Phylogenetic analysis of mitochondrial DNA in a patient with Kearns–Sayre syndrome containing a novel 7629-bp deletion

References

• Albertini AM, Hofer M, Calos MP, Miller JH. 1982. On the formation of spontaneous deletions: The importance of short sequence homologies in the generation of large deletions. Cell. 29:319–328.
   PubMed Web of Science ®Google Scholar
• Ascaso FJ, Lopez-Gallardo E, Del Prado E, Ruiz-Pesini E, Montoya J.. 2010. Macular lesion resembling adult-onset vitelliform macular dystrophy in Kearns-Sayre syndrome with multiple mtDNA deletions. Clin Experiment Ophthalmol. 38 8: 812–816.
   PubMedGoogle Scholar
• Ashizawa T, Subramony SH. 2001. What is Kearns–Sayre syndrome after all?. Arch Neurol. 58:1053–1054.
   PubMedGoogle Scholar
• Barrientos A, Casademont J, Grau JM, Cardellach F, Montoya J, Estivill X, Urbano-Márquez A, Nunes V. 1995. Oftalmoplejia externa progresiva y síndrome de Kearns–Sayre: Un estudio clínico y molecular de seis casos. Med Clin. 105:180–184.
   PubMedGoogle Scholar
• Berenbaum F, Cote D, Pradat P, Rancurel G. 1990. Kearns–Sayre syndrome. Neurology. 40:193–194.
   PubMedGoogle Scholar
• Blok RB, Thorburn DR, Danks DM, Dahl HH. 1995. A topoisomerase II cleavage site is associated with a novel mitochondrial DNA deletion. Hum Genet. 95:75–81.
   PubMedGoogle Scholar
• Bosbach S, Kornblum C, Schröder R, Wagner M. 2003. Executive and visuospatial deficits in patients with chronic progressive external ophthalmoplegia and Kearns–Sayre syndrome. Brain. 126:1231–1240.
   PubMed Web of Science ®Google Scholar
• Carling PJ, Cree LM, Chinnery PF. 2011. The implications of mitochondrial DNA copy number regulation during embryogenesis. Mitochondrion. 11:686–692.
   PubMedGoogle Scholar
• Carod-Artal FJ, Lopez Gallardo E, Solano A, Dahmani Y, Herrero MD, Montoya J. Deleciones del ADN mitocondrial asociadas al síndrome de Kearns–Sayre. Neurologia. 2006a; 21:357–366.
   PubMedGoogle Scholar
• Carod-Artal FJ, López-Gallardo E, Solano A, Dahmani Y, Ruiz-Pesini E, Montoya J. Deleciones en el ADN mitocondrial asociadas a oftalmoplejía crónica progresiva con fibras rojo rasgadas en 2 pacientes brasileños. Med Clin. 2006b; 126:457–460.
   PubMedGoogle Scholar
• Carrozzo R, Wittig I, Santorelli FM, Bertini E, Hofmann S, Brandt U, Schägger H. 2006. Subcomplexes of human ATP synthase mark mitochondrial biosynthesis disorders. Ann Neurol. 59:265–275.
   PubMed Web of Science ®Google Scholar
• Casado-Naranjo I, Cervello Donderis MA, Lluch Bellod V, Dalli Peydro E. 1988. Reversible ischemic neurologic deficit in a patient with the Kearns–Sayre syndrome. Stroke. 19 4: 533.
   PubMedGoogle Scholar
• Chabrol B, Paquis V. 1997. Cerebral infarction associated with Kearns–Sayre syndrome. Neurology. 49 1: 308.
   PubMedGoogle Scholar
• Chen T, He J, Huang Y, Zhao W. 2011. The generation of mitochondrial DNA large-scale deletions in human cells. J Hum Genet. 56:689–694.
   PubMed Web of Science ®Google Scholar
• Chiaratti MR, Meirelles FV, Wells D, Poulton J. 2011. Therapeutic treatments of mtDNA diseases at the earliest stages of human development. Mitochondrion. 11:820–828.
