A Transformative Platform Deciphers the RNA Structural Code in Living Cells

RNA structure plays critical roles in regulating various post-transcription events involved in translation, splicing, and polyadenylation. Here, we established a transformative platform to probe in vivo RNA structures at both the genome wide scale and in targeted individual cases. The genome wide study in Arabidopsis reveals native RNA structural features that relate to numerous biological processes including translation initiation and regulation, alternative polyadenylation, and alternative splicing. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. The targeted individual RNA structure study has achieved attomoler sensitivity, which allows the analysis of very low abundance mRNAs in vivo. These novel and powerful methods for the investigation of RNA structure-function relationships in plants and should be applicable to any organism.