Roles of TERRA in Telomere Maintenance and Genome Stability.. Cells 2019 Mar 15;8(3).
    doi: 10.3390/cells8030246pmc: PMC6468625pubmed: 30875900google scholar: lookup
  9. Schoeftner S, Blasco MA. Developmentally regulated transcription of mammalian telomeres by DNA-dependent RNA polymerase II.. Nat Cell Biol 2008 Feb;10(2):228-36.
    doi: 10.1038/ncb1685pubmed: 18157120google scholar: lookup
  10. 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 Jan 17;19(1).
    doi: 10.3390/ijms19010274pmc: PMC5796220pubmed: 29342094google scholar: lookup
  11. Storti CB, de Oliveira RA, de Carvalho M, Hasimoto EN, Cataneo DC, Cataneo AJM, De Faveri J, Vasconcelos EJR, Dos Reis PP, Cano MIN. Telomere-associated genes and telomeric lncRNAs are biomarker candidates in lung squamous cell carcinoma (LUSC).. Exp Mol Pathol 2020 Feb;112:104354.
    doi: 10.1016/j.yexmp.2019.104354pubmed: 31837325google scholar: lookup
  12. Meyne J, Baker RJ, Hobart HH, Hsu TC, Ryder OA, Ward OG, Wiley JE, Wurster-Hill DH, Yates TL, Moyzis RK. Distribution of non-telomeric sites of the (TTAGGG)n telomeric sequence in vertebrate chromosomes.. Chromosoma 1990 Apr;99(1):3-10.
    doi: 10.1007/BF01737283pubmed: 2340757google scholar: lookup
  13. 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 2008;122(3-4):219-28.
    doi: 10.1159/000167807pubmed: 19188690google scholar: lookup
  14. Faravelli M, Moralli D, Bertoni L, Attolini C, Chernova O, Raimondi E, Giulotto E. Two extended arrays of a satellite DNA sequence at the centromere and at the short-arm telomere of Chinese hamster chromosome 5.. Cytogenet Cell Genet 1998;83(3-4):281-6.
    doi: 10.1159/000015171pubmed: 10072604google scholar: lookup
  15. Faravelli M, Azzalin CM, Bertoni L, Chernova O, Attolini C, Mondello C, Giulotto E. Molecular organization of internal telomeric sequences in Chinese hamster chromosomes.. Gene 2002 Jan 23;283(1-2):11-6.
    doi: 10.1016/S0378-1119(01)00877-0pubmed: 11867208google scholar: lookup
  16. Nanda I, Schrama D, Feichtinger W, Haaf T, Schartl M, Schmid M. Distribution of telomeric (TTAGGG)(n) sequences in avian chromosomes.. Chromosoma 2002 Nov;111(4):215-27.
    doi: 10.1007/s00412-002-0206-4pubmed: 12424522google scholar: lookup
  17. Ventura K, Silva MJ, Fagundes V, Christoff AU, Yonenaga-Yassuda Y. Non-telomeric sites as evidence of chromosomal rearrangement and repetitive (TTAGGG)n arrays in heterochromatic and euchromatic regions in four species of Akodon (Rodentia, Muridae).. Cytogenet Genome Res 2006;115(2):169-75.
    doi: 10.1159/000095238pubmed: 17065799google scholar: lookup
  18. Rovatsos M, Kratochvíl L, Altmanová M, Johnson Pokorná M. Interstitial Telomeric Motifs in Squamate Reptiles: When the Exceptions Outnumber the Rule.. PLoS One 2015;10(8):e0134985.
    doi: 10.1371/journal.pone.0134985pmc: PMC4529230pubmed: 26252002google scholar: lookup
  19. Zattera ML, Lima L, Duarte I, de Sousa DY, Araújo OGDS, Gazoni T, Mott T, Recco-Pimentel SM, Bruschi DP. Chromosome spreading of the (TTAGGG)n repeats in the Pipa carvalhoi Miranda-Ribeiro, 1937 (Pipidae, Anura) karyotype.. Comp Cytogenet 2019;13(3):297-309.
