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52. Lu X, Song CX, Szulwach K, Wang Z, Weidenbacher P, Jin P, He C (2013) Chemical
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53. Song CX, Szulwach KE, Dai Q, Fu Y, Mao SQ, Lin L, Street C, Li Y, Poidevin M, Wu H,
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A167
35. Gasperskaja E, Kucinskas V (2017) The most common technologies and tools for functional
genome analysis. Acta Med Litu 24(1):1–11. https://doi.org/10.6001/actamedica.v24i1.3457
36. Schwartzman O, Tanay A (2015) Single-cell epigenomics: techniques and emerging applications. Nat Rev Genet 16(12):716–726. https://doi.org/10.1038/nrg3980
37. Milne TA, Zhao K, Hess JL (2009) Chromatin immunoprecipitation (ChIP) for analysis of
histone modifications and chromatin-associated proteins. Methods Mol Biol 538:409–423.
https://doi.org/10.1007/978-1-59745-418-6_21
38. Zarnegar MA, Reinitz F, Newman AM, Clarke MF (2017) Targeted chromatin ligation, a robust
epigenetic profiling technique for small cell numbers. Nucleic Acids Res 45(17):e153. https://
doi.org/10.1093/nar/gkx648
39. Teste B, Champ J, Londono-Vallejo A, Descroix S, Malaquin L, Viovy JL, Draskovic I, Mottet
G (2017) Chromatin immunoprecipitation in microfluidic droplets: towards fast and cheap
analyses. Lab Chip 17(3):530–537. https://doi.org/10.1039/c6lc01535b
40. Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE (2015) Singlecell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol 33
(11):1165–1172. https://doi.org/10.1038/nbt.3383
41. Hansel-Hertsch R, Spiegel J, Marsico G, Tannahill D, Balasubramanian S (2018) Genome-wide
mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and
high-throughput sequencing. Nat Protoc 13(3):551–564. https://doi.org/10.1038/nprot.2017.
150
42. Gaasterland T, Oprea M (2001) Whole-genome analysis: annotations and updates. Curr Opin
Struct Biol 11(3):377–381
43. Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed
98(6):236–238. https://doi.org/10.1136/archdischild-2013-304340
44. Almouzni G, Cedar H (2016) Maintenance of epigenetic information. Cold Spring Harb
Perspect Biol 8(5). https://doi.org/10.1101/cshperspect.a019372
45. Moore LD, Le T, Fan G (2013) DNA methylation and its basic function. Neuropsychopharmacology
38(1):23–38. https://doi.org/10.1038/npp.2012.112
46. Li E, Zhang Y (2014) DNA methylation in mammals. Cold Spring Harb Perspect Biol 6(5):
a019133. https://doi.org/10.1101/cshperspect.a019133
47. Tucker T, Marra M, Friedman JM (2009) Massively parallel sequencing: the next big thing in
genetic medicine. Am J Hum Genet 85(2):142–154. https://doi.org/10.1016/j.ajhg.2009.06.022
48. Li Q, Hermanson PJ, Springer NM (2018) Detection of DNA methylation by whole-genome
bisulfite sequencing. Methods Mol Biol 1676:185–196. https://doi.org/10.1007/978-1-49397315-6_11
49. Lu X, Han D, Zhao BS, Song CX, Zhang LS, Dore LC, He C (2015) Base-resolution maps of
5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics.
Cell Res 25(3):386–389. https://doi.org/10.1038/cr.2015.5
50. Yu M, Han D, Hon GC, He C (2018) Tet-assisted bisulfite sequencing (TAB-seq). Methods
Mol Biol 1708:645–663. https://doi.org/10.1007/978-1-4939-7481-8_33
51. Kawasaki Y, Kuroda Y, Suetake I, Tajima S, Ishino F, Kohda T (2017) A novel method for the
simultaneous identification of methylcytosine and hydroxymethylcytosine at a single base
resolution. Nucleic Acids Res 45(4):e24. https://doi.org/10.1093/nar/gkw994
52. Lu X, Song CX, Szulwach K, Wang Z, Weidenbacher P, Jin P, He C (2013) Chemical
modification-assisted bisulfite sequencing (CAB-seq) for 5-carboxylcytosine detection in
DNA. J Am Chem Soc 135(25):9315–9317. https://doi.org/10.1021/ja4044856
53. 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. https://doi.org/10.1016/j.cell.2013.
04.001
Advanced Assays in Epigenetics
557