   PubMedGoogle Scholar
• Chu BC, Terae S, Takahashi C, Kikuchi Y, Miyasaka K, Abe S, Minowa K, Sawamura T. 1999. MRI of the brain in the Kearns–Sayre syndrome: Report of four cases and a review. Neuroradiology. 41:759–764.
   PubMedGoogle Scholar
• Coulter-Mackie MB, Applegarth DA, Toone JR, Gagnier L. 1998. A protocol for detection of mitochondrial DNA deletions: Characterization of a novel deletion. Clin Biochem. 31:627–632.
   PubMedGoogle Scholar
• Cwerman-Thibault H, Sahel JA, Corral-Debrinski M. 2011. Mitochondrial medicine: To a new era of gene therapy for mitochondrial DNA mutations. J Inherit Metab Dis. 34:327–344.
   PubMed Web of Science ®Google Scholar
• De Coo IF, Gussinklo T, Arts PJ, Van Oost BA, Smeets HJ. 1997. A PCR test for progressive external ophtalmoplegia and Kearns–Sayre syndrome on DNA from blood samples. J Neurol Sci. 149:37–40.
   PubMedGoogle Scholar
• Degoul F, Nelson I, Amselem S, Romero N, Obermaier-Kusser B, Ponsot G, Marsac C, Lestienne P. 1991. Different mechanisms inferred from sequences of human mitochondrial DNA deletions in ocular myopathies. Nucleic Acids Res. 19:493–496.
   PubMedGoogle Scholar
• Delgado-Sánchez R, Zárate-Moysen A, Monsalvo-Reyes A, Herrero MD, Ruiz-Pesini E, López-Pérez M, Montoya J, Montiel-Sosa JF. 2007. Encefalomiopatía mitocondrial, acidosis láctica y accidentes cerebrovasculares (MELAS) con la mutación A3243G en el gen ARNtLeu(UUR) del ADNmt en el haplogrupo B2 nativoamericano. Rev Neurol. 44:18–22.
   PubMedGoogle Scholar
• De Paepe B, Smet J, Lammens M, Seneca S, Martin JJ, De Bleecker J, De Meirleir L, Lissens W, Van Coster R. 2009. Immunohistochemical analysis of the oxidative phosphorylation complexes in skeletal muscle from patients with mitochondrial DNA encoded tRNA gene defects. J Clin Pathol. 62:172–176.
   PubMedGoogle Scholar
• Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Rogalla U, Perkova M, Dambueva I, Zakharov I. 2010. Origin and post-glacial dispersal of mitochondrial DNA haplogroups C and D in northern Asia. PLoS ONE. 5 12: e15214.
   Google Scholar
• Derenko M, Malyarchuk B, Denisova G, Perkova M, Rogalla U, Grzybowski T, Khusnutdinova E, Dambueva I, Zakharov I. 2012. Complete mitochondrial DNA analysis of eastern Eurasian haplogroups rarely found in populations of northern Asia and eastern Europe. PLoS ONE. 7 2: e32179.
   Google Scholar
• DiMauro S, Hirano M, . 2003. Mitochondrial DNA deletion syndromes, GeneReviews [Internet]. In: Pagon RA, Bird TD, Dolan CR. editors. . Seattle, WA: University of Washington, Seattle Initial Posting: http://www.ncbi.nlm.nih.gov/books/NBK1203/.
   Google Scholar
• Fukui H, Moraes CT. 2008. Mechanisms of formation and accumulation of mitochondrial DNA deletions in aging neurons. Hum Mol Genet. 18:1028–1036.
   PubMed Web of Science ®Google Scholar
• Gao Y, Katyal S, Lee Y, Zhao J, Rehg JE, Russell HR, McKinnon PJ. 2011. DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair. Nature. 471:240–244.
   PubMed Web of Science ®Google Scholar
• Goebel T, Waters MR, O'Rourke DH. 2008. The late Pleistocene dispersal of modern humans in the Americas. Science. 319:1497–1502.
   PubMed Web of Science ®Google Scholar
• Gómez-Durán A, Pacheu-Grau D, López-Gallardo E, Díez-Sánchez C, Montoya J, López-Pérez MJ, Ruiz-Pesini E. 2010. Unmasking the causes of multifactorial disorders: OXPHOS differences between mitochondrial haplogroups. Hum Mol Genet. 19:3343–3353.
