Table 1.
Main epigenomics data generation methods.
| APPLICATION | METHODS | PRINCIPLE | REFS |
|---|---|---|---|
| DNA methylation pattern detection | Methylated DNA immunoprecipitation (MeDIP) | Purified DNA is immunoprecipitated with an antibody against methylated cytosines, giving rise to genomic maps of DNA methylation | 111 |
| Bisulfite sequencing | Bisulfite to convert the unmethylated cytosines to uracils | 114 | |
| Reduced representation bisulfite sequencing (RRBS) | Combines restriction enzymes and bisulfite sequencing in order to enrich for the areas of the genome that have a high CpG content | 116 | |
| Histone modification patter detection, chromatin binding protein pattern detection | ChIP chip | Specific antibodies used for enrichment of the DNA fragments at modification sites followed by array hybridazation | 119 |
| ChIP-seq | Specific antibodies used for enrichment of the DNA fragments at modification sites followed by high-throughput sequencing | 117,118 | |
| 3D structure of chromatin | DNase-seq | At Dnase I hypersensitive sites (DHSs), chromatin are sensitive to cleavage by the Dnase I enzyme. These accessible chromatin zones are functionally related to transcriptional activity | 122 |
| Hi-C chromosome conformation capturing technique | Chromosome contacts are captured by formaldehyde cross-linking | 124,125,127 | |
| RNA-protein and RNA-DNA interaction | RIP-chip | Specific antibodies used for immunopreciptation of the RNA fragments at RNA-binding sites followed by reverse transcription and microarray | 141 |
| RIP-seq | Specific antibodies used for immunopreciptation of the RNA fragments at RNA-binding sites followed by reverse transcription and high-throughput sequencing | 142 | |
| CLIP-seq | UV cross-linking with immunoprecipitation to analyze protein interactions with RNA to precisely locate RNA-protein binding site and RNA modifications. Modified versions including PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP) can improve the signal-to-noise ratio and iCLIP (Individual-nucleotide resolution CLIP) can achieve a higher efficiency in reverse-transcription. | 143,321,322 | |
| ChIRP-seq | Biotin labeled oligos that are complement to interested RNA are used to hybridize crosslinked chromatin fragments to capture biotin-oligo-RNA-DNA-protein complexes, DNA then isolated from the complexes for high-throughput sequencing to illustrate the RNA-DNA interaction | 148 |