Table 2.

The methods used to study RNA interactomes.

Method	Description	Experimental Purpose	Enhanced Version	Ref
CHIRP-seq	A method to pull down and map the RNA-associated chromatin using biotinylated antisense oligos	Identification of RNA-DNA interaction	CHART-seq, CHIRT-seq, hiCHIRP-seq	[[181], [182], [183], [184], [185]]
R-CHIP-seq	A method to pull down and map R-loops using catalytic-dead RNase H	Identification of R-loop		[186]
DRIP-seq	A method to pull down and map R-loops using S9.6 antibody	Identification of R-loop	bisDRIP-seq, DRIPc-seq	[[187], [188], [189]]
CLIP-seq	A method to pull down and map the protein-binding RNA by immunoprecipitation	Identification of RNA-protein interaction	PAR-CLIP-seq, iCLIP-seq, hiCLIP-seq	[[190], [191], [192], [193]]
SHAPE-seq	A method to predict RNA secondary structures using chemical modifiers	Prediction of RNA-RNA interaction	icSHAPE-seq, DMS-seq, SHAPE-seq2.0	[[194], [195], [196], [197]]
Frag-seq	A method to predict RNA secondary structures using endonuclease P1	Prediction of RNA-RNA interaction		[198]