REVIEW ON PROPERTIES AND METHODS OF MITOCHONDRIAL DNA RESEARCH
Abstract
About the Authors
E. N. VoropayevaRussian Federation
V. N. Maksimov
Russian Federation
S. K. Malyutina
Russian Federation
M. Bobak
Russian Federation
M. I. Voevoda
Russian Federation
References
1. Nass M. M. Intramitochondrial fibers with DNA characteristics. I. fixation and electron staining reactions / М. М. Nass, S. Nass // J. Cell. Biol. - 1963. - N 19. - Р. 593-611.
2. Schatz G. Triphosphopyridine nucleotide : cytochrome C reductase of Saccharomyces Cerevisiaea ‘microsomal enzyme / G. Schatz, J. Klima // Biochimica et Biophysica Acta. - 1964. - Vol. 81, N 3. - Р. 448-461.
3. Sequence and organization of the human mitochondrial genome / S. Anderson [et al.] // Nature. - 1981. - Vol. 290, N 5806. - Р. 457-465.
4. Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA / R. M. Andrews [et al.] // Nat. Genet. - 1999. - Vol. 23, N 2. - Р. 147.
5. Mitochondria and Cancer: Past, Present, and Future / M. L. Verschoor [et al.] // BioMed Research International. - 2013. -Article ID 612369.
6. Heinz D. Mitochondrial Quality Control : Impact on Aging and Life Span - A Mini-Review / D. Heinz, O. D. Bernhardt // Gerontology. - 2013. - N 59. - Р. 413-420.
7. Wong L. J. C. Challenges of bringing next generation sequencing technologies to clinical molecular diagnostic laboratories / L. J. C. Wong // Neurotherapeutics. - 2013. - N 10. - Р. 262-272.
8. Diagnosis and molecular basis of mitochondrial respiratory chain disorders : Exome sequencing for disease gene identification / А. Ohtake [et al.] // Biochimica et Biophysica Acta. - 2014. - N 1840. - Р. 1355-1359.
9. Techniques and pitfalls in the detection of pathogenic mitochondrial DNA mutations / С. Т. Moraes [et al.] // J. Mol. Diagn. - 2003. - N 5. - Р. 197-208.
10. Taanman J. W. The mitochondrial genome: structure, transcription, translation and replication / J. W. Taanman // Biochimica et Biophysica Acta. - 1999. - N 1410. - Р. 103-123.
11. Bogenhagen D. F. Repair of mtDNA in Vertebrates / D. F. Bogenhagen // Am. J. Hum. Genet. - 1999. - N 64. - Р. 1276-1281.
12. Quantitative assessment of heteroplasmy of mitochondrial genome : perspectives in diagnostics and methodological pitfalls / I. A. Sobenin [et al.] // BioMed Research International. - 2014. - Article ID 292017.
13. Ancient DNA studies : new perspectives on old samples / Е. Rizzi [et al.] // Genetics Selection Evolution. - 2012. - N 44. - Р. 21.
14. Mitochondrial bioenergetics in aging / G. Lenaz [et al.] // Biochimica et Biophysica Acta. - 2000. - N 1459. - Р. 397-404.
15. Segregation of point mutation heteroplasmy in the control region of dog mtDNA studied systematically in deep generation pedigrees / C. F. Klütsch [et al.] // Int. J. Legal. Med. - 2011. - Vol. 125, N 4. - Р. 527-535.
16. Zouros E. The exceptional mitochondrial DNA system of the mussel family Mytilidae / Е. Zouros // Genes Genet. Syst. - 2000. - N 75. - Р. 313-318.
17. McCormick E. Molecular genetic testing for mitochondrial disease : from one generation to the next / Е. McCormick, E. Place, M. J. Falk // Neurotherapeutics. - 2013. - Vol. 10, N 2. - Р. 251-61.
18. Nesheva D. V. Аspects of ancient mitochondrial DNA analysis in different populations for understanding human evolution / D. V. Nesheva // BJMG. - 2014. - Vol. 17, N 1. - Р. 5-14.
19. Pereira L. Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype : pathogenicity analysis of reported somatic mtDNA mutations in tumors / L. Pereira [et al.] // BMC Cancer. - 2012. - N 12. - Р. 53.
