Optimized photochemistry and enzymology enable efficient analysis of RNA structures and interactions in cells and virus infections

SUMMARY Direct determination of RNA structures and interactions in living cells is critical for understanding their functions. Current crosslinking and proximity-ligation approaches are fundamentally limited due to inefficient RNA crosslinking, purification and high-level photochemical damages. Here we present PARIS2 (psoralen analysis of RNA interactions and structures, second generation), a re-invented method for capturing RNA duplexes in cells with three orders of magnitude improved efficiency. PARIS2 captures ribosome small subunit (SSU) binding sites on mRNAs, reporting translation status on a transcriptome wide scale, and captures spliceosomal snRNP binding sites on various RNA targets. We determine the RNA genome structure of enterovirus D68, a re-emerging viral pathogen associated with severe neurological symptoms, and discover alternative conformations in the internal ribosome entry site (IRES) that controls translation initiation. Together, these results reveal new aspects of RNA photochemistry and enzymology, and enable highly efficient interrogation of the RNA structurome and interactome in cells.