Table 2.

Summary of Commonly Used Techniques for Epigenetic Profiling

Type of Epigenetic Mark	Type of Sample Preparation Approach	Type of Profiling Approach
DNA methylation	Bisulfite conversion	Microarray (Illumina), High-throughput sequencing (BS-seq, RRBS-seq), Epityper (mass spectrometry; focused) or pyrosequencing (focused)
	Methylated DNA immunoprecipitation (MeDIP)	Microarray or High-throughput sequencing (MeDIP-seq)
	Methyl-binding domain (MBD) precipitation	Microarray or high-throughput sequencing (MBD-seq)
	Restriction digest with methylation-sensitive restriction enzymes (McrBC, MspI, HpaII, MspJI etc)	Microarray (CHARM, HELP) or high-throughput sequencing (MRE-seq)
Histone modifications	Chromatin immunoprecipitation (CHIP)	Microarray (CHIP-chip), high-throughput sequencing (CHIP-seq) or quantitative PCR (focused)
DNA methylation associated with chromatin modifications	CHIP followed by bisulfite conversion	High-throughput sequencing (CHIP- BS-seq, Bis-CHIP-seq)
Noncoding RNAs	Size selection of appropriate RNA molecules	Microarray, high-throughput sequencing (miRNA-seq and RNA-seq) or quantitative RT-PCR (focused)
Chromatin accessibility	DNAse I cleavage	High-throughput sequencing (DNase sensitivity-seq)
Chromatin accessibility Chromatin spatial organization	Formaldehyde cross-linking	High-throughput sequencing (FAIRE-seq)
	Chromosome conformation capture	High-throughput sequencing (3C-seq, 4C-seq, 5C-seq)