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. 1996 Sep 15;318(Pt 3):1065–1070. doi: 10.1042/bj3181065

The unusual structures of the hot-regions flanking large-scale deletions in human mitochondrial DNA.

J H Hou 1, Y H Wei 1
PMCID: PMC1217724  PMID: 8836157

Abstract

Large-scale deletions of mitochondrial DNA (mtDNA) are common events that have been found to occur in human ageing and in patients with mitochondrial myopathies. The mechanisms by which these deletions occur remain unclear, but several mechanisms have been proposed, such as slipped-mispairing, illegitimate recombination, and oxidative reactions elicited by free radicals. In addition, the DNA topological stress and local DNA structures have been suggested as the important factors in eliciting the recombinational events. Upon examination of 128 breakpoints of human mtDNA deletions that have been published in the past 8 years, we found that these large-scale deletions often occur at some 'hot-regions'. We thus hypothesized that there exist unusual structures in these regions of human mtDNA that are important for eliciting the deletions. To test this hypothesis, we used PCR techniques to amplify the sequences of the so-called hot-regions and analysed the PCR products by two-dimensional gel electrophoresis. We found that the sequences of nucleotide position (np) 5221-5988, np 6928-7493, np 7901-8732 and np 15327-16228 exhibited retarded mobilities like bent DNA structures; np 5989-6750, np 13282-13653 and np 13282-14850 showed increased mobilities like anti-bent DNA structures. Moreover, except for the sequences of np 1175-1766 found in 12 S and 16 S rRNA genes exhibiting abnormal mobility like bent DNA structures, we did not observe significant mobility abnormalities in the np 499-5545 region where deletions rarely occurred. We thus conclude that these hot-regions assume some kinds of unusual DNA structures, which may render these regions more sensitive to the attack of free radicals or serve as recognition motifs for certain recombination machinery that is involved in the large-scale deletions of human mtDNA.

