In vivo nuclear RNA structurome reveals RNA structure regulation of mRNA processing in plants.

To investigate the role of RNA structure in mRNA processing, we performed SHAPE chemical probing on Arabidopsis nuclear RNAs and generated the in vivo RNA structure profiles with all four nucleotides. Firstly, SHAPE reagent (2-methylnicotinic acid imidazolide, NAI) treatment was applied to 5-day-old Arabidopsis seedlings. The intact nuclei were isolated and nuclear RNA extracted. We generated two independent biological replicates of (+) SHAPE and (-) SHAPE Structure-Seq libraries for high-throughput sequencing,and named our method “Nuc-SHAPE-Structure-Seq”.