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73. Siggens L, Ekwall K (2014) Epigenetics, chromatin and genome organization: recent advances
from the ENCODE project. J Intern Med 276(3):201–214. https://doi.org/10.1111/joim.12231
74. Pidsley R, Zotenko E, Peters TJ, Lawrence MG, Risbridger GP, Molloy P, van Djik S,
Muhlhausler B, Stirzaker C, Clark SJ (2016) Critical evaluation of the Illumina
MethylationEPIC BeadChip microarray for whole-genome DNA methylation profiling.
Genome Biol 17(1):208. https://doi.org/10.1186/s13059-016-1066-1
75. Chen YA, Lemire M, Choufani S, Butcher DT, Grafodatskaya D, Zanke BW, Gallinger S,
Hudson TJ, Weksberg R (2013) Discovery of cross-reactive probes and polymorphic CpGs in
the Illumina infinium HumanMethylation450 microarray. Epigenetics 8(2):203–209. https://
doi.org/10.4161/epi.23470
76. Wong NC, Ng J, Hall NE, Lunke S, Salmanidis M, Brumatti G, Ekert PG, Craig JM, Saffery R
(2013) Exploring the utility of human DNA methylation arrays for profiling mouse genomic
DNA. Genomics 102(1):38–46. https://doi.org/10.1016/j.ygeno.2013.04.014
77. Needhamsen M, Ewing E, Lund H, Gomez-Cabrero D, Harris RA, Kular L, Jagodic M (2017)
Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies. BMC Bioinf 18(1):486. https://doi.org/10.1186/s12859-017-1870-y
78. Huang Y, Pastor WA, Shen Y, Tahiliani M, Liu DR, Rao A (2010) The behaviour of
5-hydroxymethylcytosine in bisulfite sequencing. PLoS One 5(1):e8888
79. Nazor KL, Boland MJ, Bibikova M, Klotzle B, Yu M, Glenn-Pratola VL, Schell JP, Coleman
RL, Cabral-da-Silva MC, Schmidt U, Peterson SE, He C, Loring JF, Fan JB (2014) Application of a low cost array-based technique - TAB-array - for quantifying and mapping both 5mC
and 5hmC at single base resolution in human pluripotent stem cells. Genomics 104
(5):358–367. https://doi.org/10.1016/j.ygeno.2014.08.014
80. Canard B, Sarfati RS (1994) DNA polymerase fluorescent substrates with reversible 3
0 -tags.
Gene 148(1):1–6
81. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schubeler D (2005)
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37(8):853–862. https://doi.org/10.
1038/ng1598
82. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Graf S, Johnson N, Herrero J,
Tomazou EM, Thorne NP, Backdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM,
Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavare S, Beck S (2008) A Bayesian
deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat
Biotechnol 26(7):779–785. https://doi.org/10.1038/nbt1414
83. Williams K, Christensen J, Pedersen MT, Johansen JV, Cloos PA, Rappsilber J, Helin K
(2011) TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity.
Nature 473(7347):343–348. https://doi.org/10.1038/nature10066
84. Shen L, Wu H, Diep D, Yamaguchi S, D’Alessio AC, Fung HL, Zhang K, Zhang Y (2013)
Genome-wide analysis reveals TET- and TDG-dependent 5-methylcytosine oxidation dynamics. Cell 153(3):692–706. https://doi.org/10.1016/j.cell.2013.04.002
85. Pastor WA, Pape UJ, Huang Y, Henderson HR, Lister R, Ko M, McLoughlin EM, Brudno Y,
Mahapatra S, Kapranov P, Tahiliani M, Daley GQ, Liu XS, Ecker JR, Milos PM, Agarwal S,
Rao A (2011) Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells.
Nature 473(7347):394–397. https://doi.org/10.1038/nature10102
86. Huang Y, Pastor WA, Zepeda-Martinez JA, Rao A (2012) The anti-CMS technique for
genome-wide mapping of 5-hydroxymethylcytosine. Nat Protoc 7(10):1897–1908. https://
doi.org/10.1038/nprot.2012.103
87. Song CX, Sun Y, Dai Q, Lu XY, Yu M, Yang CG, He C (2011) Detection of
5-hydroxymethylcytosine in DNA by transferring a keto-glucose by using T4 phage betaglucosyltransferase. Chembiochem 12(11):1682–1685
518
C. L. Seiler et al.