Optimized photochemistry enables efficient analysis of dynamic RNA structuromes and interactomes in genetic and infectious diseases

Minjie Zhang, Kongpan Li, Jianhui Bai, Willem A. Velema, Chengqing Yu, Ryan van Damme, Wilson H. Lee, Maia L. Corpuz, Jian-Fu Chen and Zhipeng Lu ()
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Minjie Zhang: University of Southern California
Kongpan Li: University of Southern California
Jianhui Bai: University of Southern California
Willem A. Velema: Radboud University Nijmegen
Chengqing Yu: University of Southern California
Ryan van Damme: University of Southern California
Wilson H. Lee: University of Southern California
Maia L. Corpuz: University of Southern California
Jian-Fu Chen: University of Southern California
Zhipeng Lu: University of Southern California

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: Abstract Direct determination of RNA structures and interactions in living cells is critical for understanding their functions in normal physiology and disease states. Here, we present PARIS2, a dramatically improved method for RNA duplex determination in vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status on a transcriptome scale. Applying PARIS2 to the U8 snoRNA mutated in the neurological disorder LCC, we discover a network of dynamic RNA structures and interactions which are destabilized by patient mutations. We report the first whole genome structure of enterovirus D68, an RNA virus that causes polio-like symptoms, revealing highly dynamic conformations altered by antiviral drugs and different pathogenic strains. We also discover a replication-associated asymmetry on the (+) and (−) strands of the viral genome. This study establishes a powerful technology for efficient interrogation of the RNA structurome and interactome in human diseases.

Date: 2021
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DOI: 10.1038/s41467-021-22552-y

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