Table 1 In vivo mapping RNA interactomes

 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]

 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]

 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]

 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]