The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern

DNA Research

Volumn 20, Issue 6, 2013, Pages 537-547

  Bellizzi, Dina ^a   D'aquila, Patrizia ^a   Scafone, Teresa ^a   Giordano, Marco ^a   Riso, Vincenzo ^b   Riccio, Andrea ^b   Passarino, Giuseppe ^a  

^a UNIVERSITY OF CALABRIA   (Italy)

^b INSTITUTE OF GENETICS AND BIOPHYSICS ADRIANO BUZZATI TRAVERSO   (Italy)

Author keywords

5 hydromethylcytosine; 5 methylcytosine; CpG methylation; mitochondrial D loop region; non CpG methylation

Indexed keywords

5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; BISULFITE; CYTOSINE; DINUCLEOTIDE; DIOXYGENASE; DNA METHYLTRANSFERASE 1; DNA METHYLTRANSFERASE 3A; DNA METHYLTRANSFERASE 3B; MITOCHONDRIAL DNA; TET1 PROTEIN; TET2 PROTEIN; TET3 PROTEIN; UNCLASSIFIED DRUG;

ADULT; AGED; ANIMAL CELL; ARTICLE; CPG ISLAND; DNA METHYLATION; DNA MODIFICATION; DNA REPLICATION; DNA SEQUENCE; DNA STRAND; DNA STRUCTURE; DNA TRANSCRIPTION; EMBRYO; EMBRYONIC STEM CELL; FEMALE; GENOME; HUMAN; HUMAN CELL; IMMUNOPRECIPITATION; MALE; MITOCHONDRIAL DNA CONTROL REGION; MOUSE; NONHUMAN; NORMAL HUMAN; PROMOTER REGION; WILD TYPE;

5-HYDROMETHYLCYTOSINE; 5-METHYLCYTOSINE; CPG METHYLATION; MITOCHONDRIAL D-LOOP REGION; NON-CPG METHYLATION;

ADULT; AGED; AGED, 80 AND OVER; ANIMALS; CELL LINE; CPG ISLANDS; DIOXYGENASES; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA METHYLATION; DNA, MITOCHONDRIAL; FEMALE; HUMANS; LOCUS CONTROL REGION; MALE; MICE; MIDDLE AGED; MITOCHONDRIA;

EID: 84882889657     PISSN: 13402838     EISSN: 17561663     Source Type: Journal    
DOI: 10.1093/dnares/dst029     Document Type: Article

References (47)