20. The Maintenance of Mitochondrial DNA Integrity-Critical Analysis and Update / М. Alexeyev [et al.] // Cold Spring Harb Perspect Biol. - 2013. - N 5. - a012641.
21. Shokolenko I. N. Aging : A mitochondrial DNA perspective, critical analysis and an update / I. N. Shokolenko, G. L. Wilson, M. F. Alexeyev // World J. Exp. Med. - 2014. - Vol. 4, N 4. - Р. 46-57.
22. Mitochondrial DNA damage patterns and aging: revising the evidences for humans and mice / N. Kazachkova [et al.] // Аging and disease. - 2013. - Vol. 4, N 6. - Р. 337-350.
23. Decline in skeletal muscle mitochondrial function with aging in humans / K. R. Short [et al.] // Proceedings of the National Academy of Sciences of the United States of America. - 2005. - N 102. - Р. 5618-5623.
24. Lack of age-related increase of mitochondrial DNA amount in brain, skeletal muscle and human heart / Т. Frahm [et al.] // Mechanisms of ageing and development. - 2005. - N 126. - Р. 1192-1200.
25. Mitochondrial DNA deletions and the aging heart / S. A. Mohamed [et al.] // Experimental gerontology. - 2006. - N 41. - Р. 508-517.
26. Zhang Y. F. Age-dependent mitochondrial DNA 4977bp depletion in human skeletal muscle / Y. F. Zhang // Fa yi xue za zhi. - 2007. - N 23. - Р. 438-440.
27. Mitochondrial DNA 4977 bp deletion is a common phenomenon in hair and increases with age. Bosnian journal of basic medical sciences / Y. Zheng [et al.] // Udruzenje basicnih mediciniskih znanosti = Association of Basic Medical Sciences. - 2012. - N 12. - Р. 187-192.
28. Mitochondrial DNA-deletion mutations accumulate intracellularly to detrimental levels in aged human skeletal muscle fibers / Е. Bua [et al.] // American journal of human genetics. - 2006. - N 79. - Р. 469-480.
29. High levels of mitochondrial DNA deletions in substantia nigra neurons in aging and Parkinson disease / А. Bender [et al.] // Nature genetics. - 2006. - N 38. - Р. 515-517.
30. DiMauro S. Mitochondrial DNA mutations in human disease / S. DiMauro, E. A. Schon // Am. J. Med. Genet. - 2001. - N 106. - Р. 18-26.
31. Khaidakov M. Possibility of selection against mtDNA mutations in tumors / М. Khaidakov, R. J. Shmookler Reis // Molecular Cancer. - 2005. - N 4. - Р. 36.
32. Exhaustive scanning approach to screen all the mitochondrial tRNA genes for mutations and its application to the investigation of 35 independent patients with mitochondrial disorders / D. Sternberg [et al.] // Hum. Mol. Genet. - 1998. - Vol. 7, N 1. - Р. 33-42.
33. Rapid and enhanced detection of mitochondrial DNA variation using single-strand conformation analysis of superposed restriction enzyme fragments from polymerase chain reaction-amplified products / F. Barros [et al.] // Electrophoresis. - 1997. - N 18. - Р. 52-54.
34. Comprehensive scanning of the entire mitochondrial genome for mutations / L. J. Wong [et al.] // Clin. Chem. - 2002. - N 48. - Р. 1901-1912.
35. Sequence analysis of the complete mitochondrial genome in patients with Leber’s hereditary optic neuropathy lacking the three most common pathogenic DNA mutations / S. Fauser [et al.] // Biochem. Biophys. Res. Commun. - 2002. - N 295. - Р. 342-347.
36. Pareek C. S. Sequencing technologies and genome sequencing / C. S. Pareek, R. Smoczynski, A. Tretyn // J. Appl. Genetics. - 2011. - N 52. - Р. 413-435.
37. Yang Y. Application of Next-generation Sequencing Technology in Forensic Science / Y. Yang, B. Xie, J. Yan // Genomics Proteomics Bioinformatics. - 2014. - Vol. 12, N 5. - Р. 190-197.
38. Rajput N. K. Resources, challenges and way forward in rare mitochondrial diseases research / N. K. Rajput, V. Singh, A. Bhardwaj // F1000Res. - 2015. - N 4. - Р. 70.
