Table 1.

Methods for global determination of RNA structures. Methods are listed not by the labs that developed them, but by the strategy and chemical used. Regular SHAPE is very inefficient for in vivo analysis but is one of the earliest method for structure probing. Enzymatic probing is not useful for in vivo analysis but provided the first global analysis of the RNA structurome. RING-MaP and SHAPE-MaP were developed for single-RNA analysis but the strategy is useful for in vivo structurome analysis. HiCLIP and RPL has yet to achieve global analysis of RNA structurome, but represent interesting future directions

Methods	Probe	Data	Inferred	Features and limitations	References
Secondary structure in vitro
Chemical probing	1M7, DMS, CMCT, hydroxyl, etc.	1D	2D	All nucleotides, mostly in vitro, no direct base pairing information	[6,7]
Enzymatic	RNase I, V1, P1, S1	1D	2D	All nucleotides, in vitro only, no direct base pairing information	[8–11]
SHAPE-MaP, RING-MaP	1M7 and DMS	1D	2D/3D	Additional correlation for bases but only for short distance. Adaptable to in vivo and global	[26•,27•]
Secondary structure in vivo
DMS-seq	DMS	1D	2D	In vivo, only interrogates A/C, no direct base pairing information	[16••,17••,20••]
icSHAPE	NAI, NAI-N3	1D	2D	In vivo, all nucleotides, minimal background, no direct base pairing information	[18,19••]
Secondary and higher order structure in vivo
CLASH, hiCLIP	UV crosslinking	2D		In vivo, direct duplex determination, only dsRBP-bound structures	[28,29,30••]
RPL	No crosslinking	2D		Lysed cells, direct duplex determination, low efficiency and accuracy	[31]