A novel mitochondrial DNA-like sequence in the human nuclear genome

Genomics

Volumn 60, Issue 1, 1999, Pages 67-77

  Herrnstadt, Corinna ^a   Clevenger, William ^a   Ghosh, Soumitra S ^a   Anderson, Christen ^a   Fahy, Eoin ^a   Miller, Scott ^a   Howell, Neil ^b   Davis, Robert E ^a  

^a Migenix Inc   (United States)

^b University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA;

AMINO ACID SUBSTITUTION; ARTICLE; BLOOD SAMPLING; DNA FLANKING REGION; DNA SEQUENCE; DNA TRANSPOSITION; ENZYME SUBUNIT; GENE SEQUENCE; HUMAN; HUMAN CELL; MITOCHONDRIAL MEMBRANE; MULTIGENE FAMILY; NUCLEOTIDE SEQUENCE; POLYADENYLATION; POPULATION GENETICS; PRIORITY JOURNAL; PSEUDOGENE;

HOMINIDAE; PRIMATES;

EID: 0344564146     PISSN: 08887543     EISSN: None     Source Type: Journal    
DOI: 10.1006/geno.1999.5907     Document Type: Article

References (36)

1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H. L., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F., Schreier P. H., Smith A. J. H., Staden R., Young I. G. Sequence and organization of the human mitochondrial genome. Nature. 290:1981;456-465.
2. Arctander P. Comparison of a mitochondrial gene and a corresponding nuclear pseudogene. Proc. R. Soc. London B. 262:1995;13-19.
3. Blanchard J. L., Schmidt G. W. Mitochondrial DNA migration in yeast and humans: Integration by a common end-joining mechanism and alternative perspectives on nucleotide substitution patterns. Mol. Biol. Evol. 13:1996;537-548.
4. Boehnke M., Lange K., Cox D. R. Statistical methods for multipoint radiation hybrid mapping. Am. J. Hum. Genet. 49:1991;1174-1188.
5. Brown W. M., Prager E. M., Wang A., Wilson A. C. Mitochondrial DNA sequences of primates: Tempo and mode of evolution. J. Mol. Evol. 18:1982;225-239.
6. Collura R. V., Stewart C. Insertions and duplications of mtDNA in the nuclear genomes of old world monkeys and hominoids. Nature. 378:1995;485-489.
7. Collura R. V., Auerbach M. R., Stewart C. A quick, direct method that can differentiate expressed mitochondrial genes from their nuclear pseudogenes. Curr. Biol. 6:1996;1337-1339.
8. Corral M., Baffet G., Kitzis A., Paris B., Tichonicky L., Kruh J., Guguen-Guillouzo C., Defer N. DNA sequences homologous to mitochondrial genes in nuclei from normal rat tissues and from rat hepatoma cells. Biochem. Biophys. Res. Commun. 162:1989;258-264.
9. Davis R. E., Miller S., Herrnstadt C., Ghosh S. S., Fahy E., Shinobu L. A., Galasko D., Thal L. J., Beal M. F., Howell N., Parker W. D. Mutations in mitochondrial cytochrome c oxidase genes segregate with late-onset Alzheimer disease. Proc. Natl. Acad. Sci. USA. 94:1997;4526-4531.
10. Davis J. N., Parker W. D. Evidence that two reports of mtDNA cytochrome c oxidase "mutations" in Alzheimer's disease are based on nDNA pseudogenes of recent evolutionary origin. Biochem. Biophys. Res. Commun. 244:1998;877-883.
11. Fahy E., Nazarbaghi R., Zomorrodi M., Herrnstadt C., Parker W. D., Davis R. E., Ghosh S. S. Multiplex fluorescence-based primer extension method for quantitative mutation analysis of mitochondrial DNA and its diagnostic application for Alzheimer's disease. Nucleic Acids Res. 25:1997;3102-3109.
12. Fukuda M., Wakasugi S., Tsuzuki T., Nomiyama H., Shimada K. Mitochondrial DNA-like sequences in the human nuclear genome. J. Mol. Biol. 186:1985;257-266.
13. Ghosh S. S., Fahy E., Bodis-Wollner I., Sherman J., Howell N. Longitudinal study of a heteroplasmic 3460 Leber hereditary optic neuropathy family by multiplexed primer-extension analysis and nucleotide sequencing. Am. J. Hum. Genet. 58:1996;325-334.
14. Hadler H. I., Dimitrijev B., Mahalingam R. Mitochondrial DNA and nuclear DNA from normal rat liver have a common sequence. Proc. Natl. Acad. Sci. USA. 80:1983;6495-6499.