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Selected References

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  1. Anderson J. N. Detection, sequence patterns and function of unusual DNA structures. Nucleic Acids Res. 1986 Nov 11;14(21):8513–8533. doi: 10.1093/nar/14.21.8513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Behl C., Davis J. B., Lesley R., Schubert D. Hydrogen peroxide mediates amyloid beta protein toxicity. Cell. 1994 Jun 17;77(6):817–827. doi: 10.1016/0092-8674(94)90131-7. [DOI] [PubMed] [Google Scholar]
  3. Bruhn S. L., Housman D. E., Lippard S. J. Isolation and characterization of cDNA clones encoding the Drosophila homolog of the HMG-box SSRP family that recognizes specific DNA structures. Nucleic Acids Res. 1993 Apr 11;21(7):1643–1646. doi: 10.1093/nar/21.7.1643. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bruhn S. L., Pil P. M., Essigmann J. M., Housman D. E., Lippard S. J. Isolation and characterization of human cDNA clones encoding a high mobility group box protein that recognizes structural distortions to DNA caused by binding of the anticancer agent cisplatin. Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2307–2311. doi: 10.1073/pnas.89.6.2307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Dawid I. B., Horak I., Coon H. G. The use of hybrid somatic cells as an approach to mitochondrial genetics in animals. Genetics. 1974 Sep;78(1):459–471. doi: 10.1093/genetics/78.1.459. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Degoul F., Nelson I., Amselem S., Romero N., Obermaier-Kusser B., Ponsot G., Marsac C., Lestienne P. Different mechanisms inferred from sequences of human mitochondrial DNA deletions in ocular myopathies. Nucleic Acids Res. 1991 Feb 11;19(3):493–496. doi: 10.1093/nar/19.3.493. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dri A. M., Moreau P. L., Rouvière-Yaniv J. Role of the histone-like proteins OsmZ and HU in homologous recombination. Gene. 1992 Oct 12;120(1):11–16. doi: 10.1016/0378-1119(92)90003-8. [DOI] [PubMed] [Google Scholar]
  8. Hayakawa M., Hattori K., Sugiyama S., Ozawa T. Age-associated oxygen damage and mutations in mitochondrial DNA in human hearts. Biochem Biophys Res Commun. 1992 Dec 15;189(2):979–985. doi: 10.1016/0006-291x(92)92300-m. [DOI] [PubMed] [Google Scholar]
  9. Horak I., Coon H. G., Dawid I. B. Interspecific recombination of mitochondrial DNA molecules in hybrid somatic cells. Proc Natl Acad Sci U S A. 1974 May;71(5):1828–1832. doi: 10.1073/pnas.71.5.1828. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Howard M. T., Lee M. P., Hsieh T. S., Griffith J. D. Drosophila topoisomerase II-DNA interactions are affected by DNA structure. J Mol Biol. 1991 Jan 5;217(1):53–62. doi: 10.1016/0022-2836(91)90610-i. [DOI] [PubMed] [Google Scholar]
  11. Hübner P., Haffter P., Iida S., Arber W. Bent DNA is needed for recombinational enhancer activity in the site-specific recombination system Cin of bacteriophage P1. The role of FIS protein. J Mol Biol. 1989 Feb 5;205(3):493–500. doi: 10.1016/0022-2836(89)90220-9. [DOI] [PubMed] [Google Scholar]
  12. Ikeda H. Illegitimate recombination mediated by T4 DNA topoisomerase in vitro. Recombinants between phage and plasmid DNA molecules. Mol Gen Genet. 1986 Mar;202(3):518–520. doi: 10.1007/BF00333287. [DOI] [PubMed] [Google Scholar]
  13. Katayama M., Tanaka M., Yamamoto H., Ohbayashi T., Nimura Y., Ozawa T. Deleted mitochondrial DNA in the skeletal muscle of aged individuals. Biochem Int. 1991 Sep;25(1):47–56. [PubMed] [Google Scholar]
  14. Kokontis J. M., Vaughan J., Harvey R. G., Weiss S. B. Illegitimate recombination induced by benzo[a]pyrene diol epoxide in Escherichia coli. Proc Natl Acad Sci U S A. 1988 Feb;85(4):1043–1046. doi: 10.1073/pnas.85.4.1043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Krogh S., Mortensen U. H., Westergaard O., Bonven B. J. Eukaryotic topoisomerase I-DNA interaction is stabilized by helix curvature. Nucleic Acids Res. 1991 Mar 25;19(6):1235–1241. doi: 10.1093/nar/19.6.1235. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lestienne P., Bataillé N. Mitochondrial DNA alterations and genetic diseases: a review. Biomed Pharmacother. 1994;48(5-6):199–214. doi: 10.1016/0753-3322(94)90134-1. [DOI] [PubMed] [Google Scholar]
  17. Linial M., Shlomai J. A unique endonuclease from Crithidia fasciculata which recognizes a bend in the DNA helix. Specificity of the cleavage reaction. J Biol Chem. 1988 Jan 5;263(1):290–297. [PubMed] [Google Scholar]
  18. Liu L. F., Rowe T. C., Yang L., Tewey K. M., Chen G. L. Cleavage of DNA by mammalian DNA topoisomerase II. J Biol Chem. 1983 Dec 25;258(24):15365–15370. [PubMed] [Google Scholar]
  19. Mazin A., Milot E., Devoret R., Chartrand P. KIN17, a mouse nuclear protein, binds to bent DNA fragments that are found at illegitimate recombination junctions in mammalian cells. Mol Gen Genet. 1994 Aug 15;244(4):435–438. doi: 10.1007/BF00286696. [DOI] [PubMed] [Google Scholar]
  20. Milot E., Belmaaza A., Rassart E., Chartrand P. Association of a host DNA structure with retroviral integration sites in chromosomal DNA. Virology. 1994 Jun;201(2):408–412. doi: 10.1006/viro.1994.1310. [DOI] [PubMed] [Google Scholar]
