REFERENCES
- Shmookler Reis RJ, Goldstein S. 1983. Mitochondrial DNA in mortal and immortal human cells. J. Biol. Chem. 258:9078–9085.
- Pollack Y, Kasir J, Shemer R, Metzger S, Szyf M. 1984. Methylation pattern of mouse mitochondrial DNA. Nucleic Acids Res. 12:4811–4824.
- Nass MMK. 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. 80:155–175.
- Maekawa M, Taniguchi T, Higashi H, Sugimura H, Sugano K, Kanno T. 2004. Methylation of mitochondrial DNA is not a useful marker for cancer detection. Clin. Chem. 50:1480–1481.
- Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SM. 2011. DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc. Natl. Acad. Sci. U. S. A. 108:3630–3635.
- Infantino V, Castegna A, Iacobazzi F, Spera I, Scala I, Andria G, Iacobazzi V. 2011. Impairment of methyl cycle affects mitochondrial methyl availability and glutathione level in Down's syndrome. Mol. Genet. Metab. 102:378–382.
- Dzitoyeva S, Chen H, Manev H. 2012. Effect of aging on 5-hydroxymethylcytosine in brain mitochondria. Neurobiol. Aging 33:2881–2891.
- Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CLA. 1992. Genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. U. S. A. 89:1827–1831.
- Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A. 2010. The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5:e8888. doi:10.1371/journal.pone.0008888.
- Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder R, Valk GPJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. 2012. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 8:e1002781. doi:10.1371/journal.pgen.1002781.
- Heyn H, Li N, Ferreira HJ, Moran S, Pisano DG, Gomez A, Diez J, Sanchez-Mut JV, Setien F, Carmona FJ, Puca AA, Sayols S, Pujana MA, Serra-Musach J, Iglesias-Platas I, Formiga F, Fernandez AF, Fraga MF, Heath SC, Valencia A, Gut IG, Wang J, Esteller M. 2012. Distinct DNA methylomes of newborns and centenarians. Proc. Natl. Acad. Sci. U. S. A. 109:10522–10527.
- Heyn H, Vidal E, Sayols S, Sanchez-Mut JV, Moran S, Medina I, Sandoval J, Simó-Riudalbas L, Szczesna K, Huertas D, Gatto S, Matarazzo MR, Dopazo J, Esteller M. 2012. Whole-genome bisulfite DNA sequencing of a DNMT3B mutant patient. Epigenetics 7:542–550.
- Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, Pelizzola M, Valsesia A, Ye Z, Kuan S, Edsall LE, Camargo AA, Stevenson BJ, Ecker JR, Bafna V, Strausberg RL, Simpson AJ, Ren B. 2012. Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res. 22:246–258.
- Tsai AG, Chen DM, Lin M, Hsieh JC, Okitsu CY, Taghva A, Shibata D, Hsieh C-L. 2012. Heterogeneity and randomness of DNA methylation patterns in human embryonic stem cells. DNA Cell Biol. 31:893–907.
- Smith AD, Chung WY, Hodges E, Kendall J, Hannon G, Hicks J, Xuan Z, Zhang MQ. 2009. Updates to the RMAP short-read mapping software. Bioinformatics 25:2841–2842.
- Hodges E, Molaro A, Dos Santos CO, Thekkat P, Song Q, Uren PJ, Park J, Butler J, Rafii S, McCombie WR, Smith AD, Hannon GJ. 2011. Directional DNA methylation changes and complex intermediate states accompany lineage specificity in the adult hematopoietic compartment. Mol. Cell 44:1–12.
- Molaro A, Hodges E, Fang F, Song Q, McCombie WR, Hannon GJ, Smith AD. 2011. Sperm methylation profiles reveal features of epigenetic inheritance and evolution in primates. Cell 146:1029–1041.
- Kodama Y, Shumway M, Leinonen R, International Nucleotide Sequence Database Collaboration. 2012. The Sequence Read Archive: explosive growth of sequencing data. Nucleic Acids Res. 40:D54–D56.
- Lightowlers RN, Chinnery PF, Turnbull DM, Howell N. 1997. Mammalian mitochondrial genetics: heredity, heteroplasmy, and disease. Trends Genet. 13:450–455.
- Hazkani-Covo E, Graur D. 2007. A comparative analysis of numt evolution in human and chimpanzee. Mol. Biol. Evol. 24:13–18.
- Ehrlich M, Gama-Sosa MA, Huang LH, Midgett R, Kuo MKC, McCune RA, Gehrke C. 1982. Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic Acids Res. 10:2709–2721.
- Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, Low HM, Kin Sung KW, Rigoutsos I, Loring J, Wei CL. 2010. Dynamic changes in the human methylome during differentiation. Genome Res. 20:320–331.
- Li Y, Zhu J, Tian G, Li N, Li Q, Ye M, Zheng H, Yu J, Wu H, Sun J, Zhang H, Chen Q, Luo R, Chen M, He Y, Jin X, Zhang Q, Yu C, Zhou G, Sun J, Huang Y, Zheng H, Cao H, Zhou X, Guo S, Hu X, Li X, Kristiansen K, Bolund L, Xu J, Wang W, Yang H, Wang J, Li R, Beck S, Wang J, Zhang X. 2010. The DNA methylome of human peripheral blood mononuclear cells. PLoS Biol. 8:e1000533. doi:10.1371/journal.pbio.1000533.
- Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat. Genet. 37:853–862.
- Jabbar K, Bernardi G. 2004. Cytosine methylation and CpG, TpG (CpA), and TpA frequencies. Gene 333:143–149.
- Jeon JP, Shim SM, Nam HY, Baik SY, Kim JW, Han BG. 2007. Copy number increase of 1p36.33 and mitochondrial genome amplification in Epstein-Barr virus-transformed lymphoblastoid cell lines. Cancer Genet. Cytogenet. 173:122–130.
- Hirt B. 1967. Selective extraction of polyoma DNA from infected mouse cultures. J. Mol. Biol. 26:365–369.