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120. Wu H, Wu X, Zhang Y (2016) Base-resolution profiling of active DNA demethylation using
MAB-seq and caMAB-seq. Nat Protoc 11(6):1081–1100. https://doi.org/10.1038/nprot.2016.069
520
C. L. Seiler et al.
Meissner A (2010) Genome-scale DNA methylation mapping of clinical samples at singlenucleotide resolution. Nat Methods 7(2):133–136. https://doi.org/10.1038/nmeth.1414
106. Gu H, Smith ZD, Bock C, Boyle P, Gnirke A, Meissner A (2011) Preparation of reduced
representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat
Protoc 6(4):468–481. https://doi.org/10.1038/nprot.2010.190
107. Doi A, Park IH, Wen B, Murakami P, Aryee MJ, Irizarry R, Herb B, Ladd-Acosta C, Rho J,
Loewer S, Miller J, Schlaeger T, Daley GQ, Feinberg AP (2009) Differential methylation of
tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem
cells, embryonic stem cells and fibroblasts. Nat Genet 41(12):1350–1353. https://doi.org/10.
1038/ng.471
108. Wang J, Xia Y, Li L, Gong D, Yao Y, Luo H, Lu H, Yi N, Wu H, Zhang X, Tao Q, Gao F
(2013) Double restriction-enzyme digestion improves the coverage and accuracy of genomewide CpG methylation profiling by reduced representation bisulfite sequencing. BMC Genomics 14:11. https://doi.org/10.1186/1471-2164-14-11
109. Lee YK, Jin S, Duan S, Lim YC, Ng DP, Lin XM, Yeo GS, Ding C (2014) Improved reduced
representation bisulfite sequencing for epigenomic profiling of clinical samples. Biol Proced
Online 16(1):1. https://doi.org/10.1186/1480-9222-16-1
110. Hing B, Ramos E, Braun P, McKane M, Jancic D, Tamashiro KL, Lee RS, Michaelson JJ,
Druley TE, Potash JB (2015) Adaptation of the targeted capture methyl-seq platform for the
mouse genome identifies novel tissue-specific DNA methylation patterns of genes involved in
neurodevelopment. Epigenetics 10(7):581–596. https://doi.org/10.1080/15592294.2015.
1045179
111. Fu Y, Springer NM, Ying K, Yeh CT, Iniguez AL, Richmond T, Wu W, Barbazuk B,
Nettleton D, Jeddeloh J, Schnable PS (2010) High-resolution genotyping via whole genome
hybridizations to microarrays containing long oligonucleotide probes. PLoS One 5(12):
e14178. https://doi.org/10.1371/journal.pone.0014178
112. Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J,
Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM (2015) Post-conversion
targeted capture of modified cytosines in mammalian and plant genomes. Nucleic Acids Res
43:e81
113. Chen K, Zhao BS, He C (2016) Nucleic acid modifications in regulation of gene expression.
Cell Chem Biol 23(1):74–85. https://doi.org/10.1016/j.chembiol.2015.11.007
114. Jin SG, Kadam S, Pfeifer GP (2010) Examination of the specificity of DNA methylation
profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine. Nucleic Acids
Res 38(11):e125
115. Booth MJ, Branco MR, Ficz G, Oxley D, Krueger F, Reik W, Balasubramanian S (2012)
Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base
resolution. Science 336(6083):934–937. https://doi.org/10.1126/science.1220671
116. Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min
JH, Jin P, Ren B, He C (2012) Base-resolution analysis of 5-hydroxymethylcytosine in the
mammalian genome. Cell 149(6):1368–1380
117. Yu M, Hon GC, Szulwach KE, Song CX, Jin P, Ren B, He C (2012) Tet-assisted bisulfite
sequencing of 5-hydroxymethylcytosine. Nat Protoc 7(12):2159–2170
118. Chen K, Zhang J, Guo Z, Ma Q, Xu Z, Zhou Y, Xu Z, Li Z, Liu Y, Ye X, Li X, Yuan B, Ke Y,
He C, Zhou L, Liu J, Ci W (2016) Loss of 5-hydroxymethylcytosine is linked to gene body
hypermethylation in kidney cancer. Cell Res 26(1):103–118. https://doi.org/10.1038/cr.2015.150
119. Booth MJ, Marsico G, Bachman M, Beraldi D, Balasubramanian S (2014) Quantitative
sequencing of 5-formylcytosine in DNA at single-base resolution. Nat Chem 6(5):435–440.
https://doi.org/10.1038/nchem.1893
120. Wu H, Wu X, Zhang Y (2016) Base-resolution profiling of active DNA demethylation using
MAB-seq and caMAB-seq. Nat Protoc 11(6):1081–1100. https://doi.org/10.1038/nprot.2016.069
520
C. L. Seiler et al.