    doi: 10.3897/CompCytogen.v13i3.35524pmc: PMC6803351pubmed: 31649799google scholar: lookup
  20. López-Fernández C, Arroyo F, Fernández JL, Gosálvez J. Interstitial telomeric sequence blocks in constitutive pericentromeric heterochromatin from Pyrgomorpha conica (Orthoptera) are enriched in constitutive alkali-labile sites.. Mutat Res 2006 Jul 25;599(1-2):36-44.
    doi: 10.1016/j.mrfmmm.2006.01.004pubmed: 16481011google scholar: lookup
  21. He L, Liu J, Torres GA, Zhang H, Jiang J, Xie C. Interstitial telomeric repeats are enriched in the centromeres of chromosomes in Solanum species.. Chromosome Res 2013 Mar;21(1):5-13.
    doi: 10.1007/s10577-012-9332-xpubmed: 23250588google scholar: lookup
  22. IJdo JW, Baldini A, Ward DC, Reeders ST, Wells RA. Origin of human chromosome 2: an ancestral telomere-telomere fusion.. Proc Natl Acad Sci U S A 1991 Oct 15;88(20):9051-5.
    doi: 10.1073/pnas.88.20.9051pmc: PMC52649pubmed: 1924367google scholar: lookup
  23. Azzalin CM, Nergadze SG, Giulotto E. Human intrachromosomal telomeric-like repeats: sequence organization and mechanisms of origin.. Chromosoma 2001 May;110(2):75-82.
    doi: 10.1007/s004120100135pubmed: 11453557google scholar: lookup
  24. Azzalin CM, Mucciolo E, Bertoni L, Giulotto E. Fluorescence in situ hybridization with a synthetic (T2AG3)n polynucleotide detects several intrachromosomal telomere-like repeats on human chromosomes.. Cytogenet Cell Genet 1997;78(2):112-5.
    doi: 10.1159/000134640pubmed: 9371401google scholar: lookup
  25. 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 2007;8(12):R260.
    doi: 10.1186/gb-2007-8-12-r260pmc: PMC2246262pubmed: 18067655google scholar: lookup
  26. Ruiz-Herrera A, García F, Azzalin C, Giulotto E, Egozcue J, Ponsà M, Garcia M. Distribution of intrachromosomal telomeric sequences (ITS) on Macaca fascicularis (Primates) chromosomes and their implication for chromosome evolution.. Hum Genet 2002 Jun;110(6):578-86.
    doi: 10.1007/s00439-002-0730-6pubmed: 12107444google scholar: lookup
  27. Nergadze SG, Rocchi M, Azzalin CM, Mondello C, Giulotto E. Insertion of telomeric repeats at intrachromosomal break sites during primate evolution.. Genome Res 2004 Sep;14(9):1704-10.
    doi: 10.1101/gr.2778904pmc: PMC515315pubmed: 15310657google scholar: lookup
  28. 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(1-3):234-47.
    doi: 10.1159/000080822pubmed: 15545736google scholar: lookup
  29. Bertoni L, Attolini C, Faravelli M, Simi S, Giulotto E. Intrachromosomal telomere-like DNA sequences in Chinese hamster.. Mamm Genome 1996 Nov;7(11):853-5.
    doi: 10.1007/s003359900250pubmed: 8875896google scholar: lookup
  30. Simi S, Attolini C, Giulotto E. Intrachromosomal telomeric repeats and stabilization of truncated chromosomes in V79 Chinese hamster cells.. Mutat Res 1998 Feb 2;397(2):229-33.
    doi: 10.1016/S0027-5107(97)00217-0pubmed: 9541647google scholar: lookup
  31. de la Seña C, Chowdhary BP, Gustavsson I. Localization of the telomeric (TTAGGG)n sequences in chromosomes of some domestic animals by fluorescence in situ hybridization.. Hereditas 1995;123(3):269-74.