1. Lee, T., Zhai. J. and Meyers, C. 2010, Conservation and divergence in eukaryotic DNA methylation. Proc. Natl Acad. Sci. USA, 107, 9027-8.
2. Vanyushin, B.F.andAshapkin,V.V.2011,DNAmethylation in higher plants: Past, present and future, Biochim. Biophys. Acta, 1809, 360-8.
3. Ramsahoye, B.H., Biniszkiewicz, D., Lyko, F., Clark, V., Bird, A.P. and Jaenisch, R. 2000, Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc. Natl Acad. Sci. USA, 97, 5237-42.
4. Lister, R., Pelizzola, M., Dowen, R.H., et al. 2009, Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-22.
5. Xie,W., Barr, C.L., Kim, A., et al. 2012, Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell, 148, 816-31.
6. Kobayashi, H., Sakurai, T., Imai, M., et al. 2012, Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet., 8, e1002440.
7. Ichiyanagi, T., Ichiyanagi, K., Miyake, M. and Sasaki, H. Accumulation and loss of asymmetric non-CpG methylation during male germ-cell development, Nucleic Acids Res., 41, 738-45.
8. Fuso, A., Nicolia, V., Pasqualato, A., Fiorenza, M.T., Cavallaro, R.A. and Scarpa, S. 2009, Changes in Presenilin 1 gene methylation pattern in diet-induced B vitamin deficiency, Neurobiol. Aging, 32, 187-99.
9. Fuso, A., Ferraguti, G., Grandoni, F., Ruggeri, R., Scarpa, S., Strom, R. and Lucarelli, M. 2010, Early demethylation of non-CpG, CpC-rich, elements in the myogenin 50-flanking region: A priming effect on the spreading of active demethylation, Cell Cycle, 9, 3965-76.
10. Nishino, K., Hattori, N., Sato, S., Arai, Y., Tanaka, S., Nagy, A. and Shiota, K. 2011, Non-CpG methylation occurs in the regulatory region of the Sry gene. J. Reprod. Dev., 57, 586-93.
11. Goll, M.G. and Bestor, T.H. 2005, Eukaryotic cytosine methyltransferases. Annu. Rev. Biochem., 74, 481-514.
12. Grandjean, V., Yaman, R., Cuzin, F. and Rassoulzadegan, M. Inheritance of an epigenetic mark: The CpG DNA methyltransferase 1 is required for de novo establishment of a complex pattern of non-CpG methylation. PLoS One, 2, e1136.
13. Barrès, R., Osler, M.E., Yan, J., et al. 2009, Non-CpG methylation of the PGC-1alpha promoter through DNMT3B controls mitochondrial density, Cell Metab., 10, 189-98.
14. Kinney, S.R. and Pradhan, S. 2011, Regulation of expression and activity of DNA (cytosine-5) methyltransferases in mammalian cells. Prog. Mol. Biol. Transl. Sci., 101, 311-33.
15. Saxonov, S., Berg, P. and Brutlag, D.L. 2006, A genomewide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc. Natl Acad. Sci. USA, 103, 1412-7.
16. Deaton,A.M. and Bird, A. 2011,CpGislands and the regulation of transcription Genes Dev., 25, 1010-22.
17. Park, J., Xu, K., Park, T.andYi, S.V. 2012,What are the determinants of gene expression levels and breadths in the human genome? Hum. Mol. Genet, 21, 46-56.
18. Globisch,D.,Münzel,M.,Müller,M., et al. 2010, Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation intermediates. PLoS One, 5, e15367.
19. Kinney, S.M., Chin, H.G., Vaisvila, R., et al. 2011, Tissuespecific distribution and dynamic changes of 5- Hydroxymethylcytosine in mammalian genomes. J. Biol. Chem., 286, 4685-93.
20. Kriaucionis, S.andHeintz, N.2009,ThenuclearDNAbase 5- hydroxymethylcytosine is present in Purkinje neurons and the brain. Science, 324, 929-30.
21. Guo, J.U., Su, Y., Zhong, C., Ming, G.L. and Song, H. 2011, Hydroxylation of 5-methylcytosine by TET1 promotes active DNA demethylation in the adult brain. Cell, 145, 423-34.
22. Wu, H. and Zhang, Y. 2011, Mechanisms and functions of Tet protein-mediated 5-methylcytosine oxidation Genes Dev., 25, 2436-52.
23. Hashimoto, H., Liu, Y., Upadhyay, A.K., et al. 2012, Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation, Nucleic Acids Res., 40, 4841-9.
24. Tan, L. and Shi, Y.G. 2012, Tet family proteins and 5- hydroxymethylcytosine in development and disease, Development, 139, 1895-902.
25. Liutkeviciute, Z., Lukinavicius, G., Masevicius, V., Daujotyte, D. and Klimasauskas, S. 2009, Cytosine-5-methyltransferases add aldehydes to DNA. Nat. Chem. Biol., 5, 400-2.
26. Cummings, D.J., Tait, A. and Goddard, J.M. 1974, Methylated bases in DNA from Paramecium aurelia, Biochim. Biophys. Acta, 374, 1-11.
27. Dawid, I.B. 1974, 5-methylcytidylic acid: Absence from mitochondrial DNA of frogs and HeLa cells. Science, 184, 80-1.
28. Groot, G.S. and Kroon, A.M. 1979, Mitochondrial DNA from various organisms does not contain internally methylated cytosine in -CCGG- sequences, Biochim. Biophys. Acta, 564, 355-7.
29. Maekawa, M., Taniguchi, T., Higashi, H., Sugimura, H., Sugano, K. and Kanno, T.2004,Methylation of mitochondrialDNAis not ausefulmarker forcancer detection. Clin. Chem., 50, 1480-1.
30. Shmookler Reis, R.J. and Goldstein, S. 1983, Mitochondrial DNA in mortal and immortal human cells. J. Biol. Chem., 258, 9078-85.
31. Pollack, Y., Kasir, J., Shemer, R., Metzger, S. and Szyf, M. 1984, Methylation pattern of mouse mitochondrial DNA, Nucleic Acids Res., 12, 4811-24.
32. Nass, M.M. 1973, 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, 155-75.
33. Ŝimková, H. 1998, Methylation of mitochondrial DNA in carrot (Daucus carota L). Plant Cell Reports, 17, 220-4.
34. Rebelo, A.P., Williams, S.L. and Moraes, C.T. 2009, In vivo methylation of mtDNA reveals the dynamics of proteinmtDNA interactions, Nucleic Acids Res., 37, 6701-15.
35. Shock, L.S., Thakkar, P.V., Peterson, E.J., Moran, R.G. and Taylor, S.M. 2011, DNA methyltransferase 1, cytosine methylation and cytosine hydroxymethylation in mammalian mitochondria. Proc. Natl Acad. Sci. USA, 108, 3630-5.
36. Sbisà, E., Tanzariello, F., Reyes, A., Pesole, G. and Saccone, C. Mammalian mitochondrial D-loop region structural analysis: Identification of new conserved sequences and their functional and evolutionary implications, Gene, 205, 125-40.
37. Tsumura, A., Hayakawa, T., Kumaki, Y., et al. 2006, Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b Genes Cells, 11, 805-14.
38. Klose, R.J. and Bird,A.P. 2006,GenomicDNAmethylation: The mark and its mediators, Trends Biochem. Sci., 31, 89-97.
39. Weber, M. and Schübeler, D. 2007, Genomic patterns of DNA methylation: Targets and function of an epigenetic mark. Curr. Opin. Cell Biol., 19, 273-80.
40. He, X.J., Chen, T. and Zhu, J.K. 2011, Regulation and function of DNA methylation in plants and animals, Cell Res., 21, 442-65.
41. Cardon, L.R., Burge, C., Clayton, D.A. and Karlin, S. 1994, Pervasive CpG suppression in animal mitochondrial genomes. Proc. Natl Acad. Sci. USA, 91, 3799-803.
42. McClelland, M. and Ivarie, R. 1982, Asymmetrical distribution of CpG in an 'average' mammalian gene, Nucleic Acids Res., 10, 7865-77.
43. Dzitoyeva, S., Chen, H. andManev,H. 2012, Effect of aging on 5-hydroxymethylcytosine in brain mitochondria, Neurobiol. Aging, 33, 2881-91.
44. Manev, H., Dzitoyeva, S. and Chen, H. 2012, Mitochondrial DNA: A blind spot in neuroepigenetics, Biomol. Concepts, 3, 107-15.
45. Bensasson, D., Zhang, D., Hartl, D.L. and Hewitt, G.M. 2001, Mitochondrial pseudogenes: Evolution's misplaced witnesses, Trends Ecol. Evol., 16, 314-21.
46. Clayton, D.A. 2000, Transcription and replication of mitochondrial DNA, Hum. Reprod., 15, 11-7.
47. Wassenegger, M. 2000, RNA-directed DNA methylation. Plant Mol. Biol., 43, 203-20.