Table 2

Summary of experimental approaches that can be used to identify and validate bacterial RNA-human RNA interactions

MethodRequires knowledge of sRNA or mRNA beforehandUses anchor to pull or enrich RNAsCrosslinking/LigationReference
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 CLASH76
LIGR-Seq77
PARIS78
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.