TY - JOUR AU - Hagland, H. R. AU - Berg, M. AU - Jolma, I. W. AU - Carlsen, A. AU - Soreide, K. PY - 2013 DA - 2013// TI - Molecular pathways and cellular metabolism in colorectal cancer JO - Dig Surg VL - 30 UR - https://doi.org/10.1159/000347166 DO - 10.1159/000347166 ID - Hagland2013 ER - TY - JOUR AU - Wallace, D. C. PY - 2012 DA - 2012// TI - Mitochondria and cancer JO - Nat Rev Cancer VL - 12 UR - https://doi.org/10.1038/nrc3365 DO - 10.1038/nrc3365 ID - Wallace2012 ER - TY - JOUR AU - Ma, Y. AU - Zhang, P. AU - Wang, F. AU - Qin, H. PY - 2012 DA - 2012// TI - Searching for consistently reported up- and down-regulated biomarkers in colorectal cancer: a systematic review of proteomic studies JO - Mol Biol Rep VL - 39 UR - https://doi.org/10.1007/s11033-012-1702-0 DO - 10.1007/s11033-012-1702-0 ID - Ma2012 ER - TY - STD TI - Errichiello E, Venesio T. Mitochondrial DNA variants in colorectal carcinogenesis: drivers or passengers? J Cancer Res Clin Oncol. 2017;143(10):1905–1914. ID - ref4 ER - TY - JOUR AU - Law, J. A. AU - Jacobsen, S. E. PY - 2010 DA - 2010// TI - Establishing, maintaining and modifying DNA methylation patterns in plants and animals JO - Nat Rev Genet VL - 11 UR - https://doi.org/10.1038/nrg2719 DO - 10.1038/nrg2719 ID - Law2010 ER - TY - JOUR AU - Patil, V. AU - Ward, R. L. AU - Hesson, L. B. PY - 2014 DA - 2014// TI - The evidence for functional non-CpG methylation in mammalian cells JO - Epigenetics VL - 9 UR - https://doi.org/10.4161/epi.28741 DO - 10.4161/epi.28741 ID - Patil2014 ER - TY - JOUR AU - Maresca, A. AU - Zaffagnini, M. AU - Caporali, L. AU - Carelli, V. AU - Zanna, C. PY - 2015 DA - 2015// TI - DNA methyltransferase 1 mutations and mitochondrial pathology: is mtDNA methylated? JO - Front Genet VL - 6 UR - https://doi.org/10.3389/fgene.2015.00090 DO - 10.3389/fgene.2015.00090 ID - Maresca2015 ER - TY - JOUR AU - Byun, H. M. AU - Baccarelli, A. A. PY - 2014 DA - 2014// TI - Environmental exposure and mitochondrial epigenetics: study design and analytical challenges JO - Hum Genet VL - 133 UR - https://doi.org/10.1007/s00439-013-1417-x DO - 10.1007/s00439-013-1417-x ID - Byun2014 ER - TY - JOUR AU - Wijst, M. G. P. AU - Rots, M. G. PY - 2015 DA - 2015// TI - Mitochondrial epigenetics: an overlooked layer of regulation? JO - Trends Genet VL - 31 UR - https://doi.org/10.1016/j.tig.2015.03.009 DO - 10.1016/j.tig.2015.03.009 ID - Wijst2015 ER - TY - JOUR AU - Shock, L. S. AU - Thakkar, P. V. AU - Peterson, E. J. AU - Moran, R. G. AU - Taylor, S. M. PY - 2011 DA - 2011// TI - DNA methyltransferase 1, cytosine methylation, and cytosine hydroxymethylation in mammalian mitochondria JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1012311108 DO - 10.1073/pnas.1012311108 ID - Shock2011 ER - TY - JOUR AU - Saini, S. K. AU - Mangalhara, K. C. AU - Prakasam, G. AU - Bamezai, R. N. K. PY - 2017 DA - 2017// TI - DNA Methyltransferase1 (DNMT1) Isoform3 methylates mitochondrial genome and modulates its biology JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-01743-y DO - 10.1038/s41598-017-01743-y ID - Saini2017 ER - TY - JOUR AU - Wong, M. AU - Gertz, B. AU - Chestnut, B. A. AU - Martin, L. J. PY - 2013 DA - 2013// TI - Mitochondrial DNMT3A and DNA methylation in skeletal muscle and CNS of transgenic mouse models of ALS JO - Front Cell Neurosci VL - 7 ID - Wong2013 ER - TY - JOUR AU - Iacobazzi, V. AU - Castegna, A. AU - Infantino, V. AU - Andria, G. PY - 2013 DA - 2013// TI - Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool JO - Mol Genet Metab VL - 110 UR - https://doi.org/10.1016/j.ymgme.2013.07.012 DO - 10.1016/j.ymgme.2013.07.012 ID - Iacobazzi2013 ER - TY - JOUR AU - Hong, E. E. AU - Okitsu, C. Y. AU - Smith, A. D. AU - Hsieh, C. L. PY - 2013 DA - 2013// TI - Regionally specific and genome-wide analyses conclusively demonstrate the absence of CpG methylation in human mitochondrial DNA JO - Mol Cell Biol VL - 33 UR - https://doi.org/10.1128/MCB.00220-13 DO - 10.1128/MCB.00220-13 ID - Hong2013 ER - TY - JOUR AU - Maekawa, M. AU - Taniguchi, T. AU - Higashi, H. AU - Sugimura, H. AU - Sugano, K. AU - Kanno, T. PY - 2004 DA - 2004// TI - Methylation of mitochondrial DNA is not a useful marker for cancer detection JO - Clin Chem VL - 50 UR - https://doi.org/10.1373/clinchem.2004.035139 DO - 10.1373/clinchem.2004.035139 ID - Maekawa2004 ER - TY - JOUR AU - Feng, S. AU - Xiong, L. L. AU - Ji, Z. N. AU - Cheng, W. AU - Yang, H. J. PY - 2012 DA - 2012// TI - Correlation between increased ND2 expression and demethylated displacement loop of mtDNA in colorectal cancer JO - Mol Med Rep VL - 6 ID - Feng2012 ER - TY - JOUR AU - Gao, J. AU - Wen, S. AU - Zhou, H. AU - Feng, S. PY - 2015 DA - 2015// TI - 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 JO - Mol Med Rep VL - 12 UR - https://doi.org/10.3892/mmr.2015.4256 DO - 10.3892/mmr.2015.4256 ID - Gao2015 ER - TY - JOUR AU - Wijst, M. G. AU - Tilburg, A. Y. AU - Ruiters, M. H. AU - Rots, M. G. PY - 2017 DA - 2017// TI - Experimental mitochondria-targeted DNA methylation identifies GpC methylation, not CpG methylation, as potential regulator of mitochondrial gene expression JO - Sci Rep VL - 7 UR - https://doi.org/10.1038/s41598-017-00263-z DO - 10.1038/s41598-017-00263-z ID - Wijst2017 ER - TY - JOUR AU - Liu, B. AU - Du, Q. AU - Chen, L. AU - Fu, G. AU - Li, S. AU - Fu, L. AU - Zhang, X. AU - Ma, C. AU - Bin, C. PY - 2016 DA - 2016// TI - CpG methylation patterns of human mitochondrial DNA JO - Sci Rep VL - 6 UR - https://doi.org/10.1038/srep23421 DO - 10.1038/srep23421 ID - Liu2016 ER - TY - JOUR AU - Owa, C. AU - Poulin, M. AU - Yan, L. AU - Shioda, T. PY - 2018 DA - 2018// TI - Technical adequacy of bisulfite sequencing and pyrosequencing for detection of mitochondrial DNA methylation: sources and avoidance of false-positive detection JO - PLoS One VL - 13 UR - https://doi.org/10.1371/journal.pone.0192722 DO - 10.1371/journal.pone.0192722 ID - Owa2018 ER - TY - STD TI - Mechta M, Ingerslev LR, Barres R. Methodology for accurate detection of mitochondrial DNA methylation. J Vis Exp. 2018. ID - ref21 ER - TY - STD TI - Mechta M, Ingerslev LR, Fabre O, Picard M, Barres R. Evidence suggesting absence of mitochondrial DNA methylation. Front Genet. 