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) |