   PubMed Web of Science ®Google Scholar
• Gutiérrez A, Saldaña-Martínez A, García-Ramírez R, Rayo-Mares D, Carreras M, López-Pérez MJ, Ruiz-Pesini E, Montoya J, Montiel-Sosa JF. 2009. Síndrome de Leigh causado por la mutación G14459A del ADN mitocondrial en una familia mexicana. Rev Neurol. 49:248–250.
   PubMedGoogle Scholar
• Haber JE. 2000. Partners and pathwaysrepairing a double-strand break. Trends Genet. 16:259–264.
   PubMed Web of Science ®Google Scholar
• Harding AE, Hammans SR. 1992. Deletions of the mitochondrial genome. J Inherit Metab Dis. 15:480–486.
   PubMedGoogle Scholar
• Herrnstadt C, Elson JL, Fahy E, Preston G, Turnbull DM, Anderson C, Ghosh SS, Olefsky JM, Beal MF, Davis RE, Howell N. 2002. Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups. Am J Hum Genet. 70:1152–1171.
   PubMed Web of Science ®Google Scholar
• Holt IJ, Harding AE, Morgan-Hughes JA. 1988. Deletions of muscle mitochondrial DNA in patients with mitochondrial myopathies. Nature. 331:717–719.
   PubMed Web of Science ®Google Scholar
• Johns DR, Rutledge SL, Stine OC, Hurko O. 1989. Directly repeated sequences associated with pathogenic mitochondrial DNA deletions. Proc Natl Acad Sci USA. 86:8059–8062.
   PubMedGoogle Scholar
• Jonckheere AI, Huigsloot M, Lammens M, Jansen J, van den Heuvel LP, Spiekerkoetter U, von Kleist-Retzow JC, Forkink M, Koopman WJ, Szklarczyk R, Huynen MA, Fransen JA, Smeitink JA, Rodenburg RJ. 2011. Restoration of complex V deficiency caused by a novel deletion in the human TMEM70 gene normalizes mitochondrial morphology. Mitochondrion. 11:954–963.
   PubMedGoogle Scholar
• Kasiviswanathan R, Copeland WC. 2011. Ribonucleotide discrimination and reverse transcription by the human mitochondrial DNA polymerase. J Biol Chem. 286:31490–31500.
   PubMed Web of Science ®Google Scholar
• Kearns TP, Sayre GP. 1958. Retinitis pigmentosa, external ophthalmophegia, and complete heart block: Unusual syndrome with histologic study in one of two cases. AMA Arch Ophthalmol. 60:280–289.
   PubMed Web of Science ®Google Scholar
• Kosinski C, Mull M, Lethen H, Töpper R. 1995. Evidence for cardioembolic stroke in a case of Kearns–Sayre syndrome. Stroke. 26:1950–1952.
   PubMedGoogle Scholar
• Krishnan KJ, Reeve AK, Samuels DC, Chinnery PF, Blackwood JK, Taylor RW, Wanrooij S, Spelbrink JN, Lightowlers RN, Turnbull DM. 2008. What causes mitochondrial DNA deletions in human cells?. Nat Genet. 40:275–279.
   PubMed Web of Science ®Google Scholar
• Leonard JV, Schapira AH. 2000. Mitochondrial respiratory chain disorders I: Mitochondrial DNA defects. Lancet. 355:299–304.
   PubMed Web of Science ®Google Scholar
• Longo N. 2003. Mitochondrial encephalopathy. Neurol Clin N Am. 21:817–831.
   PubMedGoogle Scholar
• Malhi RS, Cybulski JS, Tito RY, Johnson J, Harry H, Dan C. 2010. Brief communication: Mitochondrial haplotype C4c confirmed as a founding genome in the Americas. Am J Phys Anthropol. 141:494–497.
   PubMed Web of Science ®Google Scholar
• Manfredi G, Vu T, Bonilla E, Schon EA, DiMauro S, Arnaudo E, Zhang L, Rowland LP, Hirano M. 1997. Association of myopathy with large-scale mitochondrial DNA duplications and deletions: Which is pathogenic?. Ann Neurol. 42:180–188.
