Prediction of Circular RNA Secondary Structures and Their Targets

At the level of secondary structure, circular RNAs (circRNAs) can be understood in terms of base pairing, base-pair stacking, and entropic loop contribution in the same way as linear RNAs and intermolecular RNA-RNA interactions. The folding problem of circular RNAs can thus be solved by dynamic programming algorithms in essentially the same manner. In this chapter, we review the similarities and differences between circular and linear RNAs with a focus on the software tools provided by the ViennaRNA package. Comparative analysis of RNA structures can also be generalized to circular RNA molecules. However, the task of constructing pairwise and multiple alignments of circular sequences is more difficult than those of their linear counterpart, whence fewer and less convenient software solutions are available. This chapter has also touched upon recent developments such as applications of chemical probing to circular RNAs and prediction of secondary structures on the interaction of circular RNAs with other molecules.