  21. Milot E., Belmaaza A., Wallenburg J. C., Gusew N., Bradley W. E., Chartrand P. Chromosomal illegitimate recombination in mammalian cells is associated with intrinsically bent DNA elements. EMBO J. 1992 Dec;11(13):5063–5070. doi: 10.1002/j.1460-2075.1992.tb05613.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Mita S., Rizzuto R., Moraes C. T., Shanske S., Arnaudo E., Fabrizi G. M., Koga Y., DiMauro S., Schon E. A. Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA. Nucleic Acids Res. 1990 Feb 11;18(3):561–567. doi: 10.1093/nar/18.3.561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Münscher C., Rieger T., Müller-Höcker J., Kadenbach B. The point mutation of mitochondrial DNA characteristic for MERRF disease is found also in healthy people of different ages. FEBS Lett. 1993 Feb 8;317(1-2):27–30. doi: 10.1016/0014-5793(93)81484-h. [DOI] [PubMed] [Google Scholar]
  24. Nicholls R. D., Fischel-Ghodsian N., Higgs D. R. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. doi: 10.1016/0092-8674(87)90289-3. [DOI] [PubMed] [Google Scholar]
  25. Ohta K., Shibata T., Nicolas A. Changes in chromatin structure at recombination initiation sites during yeast meiosis. EMBO J. 1994 Dec 1;13(23):5754–5763. doi: 10.1002/j.1460-2075.1994.tb06913.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Phillips J. W., Morgan W. F. Illegitimate recombination induced by DNA double-strand breaks in a mammalian chromosome. Mol Cell Biol. 1994 Sep;14(9):5794–5803. doi: 10.1128/mcb.14.9.5794. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Poulton J., Deadman M. E., Bindoff L., Morten K., Land J., Brown G. Families of mtDNA re-arrangements can be detected in patients with mtDNA deletions: duplications may be a transient intermediate form. Hum Mol Genet. 1993 Jan;2(1):23–30. doi: 10.1093/hmg/2.1.23. [DOI] [PubMed] [Google Scholar]
  29. Shoffner J. M., Brown M. D., Torroni A., Lott M. T., Cabell M. F., Mirra S. S., Beal M. F., Yang C. C., Gearing M., Salvo R. Mitochondrial DNA variants observed in Alzheimer disease and Parkinson disease patients. Genomics. 1993 Jul;17(1):171–184. doi: 10.1006/geno.1993.1299. [DOI] [PubMed] [Google Scholar]
  30. Shoffner J. M., Lott M. T., Voljavec A. S., Soueidan S. A., Costigan D. A., Wallace D. C. Spontaneous Kearns-Sayre/chronic external ophthalmoplegia plus syndrome associated with a mitochondrial DNA deletion: a slip-replication model and metabolic therapy. Proc Natl Acad Sci U S A. 1989 Oct;86(20):7952–7956. doi: 10.1073/pnas.86.20.7952. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Shuman S. DNA strand transfer reactions catalyzed by vaccinia topoisomerase I. J Biol Chem. 1992 Apr 25;267(12):8620–8627. [PubMed] [Google Scholar]
  32. Simonetti S., Chen X., DiMauro S., Schon E. A. Accumulation of deletions in human mitochondrial DNA during normal aging: analysis by quantitative PCR. Biochim Biophys Acta. 1992 Dec 10;1180(2):113–122. doi: 10.1016/0925-4439(92)90059-v. [DOI] [PubMed] [Google Scholar]
  33. Smith D. L., Desai A. B., Johnson A. D. DNA bending by the a1 and alpha 2 homeodomain proteins from yeast. Nucleic Acids Res. 1995 Apr 11;23(7):1239–1243. doi: 10.1093/nar/23.7.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Sperry A. O., Blasquez V. C., Garrard W. T. Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci U S A. 1989 Jul;86(14):5497–5501. doi: 10.1073/pnas.86.14.5497. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Tomkinson A. E., Linn S. Purification and properties of a single strand-specific endonuclease from mouse cell mitochondria. Nucleic Acids Res. 1986 Dec 22;14(24):9579–9593. doi: 10.1093/nar/14.24.9579. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Usdin K., Furano A. V. Insertion of L1 elements into sites that can form non-B DNA. Interactions of non-B DNA-forming sequences. J Biol Chem. 1989 Dec 5;264(34):20736–20743. [PubMed] [Google Scholar]
  37. Wallace D. C. 1994 William Allan Award Address. Mitochondrial DNA variation in human evolution, degenerative disease, and aging. Am J Hum Genet. 1995 Aug;57(2):201–223. [PMC free article] [PubMed] [Google Scholar]
  38. Wells R. D., Collier D. A., Hanvey J. C., Shimizu M., Wohlrab F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988 Nov;2(14):2939–2949. [PubMed] [Google Scholar]
  39. Welter C., Dooley S., Zang K. D., Blin N. DNA curvature in front of the human mitochondrial L-strand replication origin with specific protein binding. Nucleic Acids Res. 1989 Aug 11;17(15):6077–6086. doi: 10.1093/nar/17.15.6077. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  41. Zhang C., Baumer A., Mackay I. R., Linnane A. W., Nagley P. Unusual pattern of mitochondrial DNA deletions in skeletal muscle of an adult human with chronic fatigue syndrome. Hum Mol Genet. 1995 Apr;4(4):751–754. doi: 10.1093/hmg/4.4.751. [DOI] [PubMed] [Google Scholar]
  42. Zhang C., Linnane A. W., Nagley P. Occurrence of a particular base substitution (3243 A to G) in mitochondrial DNA of tissues of ageing humans. Biochem Biophys Res Commun. 1993 Sep 15;195(2):1104–1110. doi: 10.1006/bbrc.1993.2158. [DOI] [PubMed] [Google Scholar]

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