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Philosophical Transactions of the Royal Society B: Biological Sciences logoLink to Philosophical Transactions of the Royal Society B: Biological Sciences
. 1998 Jun 29;353(1371):955–965. doi: 10.1098/rstb.1998.0260

Molecular instability in the COII-tRNA(Lys) intergenic region of the human mitochondrial genome: multiple origins of the 9-bp deletion and heteroplasmy for expanded repeats.

M G Thomas 1, C E Cook 1, K W Miller 1, M J Waring 1, E Hagelberg 1
PMCID: PMC1692296  PMID: 9684291

Abstract

We have identified two individuals from Glasgow in Scotland who have a deletion of one of two copies of the intergenic 9-bp sequence motif CCCCCTCTA, located between the cytochrome oxidase II (COII) and lysine tRNA (tRNA(Lys)) genes of the human mitochondrial genome. Although this polymorphism is common in Africa and Asia, it has not been reported in Northern Europe. Analysis of the mitochondrial DNA control region sequences of these two individuals suggests that they belong to a lineage that originated independently of the previously characterized African and Asian 9-bp deleted lineages. Among the Scottish population we have also identified a maternal lineage of three generations exhibiting heteroplasmy for two, three and four copies of the CCCCCTCTA motif. Polymerase chain reaction amplification across the COII-tRNA(Lys) intergenic region of these individuals gives different ratios of the three product lengths that are dependent on the concentration of the DNA-binding dye crystal violet. To investigate whether changes in repeat number were generated de novo, we constructed clones containing known numbers of the CCCCCTCTA motif. In the presence of high concentrations of crystal violet we obtained two, three and four copies of this motif when the amplification template contained only four copies. Various DNA-binding drugs are known to stabilize bulged structures in DNA and contribute to the process of slipped-strand mispairing during DNA replication. These results suggest that the COII-tRNA(Lys) intergenic region is unstable owing to slipped-strand mispairing. Although sequences containing four copies of the CCCCCTCTA motif are less stable in vitro, we observed an increase in the proportion of mitochondrial genomes with four repeats between-a mother and a daughter in the heteroplasmic lineage. From this we conclude that drift in the germ-line lineage is a main factor in the maintenance or loss of heteroplasmy.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Ashley M. V., Laipis P. J., Hauswirth W. W. Rapid segregation of heteroplasmic bovine mitochondria. Nucleic Acids Res. 1989 Sep 25;17(18):7325–7331. doi: 10.1093/nar/17.18.7325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bailliet G., Rothhammer F., Carnese F. R., Bravi C. M., Bianchi N. O. Founder mitochondrial haplotypes in Amerindian populations. Am J Hum Genet. 1994 Jul;55(1):27–33. [PMC free article] [PubMed] [Google Scholar]
  4. Ballinger S. W., Schurr T. G., Torroni A., Gan Y. Y., Hodge J. A., Hassan K., Chen K. H., Wallace D. C. Southeast Asian mitochondrial DNA analysis reveals genetic continuity of ancient mongoloid migrations. Genetics. 1992 Jan;130(1):139–152. doi: 10.1093/genetics/130.1.139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Behn-Krappa A., Doerfler W. Enzymatic amplification of synthetic oligodeoxyribonucleotides: implications for triplet repeat expansions in the human genome. Hum Mutat. 1994;3(1):19–24. doi: 10.1002/humu.1380030104. [DOI] [PubMed] [Google Scholar]