15. Hirano M., Shtilbans A., Mayeux R., Davidson M. M., DiMauro S., Knowles J., Schon E. A. Apparent mtDNA heteroplasmy in Alzheimer's disease patients and in normals due to PCR amplification of nucleus-embedded mtDNA pseudogenes. Proc. Natl. Acad. Sci. USA. 94:1997;14894-14899.
16. Hu G., Thilly W. G. Evolutionary trail of the mitochondrial genome as based on human 16S DNA pseudogenes. Gene. 147:1994;197-204.
17. Hu G., Thilly W. G. Multi-copy nuclear pseudogenes of mitochondrial DNA reveal recent acute genetic changes in the human genome. Curr. Genet. 28:1995;410-414.
18. Kamimura N., Ishii S., Liandong M., Shay J. W. Three separate mitochondrial DNA sequences are contiguous in the human genomic DNA. J. Mol. Biol. 210:1989;703-707.
19. Kocher T. D., Thomas W. K., Meyer A., Edwards S. V., Pääbo S., Villablanca F. X., Wilson A. C. Dynamics of mitochondrial DNA evolution in animals: Amplification and sequencing with conserved primers. Proc. Natl. Acad. Sci. USA. 86:1989;6196-6200.
20. Lee L. G., Spurgeon S. L., Heiner C. R., Benson S. C., Rosenblum B. B., Menchen S. M., Graham R. J., Constantinescu A., Updhya K. G., Cassel J. M. New energy transfer dyes for DNA sequencing. Nucleic Acids Res. 25:1997;2816-2822.
21. Lopez J. V., Yuhki N., Masuda R., Modi W., O'Brien S. J. Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J. Mol. Evol. 39:1994;174-190.
22. Louis E. J., Haber J. E. Evolutionary recent transfer of a group I mitochondrial intron to telomere regions in Saccharomyces cerevisiae. Curr. Genet. 20:1991;411-415.
23. Mecocci P., MacGarvey U., Beal M. F. Oxidative damage to mitochondrial DNA is increased in Alzheimer's disease. Ann. Neurol. 36:1994;747-751.
24. Miller S. M., Trimmer P. A., Parker W. D., Davis R. E. Creation and characterization of mitochondrial DNA-depleted cell lines with neuronal-like properties. J. Neurochem. 67:1996;1897-1907.
25. Mullis K. B., Faloona F. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 155:1987;335-350.
26. Nomiyama H., Tsuzuki T., Wakasugi S., Fukuda M., Shimada K. Interruption of a human nuclear sequence homologous to mitochondrial DNA by a member of the KpnI 1.8 kb family. Nucleic Acids Res. 12:1984;5225-5234.
27. Nomiyama H., Fukuda M., Wakasugi S., Tsuzuki T., Shimada K., Miyata T. Molecular structures of mitochondrial-DNA-like sequences in human nuclear DNA. Nucleic Acid Res. 13:1985;1649-1658.
28. Perna N. T., Kocher T. D. Mitochondrial DNA: Molecular fossils in the nucleus. Curr. Biol. 6:1996;128-129.
29. Pichersky E., Tanksley S. D. Chloroplast DNA sequences integrated into an intron of a tomato nuclear gene. Mol. Gen. Genet. 215:1988;65-68.
30. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuschi R., Horn G. T., Mullis K. B., Ehrlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 239:1988;487-491.
31. Shay J. W., Werbin H. New evidence for the insertion of mitochondrial DNA into the human genome: Significance for cancer and aging. Mutat. Res. 275:1992;227-235.
32. Sunnucks P., Hales D. F. Numerous transposed sequences of mitochondrial cytochrome oxidase I-II in aphids of the genus sitobion (Hemiptera: Aphidae). Mol. Biol. Evol. 13:1996;510-524.
33. Tsuzuki T., Nomiyama H., Setoyama C., Maeda S., Shimada K. Presence of mitochondrial-DNA-like sequences in the human nuclear DNA. Gene. 25:1983;223-229.
34. Wallace D. C., Stugard C., Murdock D., Schurr T., Brown M. D. Ancient mtDNA sequences in the human nuclear genome: A potential source of errors in identifying pathogenic mutations. Proc. Natl. Acad. Sci. USA. 94:1997;14900-14905.
35. Walter M. A., Spillett D. J., Thomas P., Weissenbach J., Goodfellow P. N. A method for constructing radiation hybrid maps of whole genomes. Nat. Genet. 7:1994;22-28.
36. Zischler H., Gelsert H., von Haeseler A., Pääbo S. A nuclear fossil of the mitochondrial D-loop and the origin of modern humans. Nature. 378:1995;489-492.