    doi: 10.1111/j.1601-5223.1995.t01-1-00269.xpubmed: 8675441google scholar: lookup
  32. Raudsepp T, Christensen K, Chowdhar BP. Cytogenetics of donkey chromosomes: nomenclature proposal based on GTG-banded chromosomes and depiction of NORs and telomeric sites.. Chromosome Res 2000;8(8):659-70.
    doi: 10.1023/A:1026707002538pubmed: 11196129google scholar: lookup
  33. Santani A, Raudsepp T, Chowdhary BP. Interstitial telomeric sites and NORs in Hartmann's zebra (Equus zebra hartmannae) chromosomes.. Chromosome Res 2002;10(7):527-34.
    doi: 10.1023/A:1020945400949pubmed: 12498342google scholar: lookup
  34. Schlötterer C, Tautz D. Slippage synthesis of simple sequence DNA.. Nucleic Acids Res 1992 Jan 25;20(2):211-5.
    doi: 10.1093/nar/20.2.211pmc: PMC310356pubmed: 1741246google scholar: lookup
  35. 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 Mar 20;595(1-2):156-66.
    doi: 10.1016/j.mrfmmm.2005.11.002pubmed: 16413932google scholar: lookup
  36. Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski W, Jorde LB, Deininger PL, Batzer MA. Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity.. J Mol Biol 2001 Aug 3;311(1):17-40.
    doi: 10.1006/jmbi.2001.4847pubmed: 11469855google scholar: lookup
  37. Batzer MA, Deininger PL. Alu repeats and human genomic diversity.. Nat Rev Genet 2002 May;3(5):370-9.
    doi: 10.1038/nrg798pubmed: 11988762google scholar: lookup
  38. Roy-Engel AM, Salem AH, Oyeniran OO, Deininger L, Hedges DJ, Kilroy GE, Batzer MA, Deininger PL. Active Alu element "A-tails": size does matter.. Genome Res 2002 Sep;12(9):1333-44.
    doi: 10.1101/gr.384802pmc: PMC186649pubmed: 12213770google scholar: lookup
  39. Salem AH, Ray DA, Xing J, Callinan PA, Myers JS, Hedges DJ, Garber RK, Witherspoon DJ, Jorde LB, Batzer MA. Alu elements and hominid phylogenetics.. Proc Natl Acad Sci U S A 2003 Oct 28;100(22):12787-91.
    doi: 10.1073/pnas.2133766100pmc: PMC240696pubmed: 14561894google scholar: lookup
  40. Bennett EA, Coleman LE, Tsui C, Pittard WS, Devine SE. Natural genetic variation caused by transposable elements in humans.. Genetics 2004 Oct;168(2):933-51.
    doi: 10.1534/genetics.104.031757pmc: PMC1448813pubmed: 15514065google scholar: lookup
  41. Wang J, Song L, Gonder MK, Azrak S, Ray DA, Batzer MA, Tishkoff SA, Liang P. Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms.. Gene 2006 Jan 3;365:11-20.
    doi: 10.1016/j.gene.2005.09.031pmc: PMC1847407pubmed: 16376498google scholar: lookup
  42. Walker JA, Jordan VE, Storer JM, Steely CJ, Gonzalez-Quiroga P, Beckstrom TO, Rewerts LC, St Romain CP, Rockwell CE, Rogers J, Jolly CJ, Konkel MK, Batzer MA. Alu insertion polymorphisms shared by Papio baboons and Theropithecus gelada reveal an intertwined common ancestry.. Mob DNA 2019;10:46.
    doi: 10.1186/s13100-019-0187-ypmc: PMC6880559pubmed: 31788036google scholar: lookup
  43. Wang L, Rishishwar L, Mariño-Ramírez L, Jordan IK. Human population-specific gene expression and transcriptional network modification with polymorphic transposable elements.. Nucleic Acids Res 2017 Mar 17;45(5):2318-2328.
    doi: 10.1093/nar/gkw1286pmc: PMC5389732pubmed: 27998931google scholar: lookup
  44. Pitkänen E, Cajuso T, Katainen R, Kaasinen E, Välimäki N, Palin K, Taipale J, Aaltonen LA, Kilpivaara O. Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer.. Oncotarget 2014 Feb 15;5(3):853-9.
