RT Journal Article SR Electronic T1 Genome-wide Identification of Zero Nucleotide Recursive Splicing in Drosophila JF bioRxiv FD Cold Spring Harbor Laboratory SP 006163 DO 10.1101/006163 A1 Michael Duff A1 Sara Olson A1 Xintao Wei A1 Ahmad Osman A1 Alex Plocik A1 Mohan Bolisetty A1 Susan Celniker A1 Brenton R. Graveley YR 2014 UL http://biorxiv.org/content/early/2014/06/11/006163.abstract AB Recursive splicing is a process in which large introns are removed in multiple steps by resplicing at ratchet points - 5’ splice sites recreated after splicing1. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene1 and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing2,3. Here, we identify 196 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. Recursive splicing events were identified by splice junctions that map to annotated 5’ splice sites and unannotated intronic 3’ splice sites, the presence of the sequence AG/GT at the 3’ splice site, and a 5’ to 3’ gradient of decreasing RNA-Seq read density indicative of co-transcriptional splicing. 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, and that the sequence and function of ratchet points are evolutionarily conserved. Together these results indicate that recursive splicing is commonly used in Drosophila and provides insight into the mechanisms by which some introns are removed.