Table 1. Technical features of high throughput global and targeted methods for protein–RNA-binding studies using mass spectrometry or RNA sequencing.
| Method | Pub. year | Cross-link | Target /capture | MS label | Capture | Cells used in original study | Ref. |
|---|---|---|---|---|---|---|---|
| RNA interactome capture (RIC) | 2012 | 365 nm UV-4SU 254 nm UV |
RNA; poly-A tail OdT hybridisation |
SILAC Label-free |
OdT hybridisation, magnetic | HEK293T, HeLa | [6,69] |
| Orthogonal organic phase separation (OOPS) | 2019 | 254 nm UV | RNA; global Phase separation |
SILAC TMT |
Phase separation | HEK293, U2Os, MCF10A | [28] |
| Protein-cross-linked RNA extraction (XRNAX) | 2018 | 254 nm UV | RNA; global Phase separation Silica column |
SILAC | Phase separation + silica column | MCF7 | [27] |
| Phenol-toluol extraction (PTEX) | 2019 | 254 nm UV | RNA, global Phase separation |
LFQ | Phase separation | HEK293 | [29] |
| Click chemistry-assisted RNA interactome capture (CARIC) | 2018 | 365 nm UV-4SU + EU label + biotin |
RNA, labelled Click chemistry |
Dimethyl labelling | Click chemistry of metabolically labelled RNA, magnetic | HeLa | [26] |
| RNA interactome capture using click chemistry (RICK) | 2017 | 254 nm UV + EU label + biotin |
RNA, labelled Click chemistry |
Not described | Click chemistry of metabolically labelled RNA, magnetic | HeLa, HEK293T | [70] |
| Capture hybridisation analysis of RNA targets (CHART) | 2011 | Formaldehyde | RNA; sequence Hybridisation |
Western | 25mer biotinylated probe, magnetic | HeLa | [71] |
| Comprehensive identification of RNA-binding proteins by mass spectrometry (ChIRP) | 2015 | Formaldehyde | RNA; sequence Tiling hybridisation |
Not described | 20mer biotinylated tiling probe, magnetic | E36 | [42] |
| RNA affinity purification MS (RAP-MS) | 2015 | 254 nm UV | RNA; sequence Tiling hybridisation |
SILAC | 90mer biotinylated tiling probe, magnetic | SM33 | [41] |
| CRISPR-based RNA-united interacting system (CRUIS) | 2020 | Formaldehyde | Protein; label Immunoprecipitation | LFQ | sgRNA-Cas13a proximity labelling, magnetic | HEK293T | [43] |
| RNA immunoprecipitation (RIP, RIP-Seq, RIP-chip) | 2006, 2010 | None, native | Protein; epitope Immunoprecipitation | RNA-Seq only | Antibody | mESC | [72,73] |
| Cross-linking and immunoprecipitation (CLIP, CLIP-Seq, HITS-CLIP, iCLIP, eCLIP) | 2003, 2009 | 254 nm UV 365 nm UV-4SU |
Protein; epitope Immunoprecipitation | RNA-Seq only | Antibody | HepG2, K562, HeLa, mouse brain | [50–52] |