    doi: 10.18632/oncotarget.1781pmc: PMC3996660pubmed: 24553397google scholar: lookup
  45. Payer LM, Steranka JP, Yang WR, Kryatova M, Medabalimi S, Ardeljan D, Liu C, Boeke JD, Avramopoulos D, Burns KH. Structural variants caused by Alu insertions are associated with risks for many human diseases.. Proc Natl Acad Sci U S A 2017 May 16;114(20):E3984-E3992.
    doi: 10.1073/pnas.1704117114pmc: PMC5441760pubmed: 28465436google scholar: lookup
  46. Witherspoon DJ, Zhang Y, Xing J, Watkins WS, Ha H, Batzer MA, Jorde LB. Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations.. Genome Res 2013 Jul;23(7):1170-81.
    doi: 10.1101/gr.148973.112pmc: PMC3698510pubmed: 23599355google scholar: lookup
  47. Steely CJ, Walker JA, Jordan VE, Beckstrom TO, McDaniel CL, St Romain CP, Bennett EC, Robichaux A, Clement BN, Raveendran M, Worley KC, Phillips-Conroy J, Jolly CJ, Rogers J, Konkel MK, Batzer MA. Alu Insertion Polymorphisms as Evidence for Population Structure in Baboons.. Genome Biol Evol 2017 Sep 1;9(9):2418-2427.
    doi: 10.1093/gbe/evx184pmc: PMC5622324pubmed: 28957465google scholar: lookup
  48. Yu Q, Zhang W, Zhang X, Zeng Y, Wang Y, Wang Y, Xu L, Huang X, Li N, Zhou X, Lu J, Guo X, Li G, Hou Y, Liu S, Li B. Population-wide sampling of retrotransposon insertion polymorphisms using deep sequencing and efficient detection.. Gigascience 2017 Sep 1;6(9):1-11.
    doi: 10.1093/gigascience/gix066pmc: PMC5603766pubmed: 28938719google scholar: lookup
  49. 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 Oct 26;16:126.
    doi: 10.1186/s12863-015-0281-1pmc: PMC4623272pubmed: 26503543google scholar: lookup
  50. Nergadze SG, Lupotto M, Pellanda P, Santagostino M, Vitelli V, Giulotto E. Mitochondrial DNA insertions in the nuclear horse genome.. Anim Genet 2010 Dec;41 Suppl 2:176-85.
    doi: 10.1111/j.1365-2052.2010.02130.xpubmed: 21070293google scholar: lookup
  51. Trifonov VA, Stanyon R, Nesterenko AI, Fu B, Perelman PL, O'Brien PC, Stone G, Rubtsova NV, Houck ML, Robinson TJ, Ferguson-Smith MA, Dobigny G, Graphodatsky AS, Yang F. Multidirectional cross-species painting illuminates the history of karyotypic evolution in Perissodactyla.. Chromosome Res 2008;16(1):89-107.
    doi: 10.1007/s10577-007-1201-7pubmed: 18293107google scholar: lookup
  52. 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 MC, 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 Nov 6;326(5954):865-7.
    doi: 10.1126/science.1178158pmc: PMC3785132pubmed: 19892987google scholar: lookup
  53. 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 Feb 12;6(2):e1000845.
    doi: 10.1371/journal.pgen.1000845pmc: PMC2820525pubmed: 20169180google scholar: lookup
  54. Steiner CC, Ryder OA. Molecular phylogeny and evolution of the Perissodactyla. Zool. J. Linn. Soc. 2011;163:1289–1303.
    doi: 10.1111/j.1096-3642.2011.00752.xgoogle scholar: lookup
  55. Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.. Nature 2013 Jul 4;499(7456):74-8.
