Tackling Skeletal Muscle Cells Epigenome in the Next-Generation Sequencing Era

Table 1

Method	Method description	Genomewide data	Reference
4C-Seq, Hi-C-Seq	Chromatin proximity ligation and sequencing	3-Dimensional protein-DNA interaction; Long-range chromatin interaction DNA looping	[23, 24]
ChIA-PET	Chromatin interaction analysis with paired-end tag sequencing: ChIP enrichment followed by chromatin proximity ligation and sequencing	Long-range chromatin interactions mediated by a DNA binding protein; DNA looping	[25, 26]
DNase-Seq	Sequencing of DNaseI-digested DNA fragments	Chromatin accessibility and nucleosome positioning Identification of nucleosome-free regulatory regions	[28]
FAIRE-Seq	Formaldehyde-assisted isolation of regulatory elements sequencing	Chromatin accessibility; Genome-wide mapping of protein-free DNA	[29]
MNase-Seq	Sequencing of micrococcal nuclease-digested DNA	Genomewide mapping of nucleosome-protected DNA; nucleosome positioning	[27]
ChIP-Seq	Sequencing of DNA fragments obtained from chromatin immunoprecipitation assays	Genomewide mapping of protein-DNA interactions; (a) Histone posttranslational modifications; (b) Histone variants; (c) Transcription factors; (d) Chromatin modifiers and remodelers	[19, 30]
BS-seq	BS-Seq: bisulfite sequencing	DNA methylation	[31]
MeDIP-seq	MeDIP-Seq: methylated DNA immunoprecipitation sequencing	DNA methylation	[32]
MBD-seq	ChIP with methylated DNA-binding proteins	DNA methylation	[33]
RNA-Seq	Sequencing of RNA	Expression profiling; Noncoding RNA expression; Novel transcripts; Alternative splicing	[34]