Skip to main content

Mitochondrial DNA Methylation and Related Disease

  • Chapter
  • First Online:

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1038))

Abstract

Most researchers focused on methylation of genomic DNA, while methylation of mitochondrial DNA (mtDNA) is rarely tauched, and there is still controversy about the existence of mtDNA methylation. The study of cytosine methylation in mtDNA is limited. The mtDNA was recently found to exist CpG hypomethylation, and more studies provided evidence that mtDNA methylation plays an important role in mitochondrial gene regulation. In present review, we will overview recent studies of mitochondrial DNA methylation and potential influencing factors in diseases that are involved in mtDNA methylation. Thus, the further studies on mtDNA methylation will provide more evidence to explain the mechanism of mtDNA methylation and an advantageous approach for human clinical diagnosis and prevention.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  1. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, et al. MITOMAP: a human mitochondrial genome database – 2004 update. Nucleic Acids Res. 2005;33:D611–3. [PMID: 15608272]

    Article  CAS  PubMed  Google Scholar 

  2. Wallace DC. A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a Dawn for evolutionary medicine. Annu Rev Genet. 2005;39:359–407. [PMID: 16285865]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Paes B, Moco PD, Pereira CG, Porto GS, de Sousa Russo EM, Reis LCJ, et al. Ten years of iPSC: clinical potential and advances in vitro hematopoietic differentiation. Cell Biol Toxicol. 2017;33:233–50. [PMID: 28039590]

    Article  PubMed  Google Scholar 

  4. Janssen BG, Byun HM, Roels HA, Gyselaers W, Penders J, Baccarelli AA, et al. Regulating role of fetal thyroid hormones on placental mitochondrial DNA methylation: epidemiological evidence from the ENVIRONAGE birth cohort study. Clin Epigenetics. 2017;9:66. [PMID: 28649287]

    Article  PubMed  PubMed Central  Google Scholar 

  5. Byun HM, Panni T, Motta V, Hou L, Nordio F, Apostoli P, et al. Effects of airborne pollutants on mitochondrial DNA methylation. Part Fibre Toxicol. 2013;10:18. [PMID: 23656717]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SMDNA. Methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc Natl Acad Sci U S A. 2011;108:3630–5. [PMID: 21321201]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Dawid IB. 5-methylcytidylic acid: absence from mitochondrial DNA of frogs and HeLa cells. Science. 1974;184:80–1. [PMID: 4815287]

    Article  CAS  PubMed  Google Scholar 

  8. Choi YS, Hoon Jeong J, Min HK, Jung HJ, Hwang D, Lee SW, et al. Shot-gun proteomic analysis of mitochondrial D-loop DNA binding proteins: identification of mitochondrial histones. Mol BioSyst. 2011;7:1523–36. [PMID: 21359316]

    Article  CAS  PubMed  Google Scholar 

  9. Hong EE, Okitsu CY, Smith AD, Hsieh CL. Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA. Mol Cell Biol. 2013;33:2683–90. [PMID: 23671186]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Manev H, Dzitoyeva S. Progress in mitochondrial epigenetics. Biomol Concepts. 2013;4:381–9. [PMID: 25436587]

    Article  CAS  PubMed  Google Scholar 

  11. Kaarniranta K, Tokarz P, Koskela A, Paterno J, Blasiak J. Autophagy regulates death of retinal pigment epithelium cells in age-related macular degeneration. Cell Biol Toxicol. 2017;33:113–28. [PMID: 27900566]

    Article  CAS  PubMed  Google Scholar 

  12. Giromini C, Rebucci R, Fusi E, Rossi L, Saccone F, Baldi A. Cytotoxicity, apoptosis, DNA damage and methylation in mammary and kidney epithelial cell lines exposed to ochratoxin A. Cell Biol Toxicol. 2016;32:249–58. [PMID: 27154019]

    Article  CAS  PubMed  Google Scholar 

  13. Gomez-Sagasti MT, Becerril JM, Epelde L, Alkorta I, Garbisu C. Early gene expression in Pseudomonas fluorescens exposed to a polymetallic solution. Cell Biol Toxicol. 2015;31:39–81. [PMID: 25754557]

