Mapping circular RNA structures in living cells by SHAPE-MaP.

• Circular RNAs have the same sequences, but different structures from cognate linear RNAs. • NAI is used as the SHAPE reagent to probe circular RNA secondary structures in cells. • Experimental and unique computational pipelines are required for circular RNA secondary structural prediction. Circular RNAs are produced from back-splicing of exons of precursor mRNAs (pre-mRNAs). The sequences of exons in circular RNAs are identical to their linear cognate mRNAs, but the circular format may confer constraints on their folding and conformation, leading to potentially different functions from their linear RNA cognates. Here, we describe experimental and computational steps that optimize the selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) to probe circular RNA secondary structure at single-nucleotide resolution in living cells. [ABSTRACT FROM AUTHOR]