    doi: 10.1038/nature12323pubmed: 23803765google scholar: lookup
  56. Jónsson H, Schubert M, Seguin-Orlando A, Ginolhac A, Petersen L, Fumagalli M, Albrechtsen A, Petersen B, Korneliussen TS, Vilstrup JT, Lear T, Myka JL, Lundquist J, Miller DC, Alfarhan AH, Alquraishi SA, Al-Rasheid KA, Stagegaard J, Strauss G, Bertelsen MF, Sicheritz-Ponten T, Antczak DF, Bailey E, Nielsen R, Willerslev E, Orlando L. Speciation with gene flow in equids despite extensive chromosomal plasticity.. Proc Natl Acad Sci U S A 2014 Dec 30;111(52):18655-60.
    doi: 10.1073/pnas.1412627111pmc: PMC4284605pubmed: 25453089google scholar: lookup
  57. Giulotto E, Raimondi E, Sullivan KF. The Unique DNA Sequences Underlying Equine Centromeres.. Prog Mol Subcell Biol 2017;56:337-354.
    doi: 10.1007/978-3-319-58592-5_14pubmed: 28840244google scholar: lookup
  58. 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 Jun;28(6):789-799.
    doi: 10.1101/gr.231159.117pmc: PMC5991519pubmed: 29712753google scholar: lookup
  59. Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA, Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. An integrated map of structural variation in 2,504 human genomes.. Nature 2015 Oct 1;526(7571):75-81.
    doi: 10.1038/nature15394pmc: PMC4617611pubmed: 26432246google scholar: lookup
  60. Bertoni L, Attolini C, Tessera L, Mucciolo E, Giulotto E. Telomeric and nontelomeric (TTAGGG)n sequences in gene amplification and chromosome stability.. Genomics 1994 Nov 1;24(1):53-62.
    doi: 10.1006/geno.1994.1581pubmed: 7896289google scholar: lookup
  61. Kalbfleisch TS, Rice ES, DePriest MS Jr, Walenz BP, Hestand MS, Vermeesch JR, O Connell BL, Fiddes IT, Vershinina AO, Saremi NF, Petersen JL, Finno CJ, Bellone RR, McCue ME, Brooks SA, Bailey E, Orlando L, Green RE, Miller DC, Antczak DF, MacLeod JN. Improved reference genome for the domestic horse increases assembly contiguity and composition.. Commun Biol 2018;1:197.
    doi: 10.1038/s42003-018-0199-zpmc: PMC6240028pubmed: 30456315google scholar: lookup
  62. BLAST NCBI Trace Database. [(accessed on 22 January 2019)]; Available online: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Nucleotides&PROGRAM=blastn&BLAST_SPEC=TraceArchive&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch.
  63. Mondello C, Pirzio L, Azzalin CM, Giulotto E. Instability of interstitial telomeric sequences in the human genome.. Genomics 2000 Sep 1;68(2):111-7.
    doi: 10.1006/geno.2000.6280pubmed: 10964508google scholar: lookup
  64. Huang J, Zhao Y, Bai D, Shiraigol W, Li B, Yang L, Wu J, Bao W, Ren X, Jin B, Zhao Q, Li A, Bao S, Bao W, Xing Z, An A, Gao Y, Wei R, Bao Y, Bao T, Han H, Bai H, Bao Y, Zhang Y, Daidiikhuu D, Zhao W, Liu S, Ding J, Ye W, Ding F, Sun Z, Shi Y, Zhang Y, Meng H, Dugarjaviin M. Corrigendum: Donkey genome and insight into the imprinting of fast karyotype evolution.. Sci Rep 2015 Dec 18;5:17124.
    doi: 10.1038/srep17124pmc: PMC4683579pubmed: 26681131google scholar: lookup
  65. Renaud G, Petersen B, Seguin-Orlando A, Bertelsen MF, Waller A, Newton R, Paillot R, Bryant N, Vaudin M, Librado P, Orlando L. Improved de novo genomic assembly for the domestic donkey.. Sci Adv 2018 Apr;4(4):eaaq0392.
    doi: 10.1126/sciadv.aaq0392pmc: PMC5938232pubmed: 29740610google scholar: lookup
  66. Equus Asinus Assembly ASM130575v1, Breed: Guanzhong Donkey. [(accessed on 16 July 2019)]; Available online: https://www.ncbi.nlm.nih.gov/assembly/GCF_001305755.1.
