Comparison of some R-loop profiling methods
| Method | R-loop-recognizing entity | Methodologies utilized | Strand-specific | Special considerations |
|---|---|---|---|---|
| DRIP | S9.6 monoclonal antibody | Immunoprecipitation | No | Batch to batch variation in S9.6 monoclonal antibody |
| bisDRIP | S9.6 monoclonal antibody | Immunoprecipitation, bisulfite conversion | Yes | Modified nucleotides must be detected in sequencing alignment |
| DRIPc | S9.6 monoclonal antibody | Immunoprecipitation, reverse transcription | Yes | May capture non-R-loop dsRNAs |
| DRIVE | MBP-RHΔ | Amylose resin enrichment | No | Limited sensitivity |
| R-ChIP | RHΔ | Immunoprecipitation | Yes | Requires generation of RHΔ-expressing cell line |
| MapR | RHΔ–MNase fusion protein | MNase cleavage of native chromatin | No | Requires generation of recombinant RHΔ–MNase fusion protein |
| BisMapR | RHΔ–MNase fusion protein | MNase cleavage of native chromatin, bisulfite conversion | Yes | Requires generation of recombinant RHΔ–MNase fusion protein |