Skip to main content

Table 1 In vivo mapping RNA interactomes

From: Functions and properties of nuclear lncRNAs—from systematically mapping the interactomes of lncRNAs

Method Cross-linking Concept Advances Identifier Ref
RNA-chromatin
 ChIRP-seq Glutaraldehyde Use biotinylated antisense oligos to pull down a targeted RNA with its associated DNA. Robust elution by RNase A and RNase H. DNA that is associated with a specific RNA [7]
 CHART-seq Formaldehyde Use biotinylated antisense oligos to pull down a targeted RNA with its associated DNA. Apply RNase H to specifically elute RNA mediated interacting chromatin. DNA that is associated with a specific RNA [8, 9]
 CHIRT-seq Glutaraldehyde A hybrid method of ChIRP and CHART. Combination of glutaraldehyde fixation and RNase H elution. DNA that is associated with a specific RNA [10]
 MARGI-seq Formaldehyde Use a linker to ligate RNA and DNA in proximity to form of RNA-linker-DNA. Reveal all interactions between DNA and RNA. All RNA-DNA contacted sequences [11]
 ChAR-seq Formaldehyde Use a linker to ligate RNA and DNA in proximity to form of RNA-linker-DNA. Reveal all interactions between DNA and RNA. All RNA-DNA contacted sequences [12]
 GRID-seq Formaldehyde and disuccinimidyl glutarate (DSG) Use a linker to ligate RNA and DNA in proximity to form of RNA-linker-DNA. Strong crosslinking to reveal long-range interaction between DNA and RNA. All RNA-DNA contacted sequences [13]
 HiChIRP-seq Glutaraldehyde Combine ChIRP and Hi-C. Use CLICK chemistry to conjugate a biotin for subsequent contact enrichment. Characterize a specific RNA that involves in chromosomal interaction. Chromosome conformation at a specific RNA associated sites [14]
RNA-proteins
 CLIP-seq UV irradiation (254 nm) Pull down RNA-protein complexes by immunoprecipitation and perform reverse transcription. Identify all RNAs that interact with a targeted protein. RNA that binds to a specific protein [15]
 iCLIP-seq UV irradiation (254 nm) Pull down RNA-protein complexes by immunoprecipitation and perform reverse transcription. A random barcode to mark individual cDNA molecules to solve the problems of PCR duplicates. RNA that binds to a specific protein [16]
 PAR-CLIP-seq Incorporate 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA. UV (365 nm) Builds on CLIP. Incorporation of 4-SU or 6-SG results in U to C and G to A mutations respectively that allows mutational analysis to identify cross-linked sites. Use 4-SU or 6-SG incorporation to increase the crosslinking efficiency. RNA that binds to a specific protein [17]
 RAP-MS UV irradiation (254 nm) Use biotinylated antisense RNA probes to capture a specific RNA. Identify direct RNA interacting proteins. Proteins that bind to a specific RNA [18]
 ChIRP-MS Formaldehyde Use biotinylated antisense DNA probes to capture a specific RNA. Identify direct and indirect RNA interacting proteins. Proteins that bind to a specific RNA [19]
 iDRiP-MS UV irradiation (254 nm) Use biotinylated antisense DNA probes to capture a specific RNA. Identify direct RNA interacting proteins. Proteins that bind to a specific RNA [20] [10]
 RBR-ID UV (312 nm) + 4-thiouridine (4-SU) Comparison of 4-SU and non-4-SU treatments, an RNA-crosslinked peptide has a different mass. Identify all proteins bound to RNAs. All RNA binding proteins [21]
RNA structure/ RNA-RNA interactions
 FragSeq N/A RNA is digested by P1 endonuclease. Nuclease probing. Map P1 endonuclease digestion sites. In vitro RNA structure [22]
 PARS N/A RNA is digested by RNase V1 or S1 to determine double stranded or single stranded regions. Nuclease probing. Map RNase V1 or S1 digestion sites. In vitro RNA structure [23]
 SHAPE-seq Covalently modify RNA molecules in vitro. SHAPE reagents (1 M7, NAI-N3) modify RNAs. Single nucleotide resolution; each RNA in the experiment is bar-coded. In vitro RNA structure [24] [25, 26]
 icSHAPE-seq Covalently modify RNA molecules in vivo SHAPE reagent (NAI-N3). Copper-free click chemistry, a biotin moiety is selectively and efficiently added to NAI-N3-modified RNA. Identify In vivo RNA structure. In vivo RNA structure [27]
 DMS-seq (Structure-seq) Covalently modify RNA molecules Dimethyl sulphate (DMS) methylates the base-pairing faces of A and C of RNA in loops. Nucleotide resolution. Map RNA structure in vivo. In vivo RNA structure [28]
 COMRADES Psoralen + UV irradiation (365 nm) Pull down a specific RNA using biotinylated DNA oligos and perform proximity ligation. Reveal RNA structures and interactions of a specific RNA in vivo. In vivo RNA structures and interactions of a targeted RNA [29]
CLASH UV irradiation (254 nm) Immunoprecipitation to enrich a specific RNA binding protein and perform linker ligation. Find mRNA target sequences for miRNA. RNA hybrids bound by a specific RNA-binding protein [30] [31]
 hiCLIP UV irradiation (254 nm) Immunoprecipitate RNA-protein complexes by using antibodies against a specific RNA-binding protein and ligate RNA duplexes in proximity. Reveal RNA duplexes bound to a specific protein. RNA duplexes bound by a specific RNA-binding protein [32]
 MARIO Formaldehyde and EthylGlycol bis Apply a biotinylated linker to ligate two RNA fragments in proximity. Reveal all RNA-RNA interactions. All RNA fragments in proximity [33]
 PARIS Psoralen + UV irradiation (365 nm) Purify RNA-duplexes by 2D gel and ligate two RNA fragments in proximity Reveal all RNA-RNA interactions All RNA duplexes [34]
 SPLASH Psoralen + UV irradiation (365 nm) Use biotinylated psoralen to crosslink RNA and perform proximity ligation. Reveal all RNA-RNA interactions. All RNA-RNA hybrids [35]
RNA-DNA hybrids (R-loops)
 DRIP-seq N/A Pull down RNA/DNA hybrids using S9.6 antibody that specifically recognizes RNA/DNA hybrids. Reveal DNA-RNA hybrids. DNA that forms hybrids with RNA [36, 37]
 bisDRIP-seq Bisulfite modification Use bisulfite to convert cytosine residues into uracil residues within genomic DNA regions that contain single-stranded DNA. Enrich DNA/RNA hybrids by S9.6 IP. Define the boundaries of the R-loop, high resolution. Single-stranded DNA of R loops [38]
 R-ChIP Formaldehyde Use catalytic-dead RNase H to capture R loops, similar to ChIP. Reveal DNA-RNA hybrids, high resolution. RNase H target sites, R loops [39]
 DRIPc-seq N/A Builds on DRIP. Sequence RNA of DNA-RNA hybrids. Reveal DNA-RNA hybrids, high resolution. RNA of R loops [40]