  67. Equus asinus asinus assembly ASM303372v1, Willy. [(accessed on 16 July 2019)]; Available online: https://www.ncbi.nlm.nih.gov/assembly/GCA_003033725.1.
  68. Ceratotherium simum simum assembly CerSimSim1.0. [(accessed on 16 July 2019)]; Available online: https://www.ncbi.nlm.nih.gov/assembly/GCF_000283155.1/
  69. Simonet T, Zaragosi LE, Philippe C, Lebrigand K, Schouteden C, Augereau A, Bauwens S, Ye J, Santagostino M, Giulotto E, Magdinier F, Horard B, Barbry P, Waldmann R, Gilson E. The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats.. Cell Res 2011 Jul;21(7):1028-38.
    doi: 10.1038/cr.2011.40pmc: PMC3193489pubmed: 21423270google scholar: lookup
  70. Murphy WJ, Pringle TH, Crider TA, Springer MS, Miller W. Using genomic data to unravel the root of the placental mammal phylogeny.. Genome Res 2007 Apr;17(4):413-21.
    doi: 10.1101/gr.5918807pmc: PMC1832088pubmed: 17322288google scholar: lookup
  71. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann Y, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dunham I, Durbin R, French L, Grafham D, Gregory S, Hubbard T, Humphray S, Hunt A, Jones M, Lloyd C, McMurray A, Matthews L, Mercer S, Milne S, Mullikin JC, Mungall A, Plumb R, Ross M, Shownkeen R, Sims S, Waterston RH, Wilson RK, Hillier LW, McPherson JD, Marra MA, Mardis ER, Fulton LA, Chinwalla AT, Pepin KH, Gish WR, Chissoe SL, Wendl MC, Delehaunty KD, Miner TL, Delehaunty A, Kramer JB, Cook LL, Fulton RS, Johnson DL, Minx PJ, Clifton SW, Hawkins T, Branscomb E, Predki P, Richardson P, Wenning S, Slezak T, Doggett N, Cheng JF, Olsen A, Lucas S, Elkin C, Uberbacher E, Frazier M, Gibbs RA, Muzny DM, Scherer SE, Bouck JB, Sodergren EJ, Worley KC, Rives CM, Gorrell JH, Metzker ML, Naylor SL, Kucherlapati RS, Nelson DL, Weinstock GM, Sakaki Y, Fujiyama A, Hattori M, Yada T, Toyoda A, Itoh T, Kawagoe C, Watanabe H, Totoki Y, Taylor T, Weissenbach J, Heilig R, Saurin W, Artiguenave F, Brottier P, Bruls T, Pelletier E, Robert C, Wincker P, Smith DR, Doucette-Stamm L, Rubenfield M, Weinstock K, Lee HM, Dubois J, Rosenthal A, Platzer M, Nyakatura G, Taudien S, Rump A, Yang H, Yu J, Wang J, Huang G, Gu J, Hood L, Rowen L, Madan A, Qin S, Davis RW, Federspiel NA, Abola AP, Proctor MJ, Myers RM, Schmutz J, Dickson M, Grimwood J, Cox DR, Olson MV, Kaul R, Raymond C, Shimizu N, Kawasaki K, Minoshima S, Evans GA, Athanasiou M, Schultz R, Roe BA, Chen F, Pan H, Ramser J, Lehrach H, Reinhardt R, McCombie WR, de la Bastide M, Dedhia N, Blöcker H, Hornischer K, Nordsiek G, Agarwala R, Aravind L, Bailey JA, Bateman A, Batzoglou S, Birney E, Bork P, Brown DG, Burge CB, Cerutti L, Chen HC, Church D, Clamp M, Copley RR, Doerks T, Eddy SR, Eichler EE, Furey TS, Galagan J, Gilbert JG, Harmon C, Hayashizaki Y, Haussler D, Hermjakob H, Hokamp K, Jang W, Johnson LS, Jones TA, Kasif S, Kaspryzk A, Kennedy S, Kent WJ, Kitts P, Koonin EV, Korf I, Kulp D, Lancet D, Lowe TM, McLysaght A, Mikkelsen T, Moran JV, Mulder N, Pollara VJ, Ponting CP, Schuler G, Schultz J, Slater G, Smit AF, Stupka E, Szustakowki J, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Wallis J, Wheeler R, Williams A, Wolf YI, Wolfe KH, Yang SP, Yeh RF, Collins F, Guyer MS, Peterson J, Felsenfeld A, Wetterstrand KA, Patrinos A, Morgan MJ, de Jong P, Catanese JJ, Osoegawa K, Shizuya H, Choi S, Chen YJ, Szustakowki J. Initial sequencing and analysis of the human genome.. Nature 2001 Feb 15;409(6822):860-921.
