References
- Baccarelli A, Wright RO, Bollati V, Tarantini L, Litonjua A a., Suh HH, Zanobetti A, Sparrow D, Vokonas PS, Schwartz J. Rapid DNA methylation changes after exposure to traffic particles. Am J Respir Crit Care Med 2009; 179:572-8; PMID:19136372; http://dx.doi.org/10.1164/rccm.200807-1097OC
- Yauk C, Polyzos A, Rowan-Carroll A, Somers CM, Godschalk RW, Van Schooten FJ, Berndt ML, Pogribny IP, Koturbash I, Williams A, et al. Germ-line mutations, DNA damage, and global hypermethylation in mice exposed to particulate air pollution in an urban/industrial location. Proc Natl Acad Sci U S A 2008; 105:605-10; PMID:18195365; http://dx.doi.org/10.1073/pnas.0705896105
- Dolinoy DC, Das R, Weidman JR, Jirtle RL. Metastable epialleles, imprinting, and the fetal origins of adult diseases. Pediatr Res 2007; 61:30-7; PMID:17413847; http://dx.doi.org/10.1203/pdr.0b013e31804575f7
- Bernal AJ, Dolinoy DC, Huang D, Skaar DA, Weinhouse C, Jirtle RL. Adaptive radiation-induced epigenetic alterations mitigated by antioxidants. FASEB J 2013; 27:665-71; PMID:23118028; http://dx.doi.org/10.1096/fj.12-220350
- Heijmans BT, Tobi EW, Stein AD, Putter H, Blauw GJ, Susser ES, Slagboom PE, Lumey LH. Persistent epigenetic differences associated with prenatal exposure to famine in humans. Proc Natl Acad Sci U S A [Internet] 2008; 105:17046-9; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2579375&tool=pmcentrez&rendertype=abstract; PMID:18955703; http://dx.doi.org/10.1073/pnas.0806560105
- Hajkova P, Erhardt S, Lane N, Haaf T, El-Maarri O, Reik W, Walter J, Surani MA. Epigenetic reprogramming in mouse primordial germ cells. Mech Dev [Internet] 2002; 117:15-23; Available from: http://www.sciencedirect.com/science/article/pii/S0925477302001818; PMID:12204247; http://dx.doi.org/10.1016/S0925-4773(02)00181-8
- Faulk C, Dolinoy DC. Timing is everything: The when and how of environmentally induced changes in the epigenome of animals. Epigenetics 2011; 6:791-7; PMID:21636976; http://dx.doi.org/10.4161/epi.6.7.16209
- Dolinoy DC. The agouti mouse model: an epigenetic biosensor for nutritional and environmental alterations on the fetal epigenome. NIH Public Access 2008; 66:1-8
- Druker R, Bruxner TJ, Lehrbach NJ, Whitelaw E. Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic Acids Res [Internet] 2004; 32:5800-8; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=528799&tool=pmcentrez&rendertype=abstract; PMID:15520464; http://dx.doi.org/10.1093/nar/gkh914
- Faulk C, Barks A, Dolinoy DC. Phylogenetic and DNA methylation analysis reveal novel regions of variable methylation in the mouse IAP class of transposons. BMC Genomics [Internet] 2013; 14:48; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3556122&tool=pmcentrez&rendertype=abstract; PMID:23343009; http://dx.doi.org/10.1186/1471-2164-14-48
- Andreotti G, Karami S, Pfeiffer RM, Hurwitz L, Liao LM, Weinstein SJ, Albanes D, Virtamo J, Silverman DT, Rothman N, et al. LINE1 methylation levels associated with increased bladder cancer risk in pre-diagnostic blood DNA among US (PLCO) and European (ATBC) cohort study participants. Epigenetics 2013; 9:404-15; PMID:24316677; http://dx.doi.org/10.4161/epi.27386
- Castro-Diaz N, Ecco G, Coluccio A, Kapopoulou A, Yazdanpanah B, Friedli M, Duc J, Jang SM, Turelli P, Trono D. Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev [Internet] 2014; 28:1397-409; Available from: http://www.ncbi.nlm.nih.gov/pubmed/24939876; PMID:24939876; http://dx.doi.org/10.1101/gad.241661.114