2017;8:166. ID - ref22 ER - TY - STD TI - 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. ID - ref23 ER - TY - JOUR AU - Bellizzi, D. AU - D'Aquila, P. AU - Scafone, T. AU - Giordano, M. AU - Riso, V. AU - Riccio, A. AU - Passarino, G. PY - 2013 DA - 2013// TI - The control region of mitochondrial DNA shows an unusual CpG and non-CpG methylation pattern JO - DNA Res VL - 20 UR - https://doi.org/10.1093/dnares/dst029 DO - 10.1093/dnares/dst029 ID - Bellizzi2013 ER - TY - JOUR AU - Wallace, L. AU - Mehrabi, S. AU - Bacanamwo, M. AU - Yao, X. AU - Aikhionbare, F. O. PY - 2016 DA - 2016// TI - Expression of mitochondrial genes MT-ND1, MT-ND6, MT-CYB, MT-COI, MT-ATP6, and 12S/MT-RNR1 in colorectal adenopolyps JO - Tumour Biol VL - 37 UR - https://doi.org/10.1007/s13277-016-5101-3 DO - 10.1007/s13277-016-5101-3 ID - Wallace2016 ER - TY - JOUR AU - Osch, F. H. M. AU - Voets, A. M. AU - Schouten, L. J. AU - Gottschalk, R. W. H. AU - Simons, C. C. J. M. AU - Engeland, M. AU - Lentjes, M. H. F. M. AU - Brandt, P. A. AU - Smeets, H. J. M. AU - Weijenberg, M. P. PY - 2015 DA - 2015// TI - Mitochondrial DNA copy number in colorectal cancer: between tissue comparisons, clinicopathological characteristics and survival JO - Carcinogenesis VL - 36 ID - Osch2015 ER - TY - JOUR AU - Araujo, L. AU - Fonseca, A. AU - Muys, B. AU - Placa, J. R. AU - Bueno, R. B. L. AU - Lorenzi, J. C. C. AU - Santos, A. R. D. AU - Molfetta, G. A. AU - Zanette, D. L. AU - Souza, J. E. S. PY - 2015 DA - 2015// TI - Mitochondrial genome instability in colorectal adenoma and adenocarcinoma JO - Tumor Biol VL - 36 UR - https://doi.org/10.1007/s13277-015-3640-7 DO - 10.1007/s13277-015-3640-7 ID - Araujo2015 ER - TY - JOUR AU - Hesson, L. B. AU - Sloane, M. A. AU - Wong, J. W. H. AU - Nunez, A. C. AU - Srivastava, S. AU - Ng, B. AU - Hawkins, N. J. AU - Bourke, M. J. AU - Ward, R. L. PY - 2014 DA - 2014// TI - Altered promoter nucleosome positioning is an early event in gene silencing JO - Epigenetics VL - 9 UR - https://doi.org/10.4161/15592294.2014.970077 DO - 10.4161/15592294.2014.970077 ID - Hesson2014 ER - TY - JOUR AU - Hesson, L. B. AU - Ng, B. AU - Zarzour, P. AU - Srivastava, S. AU - Kwok, C. T. AU - Packham, D. AU - Nunez, A. C. AU - Beck, D. AU - Ryan, R. AU - Dower, A. PY - 2016 DA - 2016// TI - Integrated genetic, epigenetic, and transcriptional profiling identifies molecular pathways in the development of laterally spreading tumors JO - Mol Cancer Res VL - 14 UR - https://doi.org/10.1158/1541-7786.MCR-16-0175 DO - 10.1158/1541-7786.MCR-16-0175 ID - Hesson2016 ER - TY - JOUR AU - Heinz, S. AU - Benner, C. AU - Spann, N. AU - Bertolino, E. AU - Lin, Y. C. AU - Laslo, P. AU - Cheng, J. X. AU - Murre, C. AU - Singh, H. AU - Glass, C. K. PY - 2010 DA - 2010// TI - Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities JO - Mol Cell VL - 38 UR - https://doi.org/10.1016/j.molcel.2010.05.004 DO - 10.1016/j.molcel.2010.05.004 ID - Heinz2010 ER - TY - JOUR AU - Robinson, M. D. AU - Oshlack, A. PY - 2010 DA - 2010// TI - A scaling normalization method for differential expression analysis of RNA-seq data JO - Genome Biol VL - 11 UR - https://doi.org/10.1186/gb-2010-11-3-r25 DO - 10.1186/gb-2010-11-3-r25 ID - Robinson2010 ER - TY - JOUR AU - Krueger, F. AU - Andrews, S. R. PY - 2011 DA - 2011// TI - Bismark: a flexible aligner and methylation caller for bisulfite-Seq applications JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr167 DO - 10.1093/bioinformatics/btr167 ID - Krueger2011 ER - TY - JOUR AU - Krzywinski, M. AU - Schein, J. AU - Birol, I. AU - Connors, J. AU - Gascoyne, R. AU - Horsman, D. AU - Jones, S. J. AU - Marra, M. A. PY - 2009 DA - 2009// TI - Circos: an information aesthetic for comparative genomics JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.092759.109 DO - 10.1101/gr.092759.109 ID - Krzywinski2009 ER - TY - JOUR AU - Quinlan, A. R. AU - Hall, I. M. PY - 2010 DA - 2010// TI - BEDTools: a flexible suite of utilities for comparing genomic features JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq033 DO - 10.1093/bioinformatics/btq033 ID - Quinlan2010 ER - TY - JOUR AU - Liu, Y. AU - Siegmund, K. D. AU - Laird, P. W. AU - Berman, B. P. PY - 2012 DA - 2012// TI - Bis-SNP: combined DNA methylation and SNP calling for bisulfite-seq data JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-7-r61 DO - 10.1186/gb-2012-13-7-r61 ID - Liu2012 ER - TY - JOUR AU - Kim, H. C. AU - Chang, J. AU - Lee, H. S. AU - Kwon, H. J. PY - 2017 DA - 2017// TI - Mitochondrial UQCRB as a new molecular prognostic biomarker of human colorectal cancer JO - Exp Mol Med VL - 49 UR - https://doi.org/10.1038/emm.2017.152 DO - 10.1038/emm.2017.152 ID - Kim2017 ER - TY - JOUR AU - Desai, G. AU - Chu, L. AU - Guo, Y. AU - Myneni, A. A. AU - Mu, L. PY - 2017 DA - 2017// TI - Biomarkers used in studying air pollution exposure during pregnancy and perinatal outcomes: a review JO - Biomarkers VL - 22 UR - https://doi.org/10.1080/1354750X.2017.1339294 DO - 10.1080/1354750X.2017.1339294 ID - Desai2017 ER - TY - JOUR AU - Pirola, C. J. AU - Gianotti, T. F. AU - Burgueno, A. L. AU - Rey-Funes, M. AU - Loidl, C. F. AU - Mallardi, P. AU - San Martino, J. AU - Castano, G. O. AU - Sookoian, S. PY - 2013 DA - 2013// TI - Epigenetic modification of liver mitochondrial DNA is associated with histological severity of nonalcoholic fatty liver disease JO - Gut VL - 62 UR - https://doi.org/10.1136/gutjnl-2012-302962 DO - 10.1136/gutjnl-2012-302962 ID - Pirola2013 ER - TY - JOUR AU - Han, X. AU - Zhao, Z. AU - Zhang, M. AU - Li, G. AU - Yang, C. AU - Du, F. AU - Wang, J. AU - Zhang, Y. AU - Wang, Y. AU - Jia, Y. PY - 2017 DA - 2017// TI - Maternal trans-general analysis of the human mitochondrial DNA pattern JO - Biochem Biophys Res Commun