    Article  CAS  PubMed  Google Scholar 

  14. Santamaria E, Avila MA, Latasa MU, Rubio A, Martin-Duce A, SC L, et al. Functional proteomics of nonalcoholic steatohepatitis: mitochondrial proteins as targets of S-adenosylmethionine. Proc Natl Acad Sci U S A. 2003;100:3065–70. [PMID: 12631701]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Fierbinteanu-Braticevici C, Sinescu C, Moldoveanu A, Petrisor A, Diaconu S, Cretoiu D, et al. Nonalcoholic fatty liver disease: one entity, multiple impacts on liver health. Cell Biol Toxicol. 2017;33:5–14. [PMID: 27680752]

    Article  CAS  PubMed  Google Scholar 

  16. van der Wijst MG, van Tilburg AY, Ruiters MH, Rots MG. Experimental mitochondria-targeted DNA methylation identifies GpC methylation, not CpG methylation, as potential regulator of mitochondrial gene expression. Sci Rep. 2017;7:177. [PMID: 28282966]

    Article  PubMed  PubMed Central  Google Scholar 

  17. Rinaldi L, Avgustinova A, Martin M, Datta D, Solanas G, Prats N, et al. Loss of Dnmt3a and Dnmt3b does not affect epidermal homeostasis but promotes squamous transformation through PPAR-gamma. elife. 2017;6:e21697. [PMID: 28425913]

    Article  PubMed  PubMed Central  Google Scholar 

  18. Guney Eskiler G, Cecener G, Tunca B, Egeli U. An in vitro model for the development of acquired tamoxifen resistance. Cell Biol Toxicol. 2016;32:563–81. [PMID: 27585693]

    Article  CAS  PubMed  Google Scholar 

  19. Chen T, Hevi S, Gay F, Tsujimoto N, He T, Zhang B, et al. Complete inactivation of DNMT1 leads to mitotic catastrophe in human cancer cells. Nat Genet. 2007;39:391–6. [PMID: 17322882]

    Article  CAS  PubMed  Google Scholar 

  20. Wang XCBT. Profiles of cabozantinib approved for advanced renal cell carcinomas. Cell Biol Toxicol. 2016;32:259–61. [PMID: 27383755]

    Article  CAS  PubMed  Google Scholar 

  21. Mohsenzadeh M, Sadeghi RN, Vahedi M, Kamani F, Hashemi M, Asadzadeh H, et al. Promoter hypermethylation of RAR-beta tumor suppressor gene in gastric carcinoma: association with histological type and clinical outcomes. Cancer Biomark. 2017;20:7–15. [PMID: 28759951]

    Article  CAS  PubMed  Google Scholar 

  22. Lodeiro MF, Uchida A, Bestwick M, Moustafa IM, Arnold JJ, Shadel GS, et al. Transcription from the second heavy-strand promoter of human mtDNA is repressed by transcription factor A in vitro. Proc Natl Acad Sci U S A. 2012;109:6513–8. [PMID: 22493245]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Zerin T, Kim JS, Gil HW, Song HY, Hong SY. Effects of formaldehyde on mitochondrial dysfunction and apoptosis in SK-N-SH neuroblastoma cells. Cell Biol Toxicol. 2015;31:261–72. [PMID: 26728267]

    Article  CAS  PubMed  Google Scholar 

  24. Lippai M, Szatmari Z. Autophagy-from molecular mechanisms to clinical relevance. Cell Biol Toxicol. 2017;33:145–68. [PMID: 27957648]

    Article  CAS  PubMed  Google Scholar 

  25. Stoccoro A, Siciliano G, Migliore L, Coppede F. Decreased methylation of the mitochondrial D-loop region in late-onset Alzheimer’s disease. J Alzheimers Dis. 2017;59:559–64. [PMID: 28655136]

    Article  CAS  PubMed  Google Scholar 

  26. Cacabelos R, Torrellas C. Epigenetics of aging and Alzheimer’s disease: implications for pharmacogenomics and drug response. Int J Mol Sci. 2015;16:30483–543. [PMID: 26703582]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Zhou Y, Ning Z, Lee Y, Hambly BD, McLachlan CS. Shortened leukocyte telomere length in type 2 diabetes mellitus: genetic polymorphisms in mitochondrial uncoupling proteins and telomeric pathways. Clin Transl Med. 2016;5:8. [PMID: 26951191]

