CpG methylation patterns of human mitochondrial DNA

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Liu, Baojing ^a   Du, Qingqing ^a   Chen, Lu ^a   Fu, Guangping ^a   Li, Shujin ^a   Fu, Lihong ^a   Zhang, Xiaojing ^a   Ma, Chunling ^a   Bin, Cong ^a  

^a HEBEI MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

MITOCHONDRIAL DNA;

CPG ISLAND; DNA METHYLATION; GENETIC EPIGENESIS; GENETICS; HUMAN;

CPG ISLANDS; DNA METHYLATION; DNA, MITOCHONDRIAL; EPIGENESIS, GENETIC; HUMANS;

EID: 84961842166     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep23421     Document Type: Article

References (33)

1. Nass, M. M. Differential methylation of mitochondrial and nuclear DNA in cultured mouse, hamster and virus-transformed hamster cells. In vivo and in vitro methylation. J Mol Biol 80, 155-175 (1973).
2. Kirnos, M. D., Vaniushin, B. F. [Isolation of mitochondrial DNA, purified of nuclear DNA, from animal tissues (degree of methylation and level of pyrimidine nucleotide clustering-criteria of purity)]. Biokhimiia 41, 68-74 (1976).
3. Vanyushin, B. F., Kirnos, M. D. Structure of animal mitochondrial DNA: nucleotide composition, pyrimidine clusters, and methylation character. Mol Biol (Mosk) 10, 715-724 (1976).
4. Vanyushin, B. F., Kirnos, M. D. The structure of animal mitochondrial DNA (base composition, pyrimidine clusters, character of methylation). Mol Cell Biochem 14, 31-36 (1977).
5. Cummings, D. J., Tait, A., Goddard, J. M. Methylated bases in DNA from Paramecium aurelia. Biochim Biophys Acta 374, 1-11 (1974).
6. Dawid, I. B. 5-methylcytidylic acid: absence from mitochondrial DNA of frogs and HeLa cells. Science 184, 80-81 (1974).
7. Groot, G. S., Kroon, A. M. Mitochondrial DNA from various organisms does not contain internally methylated cytosine in-CCGG-sequences. Biochim Biophys Acta 564, 355-357 (1979).
8. Pollack, Y., Kasir, J., Shemer, R., Metzger, S., Szyf, M. Methylation pattern of mouse mitochondrial DNA. Nucleic Acids Res 12, 4811-4824 (1984).
9. Shmookler Reis, R. J., Goldstein, S. Mitochondrial DNA in mortal and immortal human cells. Genome number, integrity, and methylation. J Biol Chem 258, 9078-9085 (1983).
10. Iacobazzi, V., Castegna, A., Infantino, V., Andria, G. Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool. Mol Genet Metab 110, 25-34, doi: 10.1016/j.ymgme.2013.07.012 (2013).
11. Infantino, V. et al. Impairment of methyl cycle affects mitochondrial methyl availability and glutathione level in Down's syndrome. Mol Genet Metab 102, 378-382, doi: 10.1016/j.ymgme.2010.11.166 (2011).
12. Chen, H., Dzitoyeva, S., Manev, H. Effect of valproic acid on mitochondrial epigenetics. Eur J Pharmacol 690, 51-59, doi: 10.1016/j. ejphar.2012.06.019 (2012).
13. Dzitoyeva, S., Chen, H., Manev, H. Effect of aging on 5-hydroxymethylcytosine in brain mitochondria. Neurobiol Aging 33, 2881-2891, doi: 10.1016/j.neurobiolaging.2012.02.006 (2012).
14. Shock, L. S., Thakkar, P. V., Peterson, E. J., Moran, R. G., Taylor, S. M. DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc Natl Acad Sci USA 108, 3630-3635, doi: 10.1073/pnas.1012311108 (2011).
15. Bellizzi, D. et al. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res 20, 537-547, doi: 10.1093/dnares/dst029 (2013).
