Visualization of RNA Structures and Functional Annotations Using ArcPlot.

RNA molecules intrinsically fold into complex base-paired structures that critically shape RNA function and mechanisms. Recent innovations in chemical probing now make it straightforward to interrogate RNA structures in cells. New technologies, such as single-molecule chemical probing, further make it possible to directly measure secondary and tertiary base pairing interactions. However, visualizing and interpreting these structural data remains nontrivial. To address this challenge, we developed ArcPlot, a Python program for visualizing DMS and SHAPE reactivity data, PAIR and RING single-molecule probing data, and secondary structure arc diagrams. ArcPlot also facilitates the retrieval and juxtaposition of functional annotations of RNA elements from experiments such as enhanced crosslinking and immunoprecipitation (eCLIP). For advanced users, ArcPlot has an application programming interface (API) that can be used to generate highly customized data visualizations. We provide stepwise instructions and specific examples of different ArcPlot usage applications. The flexibility and ease of use of ArcPlot make visualization and interpretation of complex RNA structural datasets routine, broadly facilitating hypothesis generation and mechanistic understanding of RNA function.