    doi: 10.1038/35057062pubmed: 11237011google scholar: lookup
  72. Rosato M, Álvarez I, Feliner GN, Rosselló JA. Inter- and intraspecific hypervariability in interstitial telomeric-like repeats (TTTAGGG)n in Anacyclus (Asteraceae).. Ann Bot 2018 Aug 27;122(3):387-395.
    doi: 10.1093/aob/mcy079pmc: PMC6110349pubmed: 29800070google scholar: lookup
  73. Wakefield S, Knowles J, Zimmermann W, van Dierendonck M. Chapter 7: Status and action plan for the Przewalski’s horse (equus ferus przewalskii). Equids-Zebras, Asses, and Horses: Status Survey and Conservation Action Plan IUCN-the World Conservation Union; Gland, Switzerland: 2002.
  74. Rouet P, Smih F, Jasin M. Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease.. Mol Cell Biol 1994 Dec;14(12):8096-106.
    doi: 10.1128/MCB.14.12.8096pmc: PMC359348pubmed: 7969147google scholar: lookup
  75. 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 May 2;4(5):546-55.
    doi: 10.1016/j.dnarep.2004.12.011pubmed: 15811627google scholar: lookup
  76. Onozawa M, Zhang Z, Kim YJ, Goldberg L, Varga T, Bergsagel PL, Kuehl WM, Aplan PD. Repair of DNA double-strand breaks by templated nucleotide sequence insertions derived from distant regions of the genome.. Proc Natl Acad Sci U S A 2014 May 27;111(21):7729-34.
    doi: 10.1073/pnas.1321889111pmc: PMC4040595pubmed: 24821809google scholar: lookup
  77. Chang HHY, Pannunzio NR, Adachi N, Lieber MR. Non-homologous DNA end joining and alternative pathways to double-strand break repair.. Nat Rev Mol Cell Biol 2017 Aug;18(8):495-506.
    doi: 10.1038/nrm.2017.48pmc: PMC7062608pubmed: 28512351google scholar: lookup
  78. Ségal-Bendirdjian E, Geli V. Non-canonical Roles of Telomerase: Unraveling the Imbroglio.. Front Cell Dev Biol 2019;7:332.
    doi: 10.3389/fcell.2019.00332pmc: PMC6914764pubmed: 31911897google scholar: lookup
  79. Homo Sapiens (human) Nucleotide BLAST. [(accessed on 18 August 2016)]; Available online: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&BLAST_SPEC=OGP__9606__9558&LINK_LOC=blasthome.
  80. Galaxy. [(accessed on 18 January 2019)]; Available online: https://usegalaxy.org/
  81. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.. Nucleic Acids Res 2016 Jul 8;44(W1):W3-W10.
    doi: 10.1093/nar/gkw343pmc: PMC4987906pubmed: 27137889google scholar: lookup
  82. UCSC Genome Browser, Track “1000 Genomes Phase 3 Integrated Variant Calls: SNVs, Indels, SVs”. [(accessed on 1 March 2019)]; Available online: https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=720970681_qqmhEowWab8OoZ9mluPovptBdLXW&c=chrX&g=tgpPhase3.