- Casa V, Gabellini D. A repetitive elements perspective in Polycomb epigenetics. Front Genet 2012; 3:1-16; PMID:22303408; http://dx.doi.org/10.3389/fgene.2012.00199
- Dunican DS, Cruickshanks HA, Suzuki M, Semple C a, Davey T, Arceci RJ, Greally J, Adams IR, Meehan RR. Lsh regulates LTR retrotransposon repression independently of Dnmt3b function. Genome Biol [Internet] 2013; 14:R146; Available from: http://www.ncbi.nlm.nih.gov/pubmed/24367978/nhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4054100/pdf/gb-2013-14-12-r146.pdf; PMID:24367978; http://dx.doi.org/10.1186/gb-2013-14-12-r146
- Dolinoy DC, Weidman JR, Waterland R a., Jirtle RL. Maternal genistein alters coat color and protects Avy mouse offspring from obesity by modifying the fetal epigenome. Environ Health Perspect [Internet] 2006; 114:567-72; Available from: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1440782/\nhttp://www.ehponline.org/ambra-doi-resolver/10.1289/ehp.8700; PMID:16581547; http://dx.doi.org/10.1289/ehp.8700
- Faulk C, Liu K, Barks A, Goodrich JM, Dolinoy DC. Longitudinal epigenetic drift in mice perinatally exposed to lead. Epigenetics [Internet] 2014; 9:934-41; Available from: http://www.ncbi.nlm.nih.gov/pubmed/24786859; PMID:24786859; http://dx.doi.org/10.4161/epi.29024
- Kim JH, Sartor MA, Rozek LS, Faulk C, Anderson OS, Jones TR, Nahar MS, Dolinoy DC. Perinatal bisphenol A exposure promotes dose-dependent alterations of the mouse methylome. BMC Genomics [Internet] 2014; 15:30; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3902427&tool=pmcentrez&rendertype=abstract; PMID:24433282; http://dx.doi.org/10.1186/1471-2164-15-30
- Anderson OS, Nahar MS, Faulk C, Jones TR, Liao C, Kannan K, Weinhouse C, Rozek LS, Dolinoy DC. Epigenetic responses following maternal dietary exposure to physiologically relevant levels of bisphenol A. Environ Mol Mutagen [Internet] 2012; 53:334-42; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3570056&tool=pmcentrez&rendertype=abstract; PMID:22467340; http://dx.doi.org/10.1002/em.21692
- Kim JH, Rozek LS, Soliman AS, Sartor MA, Hablas A, Seifeldin IA, Colacino JA, Weinhouse C, Nahar MS, Dolinoy DC. Bisphenol A-associated epigenomic changes in prepubescent girls: a cross-sectional study in Gharbiah, Egypt. Environ Health [Internet] 2013; 12:33; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3655072&tool=pmcentrez&rendertype=abstract; PMID:23590724; http://dx.doi.org/10.1186/1476-069X-12-33
- Kapitonov V, Jurka J. The age of Alu subfamilies. J Mol Evol [Internet] 1996; 42:59-65; Available from: http://www.ncbi.nlm.nih.gov/pubmed/8576965; PMID:8576965; http://dx.doi.org/10.1007/BF00163212
- Price AL, Eskin E, Pevzner PA. Whole-genome analysis of Alu repeat elements reveals complex evolutionary history. Genome Res [Internet] 2004; 14:2245-52; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=525682&tool=pmcentrez&rendertype=abstract; PMID:15520288; http://dx.doi.org/10.1101/gr.2693004
- Faulk C, Kim JH, Jones TR, McEachin RC, Nahar MS, Dolinoy DC, Sartor MA. Bisphenol A-associated alterations in genome-wide DNA methylation and gene expression patterns reveal sequence-dependent and non-monotonic effects in human fetal liver. Environ Epigenetics [Internet] 2015; 1; dvv006; Available from: http://eep.oxfordjournals.org/content/1/1/dvv006.abstract; http://dx.doi.org/10.1093/eep/dvv006
- Vandenberg LN. Non-monotonic dose responses in studies of endocrine disrupting chemicals: bisphenol a as a case study. Dose Response [Internet] 2014; 12:259-76; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=4036398&tool=pmcentrez&rendertype=abstract; PMID:24910584; http://dx.doi.org/10.2203/dose-response.13-020.Vandenberg
