Acronym | Technique | Discriminating features | Reference |
---|---|---|---|
CHART | Capture hybridisation analysis of RNA targets | Tiled oligonucleotides against lncRNA, yielding bound DNA and protein | 37 |
ChIRP | Chromatin isolation by RNA purification | Pool of ∼20nt probes and gluteraldehyde crosslinking. Yields bound DNA and protein | 38 |
CLASH | Crosslinking, ligation and sequencing of hybrids | Small pool of ∼20nt probes. Partial RNaseH treatment during elution. Yields bound RNA | 39 |
iCLIP | Individual nucleotide resolution UV-crosslinking and immunoprecipitation | Antibody used against protein of interest, with interacting lncRNA nucleotide interrogated by sequencing | 40 |
RAP | RNA antisense purification | Large pool of ∼120nt probes. Yields bound DNA and RNA | 41 42 |
RIP | RNA immunoprecipitation | Antibody used against protein of interest, with presence of lncRNA interrogated. No cross-linking | 43 |
ChRIP | Chromatin RNA immunoprecipitation | Antibody used against modified chromatin, with presence of lncRNA interrogated | 44 |
ChOP | Chromatin oligo-affinity precipitation | Single ∼80nt probe, yielding interacting DNA | 45 |
All methods use biotinylated oligonucleotides as probes against the lncRNA of interest and formaldehyde cross-linking, unless otherwise stated.