88. Song CX, Szulwach KE, Fu Y, Dai Q, Yi C, Li X, Li Y, Chen CH, Zhang W, Jian X, Wang J,
Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective
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Biotechnol 29(1):68–72
89. Raiber EA, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ,
Reik W, Balasubramanian S (2012) Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.
Genome Biol 13(8):R69. https://doi.org/10.1186/gb-2012-13-8-r69
90. Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H,
Gao J, Liu P, Li L, Xu GL, Jin P, He C (2013) Genome-wide profiling of 5-formylcytosine
reveals its roles in epigenetic priming. Cell 153(3):678–691
91. Yong WS, Hsu FM, Chen PY (2016) Profiling genome-wide DNA methylation. Epigenetics
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92. Gupta R, Nagarajan A, Wajapeyee N (2010) Advances in genome-wide DNA methylation
analysis. Biotechniques 49(4):iii–ixi. https://doi.org/10.2144/000113493
93. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL
(1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine
residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831
94. Stirzaker C, Taberlay PC, Statham AL, Clark SJ (2014) Mining cancer methylomes: prospects
and challenges. Trends Genet 30(2):75–84. https://doi.org/10.1016/j.tig.2013.11.004
95. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008)
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133
(3):523–536. https://doi.org/10.1016/j.cell.2008.03.029
96. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF,
Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome
reveals DNA methylation patterning. Nature 452(7184):215–219. https://doi.org/10.1038/
nature06745
97. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L,
Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson
JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread
epigenomic differences. Nature 462(7271):315–322. https://doi.org/10.1038/nature08514
98. Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD
(2013) A reference methylome database and analysis pipeline to facilitate integrative and
comparative epigenomics. PLoS One 8(12):e81148. https://doi.org/10.1371/journal.pone.
0081148
99. Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA (2012) Genome-wide mapping of
nucleosome positioning and DNA methylation within individual DNA molecules. Genome
Res 22(12):2497–2506. https://doi.org/10.1101/gr.143008.112
100. Lay FD, Kelly TK, Jones PA (2018) Nucleosome occupancy and methylome sequencing
(NOMe-seq). Methods Mol Biol 1708:267–284. https://doi.org/10.1007/978-1-4939-7481-8_14
101. Wang L, Sun J, Wu H, Liu S, Wang J, Wu B, Huang S, Li N, Wang J, Zhang X (2012)
Systematic assessment of reduced representation bisulfite sequencing to human blood samples: a promising method for large-sample-scale epigenomic studies. J Biotechnol 157(1):1–6.
https://doi.org/10.1016/j.jbiotec.2011.06.034
102. Wetterstrand K DNA sequencing costs: data from the NHGRI genome sequencing program
(GSP). Accessed 3 Mar 2018
103. Ziller MJ, Hansen KD, Meissner A, Aryee MJ (2015) Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods 12(3):230–232. https://
doi.org/10.1038/nmeth.3152
104. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein
BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA
methylation maps of pluripotent and differentiated cells. Nature 454(7205):766–770. https://
doi.org/10.1038/nature07107
Experimental Methodologies for Detection and Mapping of Epigenetic DNA Marks
519
Zhang L, Looney TJ, Zhang B, Godley LA, Hicks LM, Lahn BT, Jin P, He C (2011) Selective
chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat
Biotechnol 29(1):68–72
89. Raiber EA, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ,
Reik W, Balasubramanian S (2012) Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase.
Genome Biol 13(8):R69. https://doi.org/10.1186/gb-2012-13-8-r69
90. Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H,
Gao J, Liu P, Li L, Xu GL, Jin P, He C (2013) Genome-wide profiling of 5-formylcytosine
reveals its roles in epigenetic priming. Cell 153(3):678–691
91. Yong WS, Hsu FM, Chen PY (2016) Profiling genome-wide DNA methylation. Epigenetics
Chromatin 9:26. https://doi.org/10.1186/s13072-016-0075-3
92. Gupta R, Nagarajan A, Wajapeyee N (2010) Advances in genome-wide DNA methylation
analysis. Biotechniques 49(4):iii–ixi. https://doi.org/10.2144/000113493
93. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL
(1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine
residues in individual DNA strands. Proc Natl Acad Sci U S A 89(5):1827–1831
94. Stirzaker C, Taberlay PC, Statham AL, Clark SJ (2014) Mining cancer methylomes: prospects
and challenges. Trends Genet 30(2):75–84. https://doi.org/10.1016/j.tig.2013.11.004
95. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR (2008)
Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133
(3):523–536. https://doi.org/10.1016/j.cell.2008.03.029
96. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF,
Pellegrini M, Jacobsen SE (2008) Shotgun bisulphite sequencing of the Arabidopsis genome
reveals DNA methylation patterning. Nature 452(7184):215–219. https://doi.org/10.1038/
nature06745
97. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, Nery JR, Lee L,
Ye Z, Ngo QM, Edsall L, Antosiewicz-Bourget J, Stewart R, Ruotti V, Millar AH, Thomson
JA, Ren B, Ecker JR (2009) Human DNA methylomes at base resolution show widespread
epigenomic differences. Nature 462(7271):315–322. https://doi.org/10.1038/nature08514
98. Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD
(2013) A reference methylome database and analysis pipeline to facilitate integrative and
comparative epigenomics. PLoS One 8(12):e81148. https://doi.org/10.1371/journal.pone.
0081148
99. Kelly TK, Liu Y, Lay FD, Liang G, Berman BP, Jones PA (2012) Genome-wide mapping of
nucleosome positioning and DNA methylation within individual DNA molecules. Genome
Res 22(12):2497–2506. https://doi.org/10.1101/gr.143008.112
100. Lay FD, Kelly TK, Jones PA (2018) Nucleosome occupancy and methylome sequencing
(NOMe-seq). Methods Mol Biol 1708:267–284. https://doi.org/10.1007/978-1-4939-7481-8_14
101. Wang L, Sun J, Wu H, Liu S, Wang J, Wu B, Huang S, Li N, Wang J, Zhang X (2012)
Systematic assessment of reduced representation bisulfite sequencing to human blood samples: a promising method for large-sample-scale epigenomic studies. J Biotechnol 157(1):1–6.
https://doi.org/10.1016/j.jbiotec.2011.06.034
102. Wetterstrand K DNA sequencing costs: data from the NHGRI genome sequencing program
(GSP). Accessed 3 Mar 2018
103. Ziller MJ, Hansen KD, Meissner A, Aryee MJ (2015) Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing. Nat Methods 12(3):230–232. https://
doi.org/10.1038/nmeth.3152
104. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein
BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES (2008) Genome-scale DNA
methylation maps of pluripotent and differentiated cells. Nature 454(7205):766–770. https://
doi.org/10.1038/nature07107
Experimental Methodologies for Detection and Mapping of Epigenetic DNA Marks
519