- Gallou-Kabani C, Gabory A, Tost J, Karimi M, Mayeur S, Lesage J, Boudadi E, Gross M-S, Taurelle J, Vigé A, et al. Sex- and diet-specific changes of imprinted gene expression and DNA methylation in mouse placenta under a high-fat diet. PLoS One [Internet] 2010; 5:e14398; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3006175&tool=pmcentrez&rendertype=abstract; PMID:21200436; http://dx.doi.org/10.1371/journal.pone.0014398
- Xiao-Jie L, Hui-Ying X, Qi X, Jiang X, Shi-Jie M. LINE-1 in cancer: multifaceted functions and potential clinical implications. Genet Med [Internet] 2015 [cited 2015 Nov 17]; 18:431-9; Available from: http://www.ncbi.nlm.nih.gov/pubmed/26334179; PMID:26334179
- Ruiz-Hernandez A, Kuo C-C, Rentero-Garrido P, Tang W-Y, Redon J, Ordovas JM, Navas-Acien A, Tellez-Plaza M. Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence. Clin Epigenetics [Internet] 2015; 7:55; Available from: http://www.clinicalepigeneticsjournal.com/content/7/1/55\nhttp://www.ncbi.nlm.nih.gov/pubmed/25984247; PMID:25984247; http://dx.doi.org/10.1186/s13148-015-0055-7
- Abdurashitov M a, Chernukhin V a, Gonchar D a, Degtyarev SK. GlaI digestion of mouse gamma-satellite DNA: study of primary structure and ACGT sites methylation. BMC Genomics 2009; 10:322; PMID:19607729; http://dx.doi.org/10.1186/1471-2164-10-322
- Crichton JH, Dunican DS, MacLennan M, Meehan RR, Adams IR. Defending the genome from the enemy within: Mechanisms of retrotransposon suppression in the mouse germline. Cell Mol Life Sci 2014; 71:1581-605; PMID:24045705; http://dx.doi.org/10.1007/s00018-013-1468-0
- Smit a F, Riggs a D. Tiggers and DNA transposon fossils in the human genome. Proc Natl Acad Sci U S A 1996; 93:1443-8; PMID:8643651; http://dx.doi.org/10.1073/pnas.93.4.1443
- Jurka J, Kapitonov VV, Pavlicek A, Klonowski P, Kohany O, Walichiewicz J. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 2005; 110:462-7; PMID:16093699; http://dx.doi.org/10.1159/000084979
- Reiss D, Zhang Y, Rouhi A, Reuter M, Mager DL. Variable DNA methylation of transposable elements: The case study of mouse early transposons. Epigenetics 2010; 5:68-79; PMID:20083901; http://dx.doi.org/10.4161/epi.5.1.10631
- Reiss D, Mager DL. Stochastic epigenetic silencing of retrotransposons: Does stability come with age?. Gene 2007; 390:130-5; PMID:16987613; http://dx.doi.org/10.1016/j.gene.2006.07.032
- Xing J, Hedges DJ, Han K, Wang H, Cordaux R, Batzer M a. Alu element mutation spectra: molecular clocks and the effect of DNA methylation. J Mol Biol [Internet] 2004; 344:675-82; Available from: http://www.ncbi.nlm.nih.gov/pubmed/15533437; PMID:15533437; http://dx.doi.org/10.1016/j.jmb.2004.09.058
- Deininger P. Alu elements: know the SINEs. Genome Biol [Internet] 2011; 12:236; Available from: http://www.ncbi.nlm.nih.gov/pubmed/22204421; PMID:22204421; http://dx.doi.org/10.1186/gb-2011-12-12-236
- Hoad G, Harrison K. The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. Methods Mol Biol [Internet] 2015; Available from: http://www.ncbi.nlm.nih.gov/pubmed/26246355; PMID:26246355
- Xie M, Hong C, Zhang B, Lowdon RF, Xing X, Li D, Zhou X, Lee HJ, Maire CL, Ligon KL, et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet [Internet] 2013; 45:836-41; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3695047&tool=pmcentrez&rendertype=abstract; PMID:23708189; http://dx.doi.org/10.1038/ng.2649
- Huang CRL, Burns KH, Boeke JD. Active transposition in genomes. Annu Rev Genet [Internet] 2012; 46:651-75; Available from: http://www.annualreviews.org/doi/abs/10.1146/annurev-genet-110711-155616; PMID:23145912; http://dx.doi.org/10.1146/annurev-genet-110711-155616
