Hagland HR, Berg M, Jolma IW, Carlsen A, Soreide K. Molecular pathways and cellular metabolism in colorectal cancer. Dig Surg. 2013;30:12–25.
Wallace DC. Mitochondria and cancer. Nat Rev Cancer. 2012;12:685–98.
Ma Y, Zhang P, Wang F, Qin H. Searching for consistently reported up- and down-regulated biomarkers in colorectal cancer: a systematic review of proteomic studies. Mol Biol Rep. 2012;39:8483–90.
Errichiello E, Venesio T. Mitochondrial DNA variants in colorectal carcinogenesis: drivers or passengers? J Cancer Res Clin Oncol. 2017;143(10):1905–1914.
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11:204–20.
Patil V, Ward RL, Hesson LB. The evidence for functional non-CpG methylation in mammalian cells. Epigenetics. 2014;9:823–8.
Maresca A, Zaffagnini M, Caporali L, Carelli V, Zanna C. DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated? Front Genet. 2015;6:90.
Byun HM, Baccarelli AA. Environmental exposure and mitochondrial epigenetics: study design and analytical challenges. Hum Genet. 2014;133:247–57.
van der Wijst MGP, Rots MG. Mitochondrial epigenetics: an overlooked layer of regulation? Trends Genet. 2015;31:353–6.
Shock LS, Thakkar PV, Peterson EJ, Moran RG, Taylor SM. DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria. Proc Natl Acad Sci U S A. 2011;108:3630–5.
Saini SK, Mangalhara KC, Prakasam G, Bamezai RNK. DNA Methyltransferase1 (DNMT1) Isoform3 methylates mitochondrial genome and modulates its biology. Sci Rep. 2017;7:1525.
Wong M, Gertz B, Chestnut BA, Martin LJ. Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS. Front Cell Neurosci. 2013;7:279.
Iacobazzi V, Castegna A, Infantino V, Andria G. Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool. Mol Genet Metab. 2013;110:25–34.
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.
Maekawa M, Taniguchi T, Higashi H, Sugimura H, Sugano K, Kanno T. Methylation of mitochondrial DNA is not a useful marker for cancer detection. Clin Chem. 2004;50:1480–1.
Feng S, Xiong LL, Ji ZN, Cheng W, Yang HJ. Correlation between increased ND2 expression and demethylated displacement loop of mtDNA in colorectal cancer. Mol Med Rep. 2012;6:125–30.
Gao J, Wen S, Zhou H, Feng S. De-methylation of displacement loop of mitochondrial DNA is associated with increased mitochondrial copy number and nicotinamide adenine dinucleotide subunit 2 expression in colorectal cancer. Mol Med Rep. 2015;12:7033–8.
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.
Liu B, Du Q, Chen L, Fu G, Li S, Fu L, Zhang X, Ma C, Bin C. CpG methylation patterns of human mitochondrial DNA. Sci Rep. 2016;6:23421.
Owa C, Poulin M, Yan L, Shioda T. Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: sources and avoidance of false-positive detection. PLoS One. 2018;13:e0192722.
Mechta M, Ingerslev LR, Barres R. Methodology for accurate detection of mitochondrial DNA methylation. J Vis Exp. 2018.
Mechta M, Ingerslev LR, Fabre O, Picard M, Barres R. Evidence suggesting absence of mitochondrial DNA methylation. Front Genet. 2017;8:166.
Tong H, Zhang L, Gao J, Wen S, Zhou H, Feng S. Methylation of mitochondrial DNA displacement loop region regulates mitochondrial copy number in colorectal cancer. Mol Med Rep. 2017;16.4:5347–5353.
Bellizzi D, D'Aquila P, Scafone T, Giordano M, Riso V, Riccio A, Passarino G. The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern. DNA Res. 2013;20:537–47.
Wallace L, Mehrabi S, Bacanamwo M, Yao X, Aikhionbare FO. Expression of mitochondrial genes MT-ND1, MT-ND6, MT-CYB, MT-COI, MT-ATP6, and 12S/MT-RNR1 in colorectal adenopolyps. Tumour Biol. 2016;37:12465–75.
van Osch FHM, Voets AM, Schouten LJ, Gottschalk RWH, Simons CCJM, van Engeland M, Lentjes MHFM, van den Brandt PA, Smeets HJM, Weijenberg MP. Mitochondrial DNA copy number in colorectal cancer: between tissue comparisons, clinicopathological characteristics and survival. Carcinogenesis. 2015;36:1502–10.
