title: Genome-wide identification of zero nucleotide recursive splicing in Drosophila.
abstract: 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. Recursive splicing was first identified in the Drosophila Ultrabithorax (Ubx) gene and only three additional Drosophila genes have since been experimentally shown to undergo recursive splicing. 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.
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Michael O
authors.initials: MO
authors.lastname: Duff
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Sara
authors.initials: S
authors.lastname: Olson
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Xintao
authors.initials: X
authors.lastname: Wei
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Sandra C
authors.initials: SC
authors.lastname: Garrett
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Ahmad
authors.initials: A
authors.lastname: Osman
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Mohan
authors.initials: M
authors.lastname: Bolisetty
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Alex
authors.initials: A
authors.lastname: Plocik
authors.affiliation: Department of Genome Dynamics, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
authors.forename: Susan E
authors.initials: SE
authors.lastname: Celniker
authors.affiliation: Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, Connecticut 06030, USA.
authors.forename: Brenton R
authors.initials: BR
authors.lastname: Graveley
mesh_terms: D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D004331:Drosophila melanogaster / Q000235:genetics*; D005091:Exons / Q000235:genetics; D005260:Female; D017344:Genes, Insect / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics*; D006801:Humans; D007438:Introns / Q000235:genetics; D008297:Male; D009687:Nuclear Proteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D009711:Nucleotides / Q000235:genetics*; D022821:RNA Splice Sites / Q000235:genetics; D012326:RNA Splicing / Q000235:genetics*; D015203:Reproducibility of Results; D012261:Ribonucleoproteins / Q000172:deficiency / Q000235:genetics / Q000378:metabolism; D000072668:Splicing Factor U2AF
chemical_list: D009687:Nuclear Proteins; D009711:Nucleotides; D022821:RNA Splice Sites; D012261:Ribonucleoproteins; D000072668:Splicing Factor U2AF; C000607494:U2AF2 protein, human