Table 1 Biochemical methods to identify lncRNA interactions
MethodFull nameUseCitation
DNA–RNA
CHAR-seqChromatin-Associated RNA sequencinggenome-wide DNA–RNA contacts[166]
CHARTCapture Hybridization Analysis of RNA Targetscandidate RNA localization on chromatin[159]
ChIRPChromatin Isolation by RNA Purificationcandidate RNA localization on chromatin[160]
dChIRPdomain-specific Chromatin Isolation by RNA Purificationcandidate RNA localization on chromatin[162]
GRID-seqGlobal RNA Interactions with DNA by deep sequencinggenome-wide DNA–RNA contacts[167]
MARGIMapping RNA-genome Interactionsgenome-wide DNA–RNA contacts[169]
RAPRNA Antisense Purificationcandidate RNA localization on chromatin[71]
RNA-DamIDRNA-DNA adenine methylase identificationcandidate RNA localization on chromatin[164]
SPRITESplit Pool Recognition of Interactions by Tag Extensiongenome-wide DNA–RNA contacts[168]
protein–RNA
IPLin vivo Proximity Labelingproximity labeling for protein–RNA[184]
CARICclick Chemistry-assisted RNA Interactome Captureproteome-scale identification of all RBPs[195]
CLIPultraviolet Crosslinking and Immunoprecipitationdiscovery of RNA interactors of a candidate protein[176]
eCLIPenhanced CLIPdiscovery of RNA interactors of a candidate protein[179]
GoldCLIPGel-omitted ligation-dependent CLIPdiscovery of RNA interactors of a candidate protein[180]
HITS-CLIPHigh-Throughput Sequencing of RNA isolated by CLIPdiscovery of RNA interactors of a candidate protein[175]
iCLIPindividual nucleotide resolution CLIPdiscovery of RNA interactors of a candidate protein[178]
iDRIPidentification of Direct RNA Interacting Proteinsdiscovery of protein interactors of a candidate RNA[121]
RaPIDRNA-protein Interaction Detectiondiscovery of protein interactors of a candidate RNA[189]
RBDmapRNA-binding Domain Mapping on a proteome scaleproteome-scale identification of polyA-bound RBPs and domains[141]
RBR-IDProteomic Identification of RNA-binding Regionsproteome scale identification of RBPs and domains[104]
RICKnewly transcribed RNA Interactome capture with Click chemistryproteome scale identification of nascent RNA-associated RBPs[194]
RIP-seqRNA Immunoprecipitation and sequencingdiscovery of RNA interactors of a candidate protein[173]
uvCLAPUltraviolet Crosslinking and Affinity Purificationdiscovery of RNA interactors of a candidate protein[181]
XRNAXprotein-crosslinked RNA extractionproteome scale identification of RBPs and domains[196]
RNA–RNA
CLASHCrosslinking Ligation and Sequencing of Hybridscandidate protein-associated RNA-RNA interactions[200]
COMRADESCrosslinking of Matched RNAsand Deep Sequencingidentification of RNA duplex interactions of candidate RNAs[203]
LIGR-seqLIGation of interacting RNA and high-throughput sequencingtrasncriptome-wide identification of RNA duplexes[202]
PARISPsoralen Analysis of RNA Interactions and Structurestranscriptome-wide identification of RNA duplexes[201]
RAP-RNARAP for RNA-RNA interactions of a target RNAintermolecular RNA interactions of candidate RNA[199]