Araujo L, Fonseca A, Muys B, Placa JR, Bueno RBL, Lorenzi JCC, Santos ARD, Molfetta GA, Zanette DL, Souza JES, et al. Mitochondrial genome instability in colorectal adenoma and adenocarcinoma. Tumor Biol. 2015;36:8869–79.
Hesson LB, Sloane MA, Wong JWH, Nunez AC, Srivastava S, Ng B, Hawkins NJ, Bourke MJ, Ward RL. Altered promoter nucleosome positioning is an early event in gene silencing. Epigenetics. 2014;9:1422–30.
Hesson LB, Ng B, Zarzour P, Srivastava S, Kwok CT, Packham D, Nunez AC, Beck D, Ryan R, Dower A, et al. Integrated genetic, epigenetic, and transcriptional profiling identifies molecular pathways in the development of laterally spreading tumors. Mol Cancer Res. 2016;14:1217–28.
Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010;38:576–89.
Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications. Bioinformatics. 2011;27:1571–2.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2.
Liu Y, Siegmund KD, Laird PW, Berman BP. Bis-SNP: combined DNA methylation and SNP calling for bisulfite-seq data. Genome Biol. 2012;13:R61.
Kim HC, Chang J, Lee HS, Kwon HJ. Mitochondrial UQCRB as a new molecular prognostic biomarker of human colorectal cancer. Exp Mol Med. 2017;49:e391.
Desai G, Chu L, Guo Y, Myneni AA, Mu L. Biomarkers used in studying air pollution exposure during pregnancy and perinatal outcomes: a review. Biomarkers. 2017;22:489–501.
Pirola CJ, Gianotti TF, Burgueno AL, Rey-Funes M, Loidl CF, Mallardi P, San Martino J, Castano GO, Sookoian S. Epigenetic modification of liver mitochondrial DNA is associated with histological severity of nonalcoholic fatty liver disease. Gut. 2013;62:1356–63.
Han X, Zhao Z, Zhang M, Li G, Yang C, Du F, Wang J, Zhang Y, Wang Y, Jia Y, et al. Maternal trans-general analysis of the human mitochondrial DNA pattern. Biochem Biophys Res Commun. 2017;493:643–9.
Warburg O. On the origin of cancer cells. Science. 1956;123:309–14.
Satoh K, Yachida S, Sugimoto M, Oshima M, Nakagawa T, Akamoto S, Tabata S, Saitoh K, Kato K, Sato S, et al. Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC. Proc Natl Acad Sci U S A. 2017;114:E7697–706.
Jiang AC, Buckingham L, Barbanera W, Korang AY, Bishehsari F, Melson J. LINE-1 is preferentially hypomethylated within adenomatous polyps in the presence of synchronous colorectal cancer (vol 9, 1, 2017). Clin Epigenetics. 2017;9:25.
Lim U, Flood A, Choi SW, Albanes D, Cross AJ, Schatzkin A, Sinha R, Katki HA, Cash B, Schoenfeld P, Stolzenberg-Solomon R. Genomic methylation of leukocyte DNA in relation to colorectal adenoma among asymptomatic women. Gastroenterology. 2008;134:47–55.
Ghosh S, Sengupta S, Scaria V. Comparative analysis of human mitochondrial methylomes shows distinct patterns of epigenetic regulation in mitochondria. Mitochondrion. 2014;18:58–62.
Pollack Y, Kasir J, Shemer R, Metzger S, Szyf M. Methylation pattern of mouse mitochondrial-DNA. Nucleic Acids Res. 1984;12:4811–24.
Huang Y, Pastor WA, Shen YH, Tahiliani M, Liu DR, Rao A. The behaviour of 5-Hydroxymethylcytosine in bisulfite sequencing. PLoS One. 2010;5(1):e8888.
Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S. Quantitative sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base resolution. Science. 2012;336:934–7.
Poulton J. Duplications of mitochondrial DNA: implications for pathogenesis. J Inherit Metab Dis. 1992;15:487–98.
Komulainen T, Hautakangas MR, Hinttala R, Pakanen S, Vahasarja V, Lehenkari P, Olsen P, Vieira P, Saarenpaa-Heikkila O, Palmio J, et al. Mitochondrial DNA depletion and deletions in Paediatric patients with neuromuscular diseases: novel phenotypes. JIMD Rep. 2015;23:91–100.