Table 3

Immunoprecipitation techniques for investigating lncRNA

AcronymTechniqueDiscriminating featuresReference
CHARTCapture hybridisation analysis of RNA targetsTiled oligonucleotides against lncRNA, yielding bound DNA and protein37
ChIRPChromatin isolation by RNA purificationPool of ∼20nt probes and gluteraldehyde crosslinking. Yields bound DNA and protein38
CLASHCrosslinking, ligation and sequencing of hybridsSmall pool of ∼20nt probes. Partial RNaseH treatment during elution. Yields bound RNA39
iCLIPIndividual nucleotide resolution UV-crosslinking and immunoprecipitationAntibody used against protein of interest, with interacting lncRNA nucleotide interrogated by sequencing40
RAPRNA antisense purificationLarge pool of ∼120nt probes. Yields bound DNA and RNA41 42
RIPRNA immunoprecipitationAntibody used against protein of interest, with presence of lncRNA interrogated. No cross-linking43
ChRIPChromatin RNA immunoprecipitationAntibody used against modified chromatin, with presence of lncRNA interrogated44
ChOPChromatin oligo-affinity precipitationSingle ∼80nt probe, yielding interacting DNA45
  • All methods use biotinylated oligonucleotides as probes against the lncRNA of interest and formaldehyde cross-linking, unless otherwise stated.