Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, these sites must be in proximity. Inverted repeat sequences, such as Alu elements, if positioned in the upstream and downstream introns, can base pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing approaches, including the recently developed SHAPE-JuMP (selective 2'-hydroxyl acylation analyzed by primer extension and juxtaposed merged pairs) strategy, to characterize secondary and tertiary interactions in the pre-mRNA that govern backsplicing. Our data confirm that the antisense Alu elements AluSz(-) and AluSq2(+), in the upstream and downstream introns, form a highly paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirms that the presence of these elements favors circularization, but with modest predictive power. Together, our study suggests that secondary structure considerations alone do not fully explain backsplicing and that additional interactions are involved.