    Article  PubMed  PubMed Central  Google Scholar 

  28. Zheng LD, Linarelli LE, Brooke J, Smith C, Wall SS, Greenawald MH, et al. Mitochondrial epigenetic changes link to increased diabetes risk and early-stage prediabetes indicator. Oxidative Med Cell Longev. 2016;2016:5290638. [PMID: 27298712]

    Google Scholar 

  29. Miko E, Vida A, Bai P. Translational aspects of the microbiome-to be exploited. Cell Biol Toxicol. 2016;32:153–6. [PMID: 27098154]

    Article  PubMed  Google Scholar 

  30. Cao T, Yang D, Zhang X, Wang Y, Qiao Z, Gao L, et al. FAM3D inhibits glucagon secretion via MKP1-dependent suppression of ERK1/2 signaling. Cell Biol Toxicol. 2017;33:457–66. [PMID: 28247283]

    Article  CAS  Google Scholar 

  31. Kuznetsova T, Knez J. Peripheral blood mitochondrial DNA and myocardial function. Adv Exp Med Biol. 2017;982:347–58. [PMID: 28551797]

    Article  PubMed  Google Scholar 

  32. Hulman A, Simmons RK, Brunner EJ, Witte DR, Faerch K, Vistisen D, et al. Trajectories of glycaemia, insulin sensitivity and insulin secretion in South Asian and white individuals before diagnosis of type 2 diabetes: a longitudinal analysis from the Whitehall II cohort study. Diabetologia. 2017;60:1252–60. [PMID: 28409212]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Tabak AG, Herder C, Rathmann W, Brunner EJ, Kivimaki M. Prediabetes: a high-risk state for diabetes development. Lancet. 2012;379:2279–90. [PMID: 22683128]

    Article  PubMed  PubMed Central  Google Scholar 

  34. Vedi M, Sabina EP. Assessment of hepatoprotective and nephroprotective potential of withaferin A on bromobenzene-induced injury in Swiss albino mice: possible involvement of mitochondrial dysfunction and inflammation. Cell Biol Toxicol. 2016;32:373–90. [PMID: 27250656]

    Article  CAS  PubMed  Google Scholar 

  35. O’Hagan HM, Wang W, Sen S, Destefano Shields C, Lee SS, Zhang YW, et al. Oxidative damage targets complexes containing DNA methyltransferases, SIRT1, and polycomb members to promoter CpG Islands. Cancer Cell. 2011;20:606–19. [PMID: 22094255]

    Article  PubMed  PubMed Central  Google Scholar 

  36. Seo JB, Jung SR, Hille B, Koh DS, Extracellular ATP. Protects pancreatic duct epithelial cells from alcohol-induced damage through P2Y1 receptor-cAMP signal pathway. Cell Biol Toxicol. 2016;32:229–47. [PMID: 27197531]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Amodio G, Sasso E, D’Ambrosio C, Scaloni A, Moltedo O, Franceschelli S, et al. Identification of a microRNA (miR-663a) induced by ER stress and its target gene PLOD3 by a combined microRNome and proteome approach. Cell Biol Toxicol. 2016;32:285–303. [PMID: 27233793]

    Article  CAS  PubMed  Google Scholar 

  38. Peng L, Yuan Z, Ling H, Fukasawa K, Robertson K, Olashaw N, et al. SIRT1 deacetylates the DNA methyltransferase 1 (DNMT1) protein and alters its activities. Mol Cell Biol. 2011;31:4720–34. [PMID: 21947282]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Engin AB, Engin A. The interactions between Kynurenine, folate, methionine and Pteridine pathways in obesity. Adv Exp Med Biol. 2017;960:511–27. [PMID: 28585214]

    Article  PubMed  Google Scholar 

  40. Petersen KF, Befroy D, Dufour S, Dziura J, Ariyan C, Rothman DL, et al. Mitochondrial dysfunction in the elderly: possible role in insulin resistance. Science. 2003;300:1140–2. [PMID: 12750520]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Infantino V, Castegna A, Iacobazzi F, Spera I, Scala I, Andria G, et al. Impairment of methyl cycle affects mitochondrial methyl availability and glutathione level in Down’s syndrome. Mol Genet Metab. 2011;102:378–82. [PMID: 21195648]

