Genome-wide identification of zero nucleotide recursive splicing in Drosophila

Recursive splicing is a process in which large introns are removed in multiple steps by re-splicing at ratchet points-5' splice sites recreated after splicing(1). Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene(1) and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing(2,3). Here we identify 197 zero nucleotide exon ratchet points in 130 introns of 115 Drosophila genes from total RNA sequencing data generated from developmental time points, dissected tissues and cultured cells. The sequential nature of recursive splicing was confirmed by identification of lariat introns generated by splicing to and from the ratchet points. We also show that recursive splicing is a constitutive process, that depletion of U2AF inhibits recursive splicing, and that the sequence and function of ratchet points are evolutionarily conserved in Drosophila. Finally, we identify four recursively spliced human genes, one of which is also recursively spliced in Drosophila. Together, these results indicate that recursive splicing is commonly used in Drosophila, occurs in humans, and provides insight into the mechanisms by which some large introns are removed.