- Juriloff DM, Harris MJ, Mager DL, Gagnier L. Epigenetic mechanism causes Wnt9b deficiency and nonsyndromic cleft lip and palate in the A/WySn mouse strain. Birth Defects Res A Clin Mol Teratol [Internet] 2014; 100:772-88; Available from: http://www.scopus.com/inward/record.url?eid=2-s2.0-84916219777&partnerID=tZOtx3y1; PMID:25257647; http://dx.doi.org/10.1002/bdra.23320
- Ekram MB, Kang K, Kim H, Kim J. Retrotransposons as a major source of epigenetic variations in the mammalian genome. Epigenetics 2012; 7:370-82; PMID:22415164; http://dx.doi.org/10.4161/epi.19462
- Day DS, Luquette LJ, Park PJ, Kharchenko P V. Estimating enrichment of repetitive elements from high-throughput sequence data. Genome Biol 2010; 11:R69; PMID:20584328; http://dx.doi.org/10.1186/gb-2010-11-6-r69
- Waterland RA, Jirtle RL. Transposable elements: targets for early nutritional effects on epigenetic gene regulation. Mol Cell Biol [Internet] 2003; 23:5293-300; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=165709&tool=pmcentrez&rendertype=abstract; PMID:12861015; http://dx.doi.org/10.1128/MCB.23.15.5293-5300.2003
- Weinhouse C, Anderson OS, Bergin IL, Vandenbergh DJ, Gyekis JP, Dingman MA, Yang J, Dolinoy DC. Dose-dependent incidence of hepatic tumors in adult mice following perinatal exposure to bisphenol A. Environ Health Perspect 2014; 122:485-91; PMID:24487385
- Nahar MS, Liao C, Kannan K, Dolinoy DC. Fetal liver bisphenol A concentrations and biotransformation gene expression reveal variable exposure and altered capacity for metabolism in humans. J Biochem Mol Toxicol [Internet] 2013; 27:116-23; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3578057&tool=pmcentrez&rendertype=abstract; PMID:23208979; http://dx.doi.org/10.1002/jbt.21459
- Kim JH, Dhanasekaran SM, Prensner JR, Cao X, Robinson D, Kalyana-Sundaram S, Huang C, Shankar S, Jing X, Iyer M, et al. Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer. Genome Res [Internet] 2011; 21:1028-41; Available from: http://genome.cshlp.org/cgi/doi/10.1101/gr.119347.110\npapers3://publication/doi/10.1101/gr.119347.110; PMID:21724842; http://dx.doi.org/10.1101/gr.119347.110
- Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A. Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat Protoc [Internet] 2011; 6:468-81; Available from: http://www.ncbi.nlm.nih.gov/pubmed/21412275; PMID:21412275; http://dx.doi.org/10.1038/nprot.2010.190
- Dobin A, Davis C a, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics [Internet] 2013; 29:15-21; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3530905&tool=pmcentrez&rendertype=abstract; PMID:23104886; http://dx.doi.org/10.1093/bioinformatics/bts635
- Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ. The UCSC Table Browser data retrieval tool. Nucleic Acids Res [Internet] 2004; 32:D493-6; Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=308837&tool=pmcentrez&rendertype=abstract; PMID:14681465; http://dx.doi.org/10.1093/nar/gkh103
- Liao Y, Smyth GK, Shi W. FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014; 30:923-30; PMID:24227677; http://dx.doi.org/10.1093/bioinformatics/btt656
- Robinson MD, McCarthy DJ, Smyth GK. edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010; 26:139-40; PMID:19910308; http://dx.doi.org/10.1093/bioinformatics/btp616
- Cavalcante RG, Sartor MA. annotatr: Associating genomic regions with genomic annotations. bioRxiv [Internet] 2016; :1–9. Available from: http://biorxiv.org/lookup/doi/10.1101/039685