  6. Bendall K. E., Macaulay V. A., Baker J. R., Sykes B. C. Heteroplasmic point mutations in the human mtDNA control region. Am J Hum Genet. 1996 Dec;59(6):1276–1287. [PMC free article] [PubMed] [Google Scholar]
  7. Bendall K. E., Sykes B. C. Length heteroplasmy in the first hypervariable segment of the human mtDNA control region. Am J Hum Genet. 1995 Aug;57(2):248–256. [PMC free article] [PubMed] [Google Scholar]
  8. Caceres-Cortes J., Wang A. H. Binding of the antitumor drug nogalamycin to bulged DNA structures. Biochemistry. 1996 Jan 16;35(2):616–625. doi: 10.1021/bi9518398. [DOI] [PubMed] [Google Scholar]
  9. Cann R. L. mtDNA and Native Americans: a Southern perspective. Am J Hum Genet. 1994 Jul;55(1):7–11. [PMC free article] [PubMed] [Google Scholar]
  10. Casane D., Dennebouy N., de Rochambeau H., Mounolou J. C., Monnerot M. Genetic analysis of systematic mitochondrial heteroplasmy in rabbits. Genetics. 1994 Oct;138(2):471–480. doi: 10.1093/genetics/138.2.471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. DeMarini D. M., Abu-Shakra A., Gupta R., Hendee L. J., Levine J. G. Molecular analysis of mutations induced by the intercalating agent ellipticine at the hisD3052 allele of Salmonella typhimurium TA98. Environ Mol Mutagen. 1992;20(1):12–18. doi: 10.1002/em.2850200104. [DOI] [PubMed] [Google Scholar]
  12. Fumagalli L., Taberlet P., Favre L., Hausser J. Origin and evolution of homologous repeated sequences in the mitochondrial DNA control region of shrews. Mol Biol Evol. 1996 Jan;13(1):31–46. doi: 10.1093/oxfordjournals.molbev.a025568. [DOI] [PubMed] [Google Scholar]
  13. Greenblatt M. S., Grollman A. P., Harris C. C. Deletions and insertions in the p53 tumor suppressor gene in human cancers: confirmation of the DNA polymerase slippage/misalignment model. Cancer Res. 1996 May 1;56(9):2130–2136. [PubMed] [Google Scholar]
  14. Hagelberg E., Clegg J. B. Genetic polymorphisms in prehistoric Pacific islanders determined by analysis of ancient bone DNA. Proc Biol Sci. 1993 May 22;252(1334):163–170. doi: 10.1098/rspb.1993.0061. [DOI] [PubMed] [Google Scholar]
  15. Hagelberg E., Quevedo S., Turbon D., Clegg J. B. DNA from ancient Easter Islanders. Nature. 1994 May 5;369(6475):25–26. doi: 10.1038/369025a0. [DOI] [PubMed] [Google Scholar]
  16. Harihara S., Hirai M., Suutou Y., Shimizu K., Omoto K. Frequency of a 9-bp deletion in the mitochondrial DNA among Asian populations. Hum Biol. 1992 Apr;64(2):161–166. [PubMed] [Google Scholar]
  17. Harrison R. G., Rand D. M., Wheeler W. C. Mitochondrial DNA size variation within individual crickets. Science. 1985 Jun 21;228(4706):1446–1448. doi: 10.1126/science.228.4706.1446. [DOI] [PubMed] [Google Scholar]
  18. Hertzberg M., Mickleson K. N., Serjeantson S. W., Prior J. F., Trent R. J. An Asian-specific 9-bp deletion of mitochondrial DNA is frequently found in Polynesians. Am J Hum Genet. 1989 Apr;44(4):504–510. [PMC free article] [PubMed] [Google Scholar]
  19. Hoelzel A. R., Hancock J. M., Dover G. A. Evolution of the cetacean mitochondrial D-loop region. Mol Biol Evol. 1991 Jul;8(4):475–493. doi: 10.1093/oxfordjournals.molbev.a040662. [DOI] [PubMed] [Google Scholar]
  20. Hoelzel A. R., Lopez J. V., Dover G. A., O'Brien S. J. Rapid evolution of a heteroplasmic repetitive sequence in the mitochondrial DNA control region of carnivores. J Mol Evol. 1994 Aug;39(2):191–199. doi: 10.1007/BF00163807. [DOI] [PubMed] [Google Scholar]