    Article  CAS  PubMed  Google Scholar 

  42. Peng C, Bind MC, Colicino E, Kloog I, Byun HM, Cantone L, et al. Particulate air pollution and fasting blood glucose in nondiabetic individuals: associations and epigenetic mediation in the normative aging study, 2000–2011. Environ Health Perspect. 2016;124:1715–21. [PMID: 27219535]

    Article  PubMed  PubMed Central  Google Scholar 

  43. Zheng LD, Linarelli LE, Liu L, Wall SS, Greenawald MH, Seidel RW, et al. Insulin resistance is associated with epigenetic and genetic regulation of mitochondrial DNA in obese humans. Clin Epigenetics. 2015;7:60. [PMID: 26110043]

    Article  PubMed  PubMed Central  Google Scholar 

  44. Thomas PD, Kahn M. Kat3 coactivators in somatic stem cells and cancer stem cells: biological roles, evolution, and pharmacologic manipulation. Cell Biol Toxicol. 2016;32:61–81. [PMID: 27008332]

    Article  CAS  PubMed  Google Scholar 

  45. Bellizzi D, D’Aquila P, Scafone T, Giordano M, Riso V, Riccio A, et al. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res. 2013;20:537–47. [PMID: 23804556]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. He J, Mao CC, Reyes A, Sembongi H, Di Re M, Granycome C, et al. The AAA+ protein ATAD3 has displacement loop binding properties and is involved in mitochondrial nucleoid organization. J Cell Biol. 2007;176:141–6. [PMID: 17210950]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Sidor-Kaczmarek J, Cichorek M, Spodnik JH, Wojcik S, Morys J. Proteasome inhibitors against amelanotic melanoma. Cell Biol Toxicol. 2017, March 9. doi:https://doi.org/10.1007/s10565-017-9390-0. [PMID: 28281027]

  48. Ganta KK, Mandal A, Chaubey B. Depolarization of mitochondrial membrane potential is the initial event in non-nucleoside reverse transcriptase inhibitor efavirenz induced cytotoxicity. Cell Biol Toxicol. 2017;33:69–82. [PMID: 27639578]

    Article  PubMed  Google Scholar 

  49. Bao L, Zhang Y, Wang J, Wang H, Dong N, Su X, et al. Variations of chromosome 2 gene expressions among patients with lung cancer or non-cancer. Cell Biol Toxicol. 2016;32:419–35. [PMID: 27301951]

    Article  CAS  PubMed  Google Scholar 

  50. Ohashi K, Munetsuna E, Yamada H, Ando Y, Yamazaki M, Taromaru N, et al. High fructose consumption induces DNA methylation at PPARalpha and CPT1A promoter regions in the rat liver. Biochem Biophys Res Commun. 2015;468:185–9. [PMID: 26519879]

    Article  CAS  PubMed  Google Scholar 

  51. Gao X, Liu YA. Transcriptomic study suggesting human iPSC-derived hepatocytes potentially offer a better in vitro model of hepatotoxicity than most hepatoma cell lines. Cell Biol Toxicol. 2017;33:407–21. [PMID: 28144825]

    Article  CAS  PubMed  Google Scholar 

  52. Yamazaki M, Munetsuna E, Yamada H, Ando Y, Mizuno G, Murase Y, et al. Fructose consumption induces hypomethylation of hepatic mitochondrial DNA in rats. Life Sci. 2016;149:146–52. [PMID: 26869391]

    Article  CAS  PubMed  Google Scholar 

  53. Crott JW, Choi SW, Branda RF, Mason JB. Accumulation of mitochondrial DNA deletions is age, tissue and folate-dependent in rats. Mutat Res. 2005;570:63–70. [PMID: 15680403]

    Article  CAS  PubMed  Google Scholar 

  54. Bao L, Diao H, Dong N, Su X, Wang B, Mo Q, et al. Histone deacetylase inhibitor induces cell apoptosis and cycle arrest in lung cancer cells via mitochondrial injury and p53 up-acetylation. Cell Biol Toxicol. 2016;32:469–82. [PMID: 27423454]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Kang SJ, Lee HM, Park YI, Yi H, Lee H. So B, et al. chemically induced hepatotoxicity in human stem cell-induced hepatocytes compared with primary hepatocytes and HepG2. Cell Biol Toxicol. 2016;32:403–17. [PMID: 27287938]

