Richardson BC. Role of DNA methylation in the regulation of cell function: autoimmunity, aging and cancer. J Nutr. 2002;132(8 Suppl):2401S–5S.
Article
CAS
Google Scholar
Khavari DA, Sen GL, Rinn JL. DNA methylation and epigenetic control of cellular differentiation. Cell Cycle. 2010;9(19):3880–3.
Article
CAS
Google Scholar
Messerschmidt DM, Knowles BB, Solter D. DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos. Genes Dev. 2014;28(8):812–28.
Article
CAS
Google Scholar
Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–92.
Article
CAS
Google Scholar
Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, Lucero J, Huang Y, Dwork AJ, Schultz MD, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013;341(6146):1237905.
Article
Google Scholar
Kass SU, Landsberger N, Wolffe AP. DNA methylation directs a time-dependent repression of transcription initiation. Current biology : CB. 1997;7(3):157–65.
Article
CAS
Google Scholar
Jones PA. The DNA methylation paradox. Trends in genetics : TIG. 1999;15(1):34–7.
Article
CAS
Google Scholar
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008;454(7205):766–70.
Article
CAS
Google Scholar
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L, Ye Z, Ngo QM, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462(7271):315–22.
Article
CAS
Google Scholar
Law JA, Jacobsen SE. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat Rev Genet. 2010;11(3):204–20.
Article
CAS
Google Scholar
Stadler MB, Murr R, Burger L, Ivanek R, Lienert F, Scholer A, van Nimwegen E, Wirbelauer C, Oakeley EJ, Gaidatzis D, et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature. 2011;480(7378):490–5.
CAS
Google Scholar
Bogdanovic O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van Kruijsbergen I et al: Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nat Genet 2016, 48(4):417–426.
Article
Google Scholar
Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, Monk D, Hata K, Marques-Bonet T, Wang L, et al. DNA methylation contributes to natural human variation. Genome Res. 2013;23(9):1363–72.
Article
CAS
Google Scholar
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30.
Article
CAS
Google Scholar
Schultz MD, He Y, Whitaker JW, Hariharan M, Mukamel EA, Leung D, Rajagopal N, Nery JR, Urich MA, Chen H, et al. Human body epigenome maps reveal noncanonical DNA methylation variation. Nature. 2015;523(7559):212–6.
Article
CAS
Google Scholar
Eichten SR, Stuart T, Srivastava A, Lister R, Borevitz JO. DNA methylation profiles of diverse Brachypodium distachyon align with underlying genetic diversity. Genome Res. 2016;26(11):1520–31.
Article
CAS
Google Scholar
Kawakatsu T, Stuart T, Valdes M, Breakfield N, Schmitz RJ, Nery JR, Urich MA, Han X, Lister R, Benfey PN, et al. Unique cell-type-specific patterns of DNA methylation in the root meristem. Nature plants. 2016;2(5):16058.
Article
CAS
Google Scholar
Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, et al. Widespread natural variation of DNA methylation within angiosperms. Genome Biol. 2016;17(1):194.
Article
Google Scholar
Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, Dempster EL, Ren B. Base-resolution analyses of sequence and parent-of-origin dependent DNA methylation in the mouse genome. Cell. 2012;148(4):816–31.
Article
CAS
Google Scholar
Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, Cross MK, Williams BA, Stamatoyannopoulos JA, Crawford GE, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23(3):555–67.
Article
CAS
Google Scholar
Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature. 2008;452(7184):215–9.
Article
CAS
Google Scholar
Guo S, Diep D, Plongthongkum N, Fung HL, Zhang K, Zhang K. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat Genet. 2017;49(4):635–42.
Article
CAS
Google Scholar
Hansen KD, Langmead B, Irizarry RA. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol. 2012;13(10):R83.
Article
Google Scholar
Dolzhenko E, Smith AD. Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments. BMC bioinformatics. 2014;15:215.
Article
Google Scholar
Lea AJ, Tung J, Zhou X. A flexible, efficient binomial mixed model for identifying differential DNA methylation in bisulfite sequencing data. PLoS Genet. 2015;11(11):e1005650.
Article
Google Scholar
Hebestreit K, Dugas M, Klein HU. Detection of significantly differentially methylated regions in targeted bisulfite sequencing data. Bioinformatics. 2013;29(13):1647–53.
Article
CAS
Google Scholar
Shafi A, Mitrea C, Nguyen T, Draghici S. A survey of the approaches for identifying differential methylation using bisulfite sequencing data. Brief Bioinform. 2018;19(5):737–53.
