Mapping In Vivo RNA Structures and Interactions

Graphical Abstract View Large Image Figure Viewer Download Hi-res image RNA folds to form diverse secondary and tertiary structures and often interacts with other biomolecules to function in cells. The technologies developed to map in vivo RNA structures and interactions can be broadly classified into four categories. (i) RNA structure probing: Methods based on chemical probing to modify RNA, followed by reverse transcriptase (RT) stop or mutation readout. (ii) RNA–RNA interaction (RRI) mapping: Methods based on chemical crosslinking agents to capture direct RNA base pairs, followed by proximity ligation and reverse crosslinking. (iii) RNA–DNA interaction mapping: Methods based on antisense hybridization probes to capture RNA-interacting DNA, bivalent linkers to ligate DNA with RNA in the vicinity, or split-pool tagging to label RNA–DNA interactions with specific barcodes. (iv) RNA–protein interaction mapping: RNA-centric methods based on the combination of mass spectrometry with antisense hybridization probe pulldown or nucleoside analog labeling