Table 1 CLIP and non-CLIP methodologies for profiling protein–RNA interactions
Identify RNAs bound to protein
Ultraviolet crosslinking
- CLIP, ultraviolet crosslinking followed by immunoprecipitation
- eCLIP, enhanced CLIP
- HITS-CLIP, high-throughput sequencing of RNA isolated by CLIP
- iCLIP, individual-nucleotide resolution CLIP
- PAR-CLIP, photoactivatable ribonucleoside-enhanced CLIP
- irCLIP, infrared CLIP
RNA base editing
- DART-seq, deamination adjacent to RNA modification targets followed by sequencing
- STAMP, surveying targets by APOBEC-mediated profiling
- TRIBE, targets of RNA-binding proteins identified by editing
- PRINTER, protein–RNA interaction-based triaging of enzymes that edit RNA
- REMORA, RNA-encoded molecular recording in adenosines
Catalytically dead Cas variant plus guide RNA
- CRUIS, CRISPR-based RNA-united interacting system
- CARPID, CRISPR-assisted RNA–protein interaction detection method
Chemical and biotin labelling
- APEX-seq, RNA sequencing based on direct proximity labelling of RNA using the peroxidase enzyme APEX2
Capture interactions of specific RNAs
Ultraviolet crosslinking and mass spectrometry
- RAP-MS, RNA antisense purification coupled with mass spectrometry
- iDRIP, identification of direct RNA-interacting proteins
- CHART, capture hybridization analysis of RNA targets
- vIPR, in vivo interactions by pulldown of RNA
- ChIRP, comprehensive identification of RNA-binding proteins by mass spectrometry
- VIR-CLASP, viral crosslinking and solid-phase purification
Proximity labelling and mass spectrometry
- RaPID, RNA–protein interaction detection
RNA–miRNA proximity ligation
- CLASH, crosslinking, ligation and sequencing of hybrids
Capture the transcriptome-wide interactome
Ultraviolet crosslinking and mass spectrometry
- CLASP, crosslinking and solid-phase purification
- RIC, RNA interactome capture
- XRNAX, protein-crosslinked RNA extraction
- OOPS, orthogonal organic phase separation
Photoreactive nucleosides
- Proximity-CLIP
Reactive nucleosides and chemical crosslinking
- RICK, capture of the newly transcribed RNA interactome using click chemistry
- CARIC, click chemistry-assisted RNA interactome capture