  21. Horai S., Hayasaka K., Kondo R., Tsugane K., Takahata N. Recent African origin of modern humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc Natl Acad Sci U S A. 1995 Jan 17;92(2):532–536. doi: 10.1073/pnas.92.2.532. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Horai S., Kondo R., Nakagawa-Hattori Y., Hayashi S., Sonoda S., Tajima K. Peopling of the Americas, founded by four major lineages of mitochondrial DNA. Mol Biol Evol. 1993 Jan;10(1):23–47. doi: 10.1093/oxfordjournals.molbev.a039987. [DOI] [PubMed] [Google Scholar]
  23. Imada M., Inouye M., Eda M., Tsugita A. Frameshift mutation in the lysozyme gene of bacteriophage T4: demonstration of the insertion offour bases and the preferential occurrence of base addition in acridine mutagenesis. J Mol Biol. 1970 Dec 14;54(2):199–217. doi: 10.1016/0022-2836(70)90427-4. [DOI] [PubMed] [Google Scholar]
  24. Ivanov P. L., Wadhams M. J., Roby R. K., Holland M. M., Weedn V. W., Parsons T. J. Mitochondrial DNA sequence heteroplasmy in the Grand Duke of Russia Georgij Romanov establishes the authenticity of the remains of Tsar Nicholas II. Nat Genet. 1996 Apr;12(4):417–420. doi: 10.1038/ng0496-417. [DOI] [PubMed] [Google Scholar]
  25. Jenuth J. P., Peterson A. C., Fu K., Shoubridge E. A. Random genetic drift in the female germline explains the rapid segregation of mammalian mitochondrial DNA. Nat Genet. 1996 Oct;14(2):146–151. doi: 10.1038/ng1096-146. [DOI] [PubMed] [Google Scholar]
  26. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980 Dec;16(2):111–120. doi: 10.1007/BF01731581. [DOI] [PubMed] [Google Scholar]
  27. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Päbo S., Villablanca F. X., Wilson A. C. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proc Natl Acad Sci U S A. 1989 Aug;86(16):6196–6200. doi: 10.1073/pnas.86.16.6196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Levinson G., Gutman G. A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol Biol Evol. 1987 May;4(3):203–221. doi: 10.1093/oxfordjournals.molbev.a040442. [DOI] [PubMed] [Google Scholar]
  29. Lum J. K., Rickards O., Ching C., Cann R. L. Polynesian mitochondrial DNAs reveal three deep maternal lineage clusters. Hum Biol. 1994 Aug;66(4):567–590. [PubMed] [Google Scholar]
  30. Marchington D. R., Hartshorne G. M., Barlow D., Poulton J. Homopolymeric tract heteroplasmy in mtDNA from tissues and single oocytes: support for a genetic bottleneck. Am J Hum Genet. 1997 Feb;60(2):408–416. [PMC free article] [PubMed] [Google Scholar]
  31. Melton T., Peterson R., Redd A. J., Saha N., Sofro A. S., Martinson J., Stoneking M. Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am J Hum Genet. 1995 Aug;57(2):403–414. [PMC free article] [PubMed] [Google Scholar]
  32. Merriwether D. A., Rothhammer F., Ferrell R. E. Genetic variation in the New World: ancient teeth, bone, and tissue as sources of DNA. Experientia. 1994 Jun 15;50(6):592–601. doi: 10.1007/BF01921730. [DOI] [PubMed] [Google Scholar]
  33. Monsalve M. V., Groot de Restrepo H., Espinel A., Correal G., Devine D. V. Evidence of mitochondrial DNA diversity in South American aboriginals. Ann Hum Genet. 1994 Jul;58(Pt 3):265–273. doi: 10.1111/j.1469-1809.1994.tb01890.x. [DOI] [PubMed] [Google Scholar]
