Table 1. Current approaches used to map distal enhancers genome-wide.
| Approach | Activity1 | Specificity2 | Examples |
|---|---|---|---|
| DNase I-seq |
Open |
Non |
refs. 6, 7 |
| NA-seq |
Open |
Non |
ref. 8 |
| FAIRE |
Open |
Non |
refs. 9, 10 |
| P300 (ChIP-seq) |
Open |
Enh. = Prom. |
refs. 11–13 |
| H3K4me1 (ChIP-seq) |
Open |
Enh. > Prom. |
refs. 11, 14 |
| H3K4me2 (ChIP-seq) |
Open |
Enh. = Prom. |
ref. 15 |
| H3K27ac (ChIP-seq) |
Active |
Enh. > Prom. |
refs. 16, 17 |
| H3K4me3 (ChIP-seq) |
Active |
Prom. > Enh. |
ref. 18 |
| Pol II (ChIP-seq) |
Active |
Prom. > Enh. |
refs. 19–21 |
| BRG1 (ChIP-Seq) | Active | Enh. = Prom. | ref. 22 |
1Refers to whether the approach allows the discrimination between poised and active enhancers. “Open” means that the approach identifies both poised and active enhancers without discrimination. In some cases, a quantitative difference in either chromatin accessibility or the enrichment of the specified factor or histone modification might be observed between poised and active enhancers.
2Refers to whether the approach preferentially marks enhancers (Enh. > Prom.), promoters (Prom. > Enh.) or both regions (Enh. = Prom.).