VL - 493 UR - https://doi.org/10.1016/j.bbrc.2017.08.138 DO - 10.1016/j.bbrc.2017.08.138 ID - Han2017 ER - TY - JOUR AU - Warburg, O. PY - 1956 DA - 1956// TI - On the origin of cancer cells JO - Science VL - 123 UR - https://doi.org/10.1126/science.123.3191.309 DO - 10.1126/science.123.3191.309 ID - Warburg1956 ER - TY - JOUR AU - Satoh, K. AU - Yachida, S. AU - Sugimoto, M. AU - Oshima, M. AU - Nakagawa, T. AU - Akamoto, S. AU - Tabata, S. AU - Saitoh, K. AU - Kato, K. AU - Sato, S. PY - 2017 DA - 2017// TI - Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC JO - Proc Natl Acad Sci U S A VL - 114 UR - https://doi.org/10.1073/pnas.1710366114 DO - 10.1073/pnas.1710366114 ID - Satoh2017 ER - TY - STD TI - 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. ID - ref42 ER - TY - JOUR AU - Lim, U. AU - Flood, A. AU - Choi, S. W. AU - Albanes, D. AU - Cross, A. J. AU - Schatzkin, A. AU - Sinha, R. AU - Katki, H. A. AU - Cash, B. AU - Schoenfeld, P. AU - Stolzenberg-Solomon, R. PY - 2008 DA - 2008// TI - Genomic methylation of leukocyte DNA in relation to colorectal adenoma among asymptomatic women JO - Gastroenterology VL - 134 UR - https://doi.org/10.1053/j.gastro.2007.10.013 DO - 10.1053/j.gastro.2007.10.013 ID - Lim2008 ER - TY - JOUR AU - Ghosh, S. AU - Sengupta, S. AU - Scaria, V. PY - 2014 DA - 2014// TI - Comparative analysis of human mitochondrial methylomes shows distinct patterns of epigenetic regulation in mitochondria JO - Mitochondrion VL - 18 UR - https://doi.org/10.1016/j.mito.2014.07.007 DO - 10.1016/j.mito.2014.07.007 ID - Ghosh2014 ER - TY - JOUR AU - Pollack, Y. AU - Kasir, J. AU - Shemer, R. AU - Metzger, S. AU - Szyf, M. PY - 1984 DA - 1984// TI - Methylation pattern of mouse mitochondrial-DNA JO - Nucleic Acids Res VL - 12 UR - https://doi.org/10.1093/nar/12.12.4811 DO - 10.1093/nar/12.12.4811 ID - Pollack1984 ER - TY - STD TI - 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. ID - ref46 ER - TY - JOUR AU - Booth, M. J. AU - Branco, M. R. AU - Ficz, G. AU - Oxley, D. AU - Krueger, F. AU - Reik, W. AU - Balasubramanian, S. PY - 2012 DA - 2012// TI - Quantitative sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base resolution JO - Science VL - 336 UR - https://doi.org/10.1126/science.1220671 DO - 10.1126/science.1220671 ID - Booth2012 ER - TY - JOUR AU - Poulton, J. PY - 1992 DA - 1992// TI - Duplications of mitochondrial DNA: implications for pathogenesis JO - J Inherit Metab Dis VL - 15 UR - https://doi.org/10.1007/BF01799607 DO - 10.1007/BF01799607 ID - Poulton1992 ER - TY - JOUR AU - Komulainen, T. AU - Hautakangas, M. R. AU - Hinttala, R. AU - Pakanen, S. AU - Vahasarja, V. AU - Lehenkari, P. AU - Olsen, P. AU - Vieira, P. AU - Saarenpaa-Heikkila, O. AU - Palmio, J. PY - 2015 DA - 2015// TI - Mitochondrial DNA depletion and deletions in Paediatric patients with neuromuscular diseases: novel phenotypes JO - JIMD Rep VL - 23 UR - https://doi.org/10.1007/8904_2015_438 DO - 10.1007/8904_2015_438 ID - Komulainen2015 ER -