  83. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS. Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area.. Am J Hum Genet 2004 May;74(5):1023-34.
    doi: 10.1086/386295pmc: PMC1181965pubmed: 15069642google scholar: lookup
  84. UCSC Genome Browser Gateway. [(accessed on 16 July 2019)]; Available online: https://genome.ucsc.edu/cgi-bin/hgGateway.
  85. Anglana M, Bertoni L, Giulotto E. Cloning of a polymorphic sequence from the nontranscribed spacer of horse rDNA.. Mamm Genome 1996 Jul;7(7):539-41.
    doi: 10.1007/s003359900159pubmed: 8672135google scholar: lookup
  86. Multalin. [(accessed on 16 July 2019)]; Available online: http://multalin.toulouse.inra.fr/multalin/
  87. Corpet F. Multiple sequence alignment with hierarchical clustering.. Nucleic Acids Res 1988 Nov 25;16(22):10881-90.
    doi: 10.1093/nar/16.22.10881pmc: PMC338945pubmed: 2849754google scholar: lookup
  88. Vidale P, Magnani E, Nergadze SG, Santagostino M, Cristofari G, Smirnova A, Mondello C, Giulotto E. The catalytic and the RNA subunits of human telomerase are required to immortalize equid primary fibroblasts.. Chromosoma 2012 Oct;121(5):475-88.
    doi: 10.1007/s00412-012-0379-4pmc: PMC3443485pubmed: 22797876google scholar: lookup
  89. 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(1-2):165-72.
    doi: 10.1159/000245916pubmed: 20016166google scholar: lookup

Citations

This article has been cited 6 times.
  1. Piras FM, Cappelletti E, Abdelgadir WA, Salamon G, Vignati S, Santagostino M, Sola L, Nergadze SG, Giulotto E. A Satellite-Free Centromere in Equus przewalskii Chromosome 10.. Int J Mol Sci 2023 Feb 18;24(4).
    doi: 10.3390/ijms24044134pubmed: 36835543google scholar: lookup
  2. Piras FM, Cappelletti E, Santagostino M, Nergadze SG, Giulotto E, Raimondi E. Molecular Dynamics and Evolution of Centromeres in the Genus Equus.. Int J Mol Sci 2022 Apr 10;23(8).
    doi: 10.3390/ijms23084183pubmed: 35457002google scholar: lookup
  3. Ahmad HI, Afzal G, Sadia S, Haider G, Ahmed S, Saeed S, Chen J. Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates.. Oxid Med Cell Longev 2022;2022:1144387.
    doi: 10.1155/2022/1144387pubmed: 35419164google scholar: lookup
  4. Sola L, Nergadze SG, Cappelletti E, Piras FM, Giulotto E, Santagostino M. Telomeric-Like Repeats Flanked by Sequences Retrotranscribed from the Telomerase RNA Inserted at DNA Double-Strand Break Sites during Vertebrate Genome Evolution.. Int J Mol Sci 2021 Oct 13;22(20).
    doi: 10.3390/ijms222011048pubmed: 34681704google scholar: lookup
  5. Bugno-Poniewierska M, Raudsepp T. Horse Clinical Cytogenetics: Recurrent Themes and Novel Findings.. Animals (Basel) 2021 Mar 16;11(3).
    doi: 10.3390/ani11030831pubmed: 33809432google scholar: lookup
  6. Clemente L, Mazzoleni S, Pensabene Bellavia E, Augstenová B, Auer M, Praschag P, Protiva T, Velenský P, Wagner P, Fritz U, Kratochvíl L, Rovatsos M. Interstitial Telomeric Repeats Are Rare in Turtles.. Genes (Basel) 2020 Jun 16;11(6).
    doi: 10.3390/genes11060657pubmed: 32560114google scholar: lookup
Subscribe to our newsletter
Join 99,344 horse owners like you who receive our email updates on horse health and nutrition.