smartSHAPE: a low-input method for transcriptome-wide RNA structure probing uncovers RNA structure landscape in mouse colonic macrophages

Here, we report the development and application of smartSHAPE, a SHAPE-like RNA structure probing method that requires low amounts of input due to the largely reduced artefact signals of premature RT stops and increased efficiency of library construction. We used smartSHAPE to profile the global RNA secondary structures of two subtypes of mouse colonic macrophages upon inflammation, and provided evidence that RNA conformational changes at protein binding sites regulate gene expression and, in turn, immune responses. We predicted functional RNA structure elements based on smartSHAPE structure data, and discovered that PD-L1 contains a YRY-motif stem-loop structural element within the 3'UTR, which triggers RNA degradation mediated by Regnase-1. Overall design: smartSHAPE was systematically evaluated by structure probing using different amounts of RNAs from HEK293T cells and applied to RNA structure probing in two subtypes of mouse colonic macrophages. To validate structure elements predicted based on structure data, we constructed RNA-Seq libraries in Reg1 KO or WT iBMDMs and uvCLAP libraries in Raw264.7 cells overexpressing FLAG-tagged Reg1 or GFP.