   PubMedGoogle Scholar
• Marin-Garcia J, Goldenthal MJ, Sarnat HB. 2000. Kearns–Sayre syndrome with a novel mitochondrial DNA deletion. J Child Neurol. 15:555–558.
   PubMedGoogle Scholar
• Mkaouar-Rebai E, Chamkha I, Kammoun T, Chabchoub I, Aloulou H, Fendri N, Hachicha M, Fakhfakh F. 2010. A case of Kearns–Sayre syndrome with two novel deletions (9.768 and 7.253 kb) of the mtDNA associated with the common deletion in blood leukocytes, buccal mucosa and hair follicles. Mitochondrion. 10:449–455.
   PubMed Web of Science ®Google Scholar
• Mita S, Rizzuto R, Moraes CT, Shanske S, Arnaudo E, Fabrizi GM, Koga Y, DiMauro S, Schon EA. 1990. Recombination via flanking direct repeats is a major cause of large-scale deletions of human mitochondrial DNA. Nucleic Acids Res. 18:561–567.
   PubMed Web of Science ®Google Scholar
• Mohri I, Taniike M, Fujimura H, Matsuoka T, Inui K, Nagai T, Okada S. 1998. A case of Kearns–Sayre syndrome showing a constant proportion of deleted mitochondrial DNA in blood cells during 6 years of follow-up. J Neurol Sci. 158:106–109.
   PubMedGoogle Scholar
• Montiel-Sosa F, Ruiz-Pesini E, Enríquez JA, Marcuello A, Díez-Sánchez C, Montoya J, Wallace DC, López-Pérez MJ. 2006. Differences of sperm motility in mitochondrial DNA haplogroup U sublineages. Gene. 368:21–27.
   PubMedGoogle Scholar
• Provenzale JM, VanLandingham K. 1996. Cerebral infarction associated with Kearns–Sayre syndrome-related cardiomyopathy. Neurology. 46:826–828.
   PubMedGoogle Scholar
• Puoti G, Carrara F, Sampaolo S, De Caro M, Vincitorio CM, Invernizzi F, Zeviani M. 2003. Identical large scale rearrangement of mitochondrial DNA causes Kearns–Sayre syndrome in a mother and her son. Med Genet. 40:858–863.
   Google Scholar
• Remes AM, Peuhkurinen KJ, Herva R, Majamaa K, Hassinen IE. 1993. Kearns–Sayre syndrome case presenting a mitochondrial DNA deletion with unusual direct repeats and a rudimentary RNAase mitochondrial ribonucleotide processing target sequence. Genomics. 16:256–258.
   PubMedGoogle Scholar
• Richardson C, Jasin M. 2000. Coupled homologous and nonhomologous repair of a doublestrand break preserves genomic integrity in mammalian cells. Mol Cell Biol. 20:9068–9075.
   PubMed Web of Science ®Google Scholar
• Roels F, Verloo P, Eyskens F, François B, Seneca S, De Paepe B, JJ Martin, Meersschaut V, Praet M, Scalais E, Espeel M, Smet J, Van Goethem G, Van Coster R. 2009. Mitochondrial mosaics in the liver of 3 infants with mtDNA defects. BMC Clin Pathol. 9:4.
   PubMedGoogle Scholar
• Sadikovic B, Wang J, El-Hattab A, Landsverk M, Douglas G, Brundage EK, Craigen WJ, Schmitt ES, Wong LJ. 2010. Sequence homology at the breakpoint and clinical phenotype of mitochondrial DNA deletion syndromes. PLoS ONE. 5 12: e15687.
   PubMed Web of Science ®Google Scholar
• Samuels DC, Schon EA, Chinnery PF. 2004. Two direct repeats cause most human mtDNA deletions. Trends Genet. 20:393–398.
   PubMed Web of Science ®Google Scholar
• Santos JH, Mandavilli BS, Van Houten B. 2002. Measuring oxidative mtDNA damage and repair using quantitative PCR. Methods Mol Biol. 197:159–176.