  34. Nagafuchi S., Yanagisawa H., Sato K., Shirayama T., Ohsaki E., Bundo M., Takeda T., Tadokoro K., Kondo I., Murayama N. Dentatorubral and pallidoluysian atrophy expansion of an unstable CAG trinucleotide on chromosome 12p. Nat Genet. 1994 Jan;6(1):14–18. doi: 10.1038/ng0194-14. [DOI] [PubMed] [Google Scholar]
  35. Nei M., Li W. H. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979 Oct;76(10):5269–5273. doi: 10.1073/pnas.76.10.5269. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Passarino G., Semino O., Modiano G., Santachiara-Benerecetti A. S. COII/tRNA(Lys) intergenic 9-bp deletion and other mtDNA markers clearly reveal that the Tharus (southern Nepal) have Oriental affinities. Am J Hum Genet. 1993 Sep;53(3):609–618. [PMC free article] [PubMed] [Google Scholar]
  37. Piercy R., Sullivan K. M., Benson N., Gill P. The application of mitochondrial DNA typing to the study of white Caucasian genetic identification. Int J Legal Med. 1993;106(2):85–90. doi: 10.1007/BF01225046. [DOI] [PubMed] [Google Scholar]
  38. Pikó L., Matsumoto L. Number of mitochondria and some properties of mitochondrial DNA in the mouse egg. Dev Biol. 1976 Mar;49(1):1–10. doi: 10.1016/0012-1606(76)90253-0. [DOI] [PubMed] [Google Scholar]
  39. Redd A. J., Takezaki N., Sherry S. T., McGarvey S. T., Sofro A. S., Stoneking M. Evolutionary history of the COII/tRNALys intergenic 9 base pair deletion in human mitochondrial DNAs from the Pacific. Mol Biol Evol. 1995 Jul;12(4):604–615. doi: 10.1093/oxfordjournals.molbev.a040240. [DOI] [PubMed] [Google Scholar]
  40. Rentzeperis D., Medero M., Marky L. A. Thermodynamic investigation of the association of ethidium, propidium and bis-ethidium to DNA hairpins. Bioorg Med Chem. 1995 Jun;3(6):751–759. doi: 10.1016/0968-0896(95)00056-m. [DOI] [PubMed] [Google Scholar]
  41. Rosche W. A., Trinh T. Q., Sinden R. R. Differential DNA secondary structure-mediated deletion mutation in the leading and lagging strands. J Bacteriol. 1995 Aug;177(15):4385–4391. doi: 10.1128/jb.177.15.4385-4391.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Schurr T. G., Ballinger S. W., Gan Y. Y., Hodge J. A., Merriwether D. A., Lawrence D. N., Knowler W. C., Weiss K. M., Wallace D. C. Amerindian mitochondrial DNAs have rare Asian mutations at high frequencies, suggesting they derived from four primary maternal lineages. Am J Hum Genet. 1990 Mar;46(3):613–623. [PMC free article] [PubMed] [Google Scholar]
  43. Shields G. F., Hecker K., Voevoda M. I., Reed J. K. Absence of the Asian-specific region V mitochondrial marker in Native Beringians. Am J Hum Genet. 1992 Apr;50(4):758–765. [PMC free article] [PubMed] [Google Scholar]
  44. Soodyall H., Jenkins T., Stoneking M. 'Polynesian' mtDNA in the Malagasy. Nat Genet. 1995 Aug;10(4):377–378. doi: 10.1038/ng0895-377. [DOI] [PubMed] [Google Scholar]
  45. Soodyall H., Vigilant L., Hill A. V., Stoneking M., Jenkins T. mtDNA control-region sequence variation suggests multiple independent origins of an "Asian-specific" 9-bp deletion in sub-Saharan Africans. Am J Hum Genet. 1996 Mar;58(3):595–608. [PMC free article] [PubMed] [Google Scholar]
  46. Stoneking M., Sherry S. T., Redd A. J., Vigilant L. New approaches to dating suggest a recent age for the human mtDNA ancestor. Philos Trans R Soc Lond B Biol Sci. 1992 Aug 29;337(1280):167–175. doi: 10.1098/rstb.1992.0094. [DOI] [PubMed] [Google Scholar]
  47. Streisinger G., Okada Y., Emrich J., Newton J., Tsugita A., Terzaghi E., Inouye M. Frameshift mutations and the genetic code. This paper is dedicated to Professor Theodosius Dobzhansky on the occasion of his 66th birthday. Cold Spring Harb Symp Quant Biol. 1966;31:77–84. doi: 10.1101/sqb.1966.031.01.014. [DOI] [PubMed] [Google Scholar]