39. Kogelnik A. M. MITOMAP : a human mitochondrial genome database / А. М. Kogelnik, M. T. Lott, M. D. Brown // Nucleic Acids Res. - 1996. - Vol. 24, N 1. - Р. 177-179.
40. Shamnamole K. MitoLSDB : a comprehensive resource to study genotype to phenotype correlations in human mitochondrial DNA variations / K. Shamnamole, S. Jalali, V. Scaria // PLoS One. - 2013. - Vol. 8, N 4. - e60066.
41. Damas J. MitoBreak : the mitochondrial DNA breakpoints database / J. Damas, J. Carneiro, A. Amorim // Nucleic Acids Res. - 2014. - N 42. - D1261-8.
42. Rubino F. HmtDB, a genomic resource for mitochondrion-based human variability studies / F. Rubino, R. Piredda, F. M. Calabrese // Nucleic Acids Res. - 2012. - N 40. - D1150-9.
43. Scheibye-Knudsen M. A novel diagnostic tool reveals mitochondrial pathology in human diseases and aging / М. Scheibye-Knudsen, K. Scheibye-Alsing, C. Canugovi // Aging. - 2013. - Vol. 5, N 3. - Р. 192-208.
44. mtDNAprofiler : a Web application for the nomenclature and comparison of human mitochondrial DNA sequences / I. S. Yang [et al.] // J. Forensic. Sci. - 2013. - Vol. 58, N 4. - Р. 972-80.
45. HAPLOFIND : a new method for high-throughput mtDNA haplogroup assignment / D. Vianello [et al.] // Hum. Mutat. - 2013. - Vol. 34, N 9. - Р. 1189-94.
46. Моlecular oncology focus - Is carcinogenesis a ’mitochondriopathy’? / А. М. Czarnecka [et al.] // Journal of Biomedical Science. - 2012. - N 17. - Р. 31.
47. Tengan C. H. Detection and analysis of mitochondrial DNA deletions by whole genome PCR / С. Н. Tengan, C. T. Moraes // Biochem. Mol. Med. - 1996. - N 58. - Р. 130-134.
48. Efficient and specific amplification of identified partial duplications of human mitochondrial DNA by long PCR / В. Fromenty [et al.] // Biochim. Biophys. Acta. - 1996. - N 1308. - Р. 222-230.
49. Meyer J. N. QPCR : a tool for analysis of mitochondrial and nuclear DNA damage in ecotoxicology / J. N. Meyer // Ecotoxicology. - 2010. - N 19. - Р. 804-811.
50. Lee H. C. Mitochondrial biogenesis and mitochondrial DNA maintenance of mammalian cells under oxidative stress / Н. С. Lee, Y. H. Wei // Int. J. Biochem. Cell. Biol. - 2005. - N 37. - Р. 822-834.
51. Exercise intolerance due to mutations in the cytochrome b gene of mitochondrial DNA / A. L. Andreu [et al.] // N. Engl. J. Med. - 1999. - N 341. - Р. 1037-1044.
52. Telomere length measurement and comparison in skeletal muscle, adipose tissue, skin and leukocytes : methodological aspects and preliminary results / S. Toupance [et al.] // Arch. Cardiovasc. Dis. - 2014. - Suppl. 6. - Р. 18-19.
53. Mitochondrial base excision repair assays / S. Maynard [et al.] // Methods. - 2010. - Vol. 51, N 4. - Р. 416-425.
54. Pallotti F. Isolation and subfractionation of mitochondria from animal cells and tissue culture lines / F. Pallotti, G. Lenaz // Methods Cell Biol. - 2007. - N 80. - Р. 3-44.
55. Quantitative PCR-based measurement of nuclear and mitochondrial DNA damage and repair in mammalian cells / J. H. Santos [et al.] // Methods Mol. Biol. - 2006. - N 314. - 183-99.
Review
For citations:
Voropayeva E.N., Maksimov V.N., Malyutina S.K., Bobak M., Voevoda M.I. REVIEW ON PROPERTIES AND METHODS OF MITOCHONDRIAL DNA RESEARCH. Journal of Siberian Medical Sciences. 2016;(3):8.