   PubMedGoogle Scholar
• Shoffner JM, Lott MT, Voljavec AS, Soueidan SA, Costigan DA, Wallace DC. 1989. 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 USA. 86:7952–7956.
   PubMed Web of Science ®Google Scholar
• Schon EA, Rizzuto R, Moraes CT, Nakase H, Zeviani M, DiMauro S. 1989. A direct repeat is a hotspot for large-scale deletion of human mitochondrial DNA. Science. 244:346–349.
   PubMed Web of Science ®Google Scholar
• Solano A, Gámez J, Carod FJ, Pineda M, Playán A, López-Gallardo E, Andreu AL, Montoya J. 2003. Characterisation of repeat and palindrome elements in patients harbouring single deletions of mitochondrial DNA. J Med Genet. 40 7: e86.
   Google Scholar
• Srivastava S, Moraes CT. 2005. Double-strand breaks of mouse muscle mtDNA promote large deletions similar to multiple mtDNA deletions in humans. Hum Mol Genet. 14:893–902.
   PubMed Web of Science ®Google Scholar
• Tamm E, Kivisild T, Reidla M, Metspalu M, Smith DG, Mulligan CJ, Bravi CM, Rickards O, Martinez-Labarga C, Khusnutdinova EK, Fedorova SA, Golubenko MV, Stepanov VA, Gubina MA, Zhadanov SI, Ossipova LP, Damba L, Voevoda MI, Dipierri JE, Villems R, Malhi RS. 2007. Beringian standstill and spread of Native American founders. PLoS ONE. 2 9: e829.
   PubMed Web of Science ®Google Scholar
• Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731–2739.
   PubMed Web of Science ®Google Scholar
• Tanji K, DiMauro S, Bonilla E. Disconnection of cerebellar Purkinje cells in Kearns–Sayre syndrome. J Neurol Sci. 1999b; 166:64–70.
   PubMedGoogle Scholar
• Tanji K, Vu TH, Schon EA, DiMauro S, Bonilla E. Kearns–Sayre syndrome: Unusual pattern of expression of subunits of the respiratory chain in the cerebellar system. Ann Neurol. 1999a; 45:377–383.
   PubMedGoogle Scholar
• Tengan CH, Moraes CT. 1996. Detection and analysis of mitochondrial DNA deletions by whole genome PCR. Biochem Mol Med. 58:130–134.
   PubMedGoogle Scholar
• Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673–4680.
   PubMed Web of Science ®Google Scholar
• van der Westhuizen FH, Smet J, Levanets O, Meissner-Roloff M, Louw R, Van Coster R, Smuts I. Aberrant synthesis of ATP synthase resulting from a novel deletion in mitochondrial DNA in an African patient with progressive external ophthalmoplegia. J Inherit Metab Dis. 2010 Epub ahead of print. DOI: 10.1007/s10545-009-9020-y.
   Google Scholar
• Vázquez-Acevedo M, Vázquez-Memije ME, Mutchinick OM, Morales JJ, García-Ramos G, González-Halphen D. 2002. A case of Kearns–Sayre syndrome with the 4,977-bp common deletion associated with a novel 7,704-bp deletion. Neurol Sci. 23:247–250.
   PubMedGoogle Scholar
• Wilichowski E, Grüters A, Kruse K, Rating D, Beetz R, Korenke GC, Ernst BP, Christen HJ, Hanefeld F. 1997. Hypoparathyroidism and deafness associated with pleioplasmic large scale rearrangements of the mitochondrial DNA: A clinical and molecular genetic study of four children with Kearns–Sayre syndrome. Pediatr Res. 41:193–200.
   PubMed Web of Science ®Google Scholar
• Yakes FM, Van Houten B. 1997. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress. Proc Natl Acad Sci USA. 94:514–519.
   PubMed Web of Science ®Google Scholar
• Zeviani M, Moraes CT, DiMauro S, Nakase H, Bonilla E, Schon EA, Rowland LP. 1988. Deletions of mitochondrial DNA in Kearns–Sayre syndrome. Neurology. 38:1339–1346.
   PubMed Web of Science ®Google Scholar