  48. Sykes B., Leiboff A., Low-Beer J., Tetzner S., Richards M. The origins of the Polynesians: an interpretation from mitochondrial lineage analysis. Am J Hum Genet. 1995 Dec;57(6):1463–1475. [PMC free article] [PubMed] [Google Scholar]
  49. Thomas M. G., Miller K. W., Cook C. E., Jr, Hagelberg E. A method for avoiding mis-priming when sequencing with Dynabeads. Nucleic Acids Res. 1994 Aug 11;22(15):3243–3244. doi: 10.1093/nar/22.15.3243. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Torroni A., Petrozzi M., Santolamazza P., Sellitto D., Cruciani F., Scozzari R. About the "Asian"-specific 9-bp deletion of mtDNA.... Am J Hum Genet. 1995 Aug;57(2):507–508. [PMC free article] [PubMed] [Google Scholar]
  51. Torroni A., Schurr T. G., Cabell M. F., Brown M. D., Neel J. V., Larsen M., Smith D. G., Vullo C. M., Wallace D. C. Asian affinities and continental radiation of the four founding Native American mtDNAs. Am J Hum Genet. 1993 Sep;53(3):563–590. [PMC free article] [PubMed] [Google Scholar]
  52. Torroni A., Schurr T. G., Yang C. C., Szathmary E. J., Williams R. C., Schanfield M. S., Troup G. A., Knowler W. C., Lawrence D. N., Weiss K. M. Native American mitochondrial DNA analysis indicates that the Amerind and the Nadene populations were founded by two independent migrations. Genetics. 1992 Jan;130(1):153–162. doi: 10.1093/genetics/130.1.153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Torroni A., Sukernik R. I., Schurr T. G., Starikorskaya Y. B., Cabell M. F., Crawford M. H., Comuzzie A. G., Wallace D. C. mtDNA variation of aboriginal Siberians reveals distinct genetic affinities with Native Americans. Am J Hum Genet. 1993 Sep;53(3):591–608. [PMC free article] [PubMed] [Google Scholar]
  54. Tran H. T., Degtyareva N. P., Koloteva N. N., Sugino A., Masumoto H., Gordenin D. A., Resnick M. A. Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes. Mol Cell Biol. 1995 Oct;15(10):5607–5617. doi: 10.1128/mcb.15.10.5607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Tuite E., Nordén B. Intercalative interactions of ethidium dyes with triplex structures. Bioorg Med Chem. 1995 Jun;3(6):701–711. doi: 10.1016/0968-0896(95)00061-k. [DOI] [PubMed] [Google Scholar]
  56. Wakelin L. P., Adams A., Hunter C., Waring M. J. Interaction of crystal violet with nucleic acids. Biochemistry. 1981 Sep 29;20(20):5779–5787. doi: 10.1021/bi00523a021. [DOI] [PubMed] [Google Scholar]
  57. Wallace D. C., Torroni A. American Indian prehistory as written in the mitochondrial DNA: a review. Hum Biol. 1992 Jun;64(3):403–416. [PubMed] [Google Scholar]
  58. Wilkinson G. S., Chapman A. M. Length and sequence variation in evening bat D-loop mtDNA. Genetics. 1991 Jul;128(3):607–617. doi: 10.1093/genetics/128.3.607. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Wrischnik L. A., Higuchi R. G., Stoneking M., Erlich H. A., Arnheim N., Wilson A. C. Length mutations in human mitochondrial DNA: direct sequencing of enzymatically amplified DNA. Nucleic Acids Res. 1987 Jan 26;15(2):529–542. doi: 10.1093/nar/15.2.529. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Zharkikh A., Li W. H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol Biol Evol. 1992 Nov;9(6):1119–1147. doi: 10.1093/oxfordjournals.molbev.a040782. [DOI] [PubMed] [Google Scholar]

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