Epigenomics of human embryonic stem cells and induced pluripotent stem cells: insights into pluripotency and implications for disease

Table 1 Next-generation sequencing-based methods used in epigenomic studies

Epigenetic modification	Method	Reference(s)
DNA methylation	MethylC-seq	[40]
	BS-seq	[31]
	MeDIP-seq	[33]
	MRE-seq	[37]
	MethylCap-seq	[30]
	RRBS	[41]
Histone post-translational modifications	ChIP-seq	[22, 42]
Histone variants	ChIP-seq	[36]
Chromatin modifiers and remodelers	ChIP-seq	[38, 43]
Chromatin accessibility	DNAseI-seq	[29]
	FAIRE-seq	[35]
	Sono-seq	[28]
Nucleosome positioning and turnover	MNase-seq	[44]
	CATCH-IT	[32]
Long-range chromatin interactions	Hi-C	[39]
	ChIA-PET	[34]
Allele-specific chromatin signatures	haploChIP	[42, 97, 124]

BS-seq, bisulfite sequencing; CATCH-IT, covalent attachment of tags to capture histones and identify turnover; ChIA-PET, chromatin interaction analysis with paired-end tag sequencing; ChIP-seq, chromatin immunoprecipitation sequencing; DNAseI-seq, DNAseI sequencing; FAIRE-seq, formaldehyde-assisted isolation of regulatory elements sequencing; haploChIP, haplotype-specific ChIP; Hi-C, high-throughput chromosome capture; MeDIP-seq, methylated DNA immunoprecipitation sequencing; MethylCap-seq, MethylCap sequencing; MethylC-seq, MethylC sequencing; MNase-seq, micrococcal nuclease sequencing; MRE-seq, methylation-sensitive restriction enzyme sequencing; RRBS, reduced representation bisulfite sequencing; Sono-seq, sonicated chromatin sequencing.