PaperRead-CLIP-moethod


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

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