Article
Google Scholar
Saito Y, Tsuji J, Mituyama T. Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions. Nucleic Acids Res. 2014;42(6):e45.
Article
CAS
Google Scholar
Wang Z, Li X, Jiang Y, Shao Q, Liu Q, Chen B, Huang D. swDMR: a sliding window approach to identify differentially methylated regions based on whole genome bisulfite sequencing. PLoS One. 2015;10(7):e0132866.
Article
Google Scholar
Feng H, Conneely KN, Wu H. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res. 2014;42(8):e69.
Article
CAS
Google Scholar
Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely KN. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Res. 2015;43(21):e141.
PubMed
PubMed Central
Google Scholar
Juhling F, Kretzmer H, Bernhart SH, Otto C, Stadler PF, Hoffmann S. Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data. Genome Res. 2016;26(2):256–62.
Article
Google Scholar
Eckhardt F, Lewin J, Cortese R, Rakyan VK, Attwood J, Burger M, Burton J, Cox TV, Davies R, Down TA, et al. DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet. 2006;38(12):1378–85.
Article
CAS
Google Scholar
Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics. 2012;13(1):166–78.
Article
Google Scholar
Cortes C, Vapnik V. Support-vector networks. Mach Learn. 1995;20(3):273.
Google Scholar
Mo A, Mukamel EA, Davis FP, Luo C, Henry GL, Picard S, Urich MA, Nery JR, Sejnowski TJ, Lister R, et al. Epigenomic signatures of neuronal diversity in the mammalian brain. Neuron. 2015;86(6):1369–84.
Article
CAS
Google Scholar
Breiman L. Random forests. Mach Learn. 2001;45(1):5–32.
Article
Google Scholar
Karpievitch YV, Hill EG, Leclerc AP, Dabney AR, Almeida JS. An introspective comparison of random forest-based classifiers for the analysis of cluster-correlated data by way of RF++. PLoS One. 2009;4(9):e7087.
Article
Google Scholar
Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, et al. Scikit-learn: machine learning in python. J Mach Learn Res. 2011;12:2825–30.
Google Scholar
Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12(8):529–41.
Article
CAS
Google Scholar
Wen Y, Chen F, Zhang Q, Zhuang Y, Li Z. Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics. Bioinformatics. 2016;32(22):3396–404.
CAS
PubMed
Google Scholar
McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol. 2010;28(5):495–501.
Article
CAS
Google Scholar
Stroud H, Do T, Du J, Zhong X, Feng S, Johnson L, Patel DJ, Jacobsen SE. Non-CG methylation patterns shape the epigenetic landscape in Arabidopsis. Nat Struct Mol Biol. 2014;21(1):64–72.
Article
CAS
Google Scholar
Zemach A, Kim MY, Hsieh PH, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer SL, Zilberman D. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin. Cell. 2013;153(1):193–205.
Article
CAS
Google Scholar
Crisp PA, Ganguly DR, Smith AB, Murray KD, Estavillo GM, Searle I, Ford E, Bogdanovic O, Lister R, Borevitz JO, et al. Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis. Plant Cell. 2017;29(8):1836–63.
Article
CAS
Google Scholar
Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell. 2008;133(3):523–36.
Article
CAS
Google Scholar
Narsai R, Secco D, Schultz MD, Ecker JR, Lister R, Whelan J. Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The Plant journal : for cell and molecular biology. 2017;89(4):805–24.
Article
CAS
Google Scholar
Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, Antosiewicz-Bourget J, O’Malley R, Castanon R, Klugman S, et al. Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011;471(7336):68–73.
Article
CAS
Google Scholar
Lee DS, Shin JY, Tonge PD, Puri MC, Lee S, Park H, Lee WC, Hussein SM, Bleazard T, Yun JY, et al. An epigenomic roadmap to induced pluripotency reveals DNA methylation as a reprogramming modulator. Nat Commun. 2014;5:5619.
Article
CAS
Google Scholar
Knaupp AS, Buckberry S, Pflueger J, Lim SM, Ford E, Larcombe MR, Rossello FJ, de Mendoza A, Alaei S, Firas J, et al. Transient and permanent reconfiguration of chromatin and transcription factor occupancy drive reprogramming. Cell Stem Cell. 2017;21(6):834–845 e836.
Article
CAS
Google Scholar
Dowen RH, Pelizzola M, Schmitz RJ, Lister R, Dowen JM, Nery JR, Dixon JE, Ecker JR. Widespread dynamic DNA methylation in response to biotic stress. Proc Natl Acad Sci U S A. 2012;109(32):E2183–91.
Article
CAS
Google Scholar