16. Byun, H. M. et al. Effects of airborne pollutants on mitochondrial DNA methylation. Part Fibre Toxicol 10, 18, doi: 10.1186/1743-8977-10-18 (2013).
17. Wong, M., Gertz, B., Chestnut, B. A., Martin, L. J. Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS. Front Cell Neurosci 7, 279, doi: 10.3389/fncel.2013.00279 (2013).
18. Janssen, B. G. et al. Variation of DNA methylation in candidate age-related targets on the mitochondrial-telomere axis in cord blood and placenta. Placenta 35, 665-672, doi: 10.1016/j.placenta.2014.06.371 (2014).
19. Byun, H. M., Barrow, T. M. Analysis of pollutant-induced changes in mitochondrial DNA methylation. Methods Mol Biol 1265, 271-283, doi: 10.1007/978-1-4939-2288-8-19 (2015).
20. Hong, E. E., Okitsu, C. Y., Smith, A. D., Hsieh, C. L. Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. Mol Cell Biol 33, 2683-2690, doi: 10.1128/MCB.00220-13 (2013).
21. Maekawa, M. et al. Methylation of mitochondrial DNA is not a useful marker for cancer detection. Clin Chem 50, 1480-1481, doi: 10.1373/clinchem.2004.035139 (2004).
22. Ghosh, S., Sengupta, S., Scaria, V. Comparative analysis of human mitochondrial methylomes shows distinct patterns of epigenetic regulation in mitochondria. Mitochondrion 18, 58-62, doi: 10.1016/j.mito.2014.07.007 (2014).
23. Reed, K., Poulin, M. L., Yan, L., Parissenti, A. M. Comparison of bisulfite sequencing PCR with pyrosequencing for measuring differences in DNA methylation. Anal Biochem 397, 96-106, doi: 10.1016/j.ab.2009.10.021 (2010).
24. Migheli, F. et al. Comparison study of MS-HRM and pyrosequencing techniques for quantification of APC and CDKN2A gene methylation. PLoS One 8, e52501, doi: 10.1371/journal.pone.0052501 (2013).
25. Frommer, M. et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89, 1827-1831 (1992).
26. Grunau, C., Clark, S. J., Rosenthal, A. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters. Nucleic Acids Res 29, E65-65 (2001).
27. Ehrich, M. et al. Quantitative high-throughput analysis of DNA methylation patterns by base-specific cleavage and mass spectrometry. Proc Natl Acad Sci USA 102, 15785-15790, doi: 10.1073/pnas.0507816102 (2005).
28. Coolen, M. W., Statham, A. L., Gardiner-Garden, M., Clark, S. J. Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements. Nucleic Acids Res 35, e119, doi: 10.1093/nar/gkm662 (2007).
29. Wong, J. M. C. a. N. C. Epigenetics: A Reference Manual. (Caister Academic Press, 2011).
30. Manev, H., Dzitoyeva, S., Chen, H. Mitochondrial DNA: A Blind Spot in Neuroepigenetics. Biomol Concepts 3, 107-115, doi: 10.1515/bmc-2011-0058 (2012).
31. Minocherhomji, S., Tollefsbol, T. O., Singh, K. K. Mitochondrial regulation of epigenetics and its role in human diseases. Epigenetics 7, 326-334, doi: 10.4161/epi.19547 (2012).
32. Chinnery, P. F., Elliott, H. R., Hudson, G., Samuels, D. C., Relton, C. L. Epigenetics, epidemiology and mitochondrial DNA diseases. Int J Epidemiol 41, 177-187, doi: 10.1093/ije/dyr232 (2012).
33. Agrimi, G. et al. Identification of the human mitochondrial S-adenosylmethionine transporter: bacterial expression, reconstitution, functional characterization and tissue distribution. Biochem J 379, 183-190, doi: 10.1042/BJ20031664 (2004).