Method | Requires knowledge of sRNA or mRNA beforehand | Uses anchor to pull or enrich RNAs | Crosslinking/Ligation | Reference |
EMSA | ✓ (both) | 49 67–69 | ||
Reporter systems | ✓ (both) | 29 49 | ||
Expression alteration | ✓ (both) | 70 71 | ||
RNA Pull-Down | ✓ (both) | 72 | ||
MAPS | ✓ (one) | ✓ (MS2-RNA) | 73–75 | |
RIP-Seq | ✓ (Ago) | 29 33 | ||
qCLASH | ✓ (Ago, Hfq) | ✓ | 84 85 | |
RIL-Seq | ✓ (Hfq) | ✓ | 86 | |
RAP-RNA | ✓ (biotinylated probe) | ✓ | 80 | |
MARIO | ✓ (biotinylated cysteine residues) | ✓ | 88 | |
Modified CLASH | ✓ | 76 | ||
LIGR-Seq | ✓ | 77 | ||
PARIS | ✓ | 78 | ||
SPLASH | ✓ (biotinylated psoralin) | ✓ | 79 | |
RIC-Seq | ✓ (biotinylated cytidine (bis) phosphate-3’ RNA ends) | ✓ | 87 |
EMSA, electrophoretic mobility shift assay; LIGR-Seq, ligation of interacting RNA followed by high throughput sequencing; MAPS, MS2-affinity purification coupled with RNA sequencing; MARIO, mapping RNA interactome in vivo; mRNA, messenger RNA; PARIS, psoralen analysis of RNA interactions and structures; qCLASH, quick cross-linking and sequencing of hybrids; RAP-RNA, RNA antisense purification to systemically map RNA-RNA interactions; RIC-Seq, RNA in situ conformation; RIP-Seq, RNA immunoprecipitation and sequencing; SPLASH, sequencing of psoralen crosslinked, ligated, and selected hybrids; sRNA, small RNA.