    Article  CAS  PubMed  Google Scholar 

  56. Blanch M, Mosquera JL, Ansoleaga B, Ferrer I, Barrachina M, Altered Mitochondrial DNA. Methylation pattern in Alzheimer disease-related pathology and in Parkinson disease. Am J Pathol. 2016;186:385–97. [PMID: 26776077]

    Article  CAS  PubMed  Google Scholar 

  57. Domcke S, Bardet AF, Adrian Ginno P, Hartl D, Burger L, Schubeler D. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature. 2015;528:575–9. [PMID: 26675734]

    Article  CAS  PubMed  Google Scholar 

  58. Kornicka K, Marycz K, Maredziak M, Tomaszewski KA, Nicpon J. The effects of the DNA methyltranfserases inhibitor 5-Azacitidine on ageing, oxidative stress and DNA methylation of adipose derived stem cells. J Cell Mol Med. 2017;21:387–401. [PMID: 27998022]

    Article  CAS  PubMed  Google Scholar 

  59. Gu J, Wang X. New future of cell biology and toxicology: thinking deeper. Cell Biol Toxicol. 2016;32:1–3. [PMID: 26874518]

    Article  PubMed  Google Scholar 

  60. Kelly RD, Mahmud A, McKenzie M, Trounce IA, St John JC. Mitochondrial DNA copy number is regulated in a tissue specific manner by DNA methylation of the nuclear-encoded DNA polymerase gamma A. Nucleic Acids Res. 2012;40:10124–38. [PMID: 22941637]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Bestwick ML, Shadel GS. Accessorizing the human mitochondrial transcription machinery. Trends Biochem Sci. 2013;38:283–91. [PMID: 23632312]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Liu T, Liu WH, Zhao JS, Meng FZ, Wang H. Lutein protects against beta-amyloid peptide-induced oxidative stress in cerebrovascular endothelial cells through modulation of Nrf-2 and NF-kappa b. Cell Biol Toxicol. 2017;33:57–67. [PMID: 27878403]

    Article  PubMed  Google Scholar 

  63. Zhu LZ, Hou YJ, Zhao M, Yang MF, XT F, Sun JY, et al. Caudatin induces caspase-dependent apoptosis in human glioma cells with involvement of mitochondrial dysfunction and reactive oxygen species generation. Cell Biol Toxicol. 2016;32:333–45. [PMID: 27184666]

    Article  CAS  PubMed  Google Scholar 

  64. Wang W, Wang X, Single-cell CRISPR. Screening in drug resistance. Cell Biol Toxicol. 2017;33:207–10. [PMID: 28474250]

    Article  CAS  PubMed  Google Scholar 

  65. Wang W, Gao D, Wang X. Can single-cell RNA sequencing crack the mystery of cells? Cell Biol Toxicol. 2017, July 21. doi:https://doi.org/10.1007/s10565-017-9404-y. [PMID: 28733864]

  66. Wang W, Zhu B, Wang X. Dynamic phenotypes: illustrating a single-cell odyssey. Cell Biol Toxicol. 2017;33:423–7. [PMID: 28638956]

    Article  Google Scholar 

  67. Liu B, Du Q, Chen L, Fu G, Li S, Fu L, et al. CpG methylation patterns of human mitochondrial DNA. Sci Rep. 2016;6:23421. [PMID: 26996456]

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

The work was supported by the Zhongshan Distinguished Professor Grant (XDW), the National Nature Science Foundation of China (91230204, 81270099, 81320108001, 81270131, 81300010), the Shanghai Committee of Science and Technology (12JC1402200, 12431900207, 11410708600, 14431905100), the operation funding of Shanghai Institute of Clinical Bioinformatics, the Ministry of Education for Academic Special Science and Research Foundation for PhD Education (20130071110043), and the National Key Research and Development Program (2016YFC0902400, 2017YFSF090207).

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Hongzhi Sun or Xiangdong Wang .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2017 The Editor(s) (if applicable) and The Author(s) 2018

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Gao, D., Zhu, B., Sun, H., Wang, X. (2017). Mitochondrial DNA Methylation and Related Disease. In: Sun, H., Wang, X. (eds) Mitochondrial DNA and Diseases. Advances in Experimental Medicine and Biology, vol 1038. Springer, Singapore. https://doi.org/10.1007/978-981-10-6674-0_9

Download citation

Publish with us

Policies and ethics