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.