Widespread alternative and aberrant splicing revealed by lariat sequencing.
Alternative splicing is an important and ancient feature of eukaryotic gene structure, the existence of which has likely facilitated eukaryotic proteome expansions. Here, we have used intron lariat sequencing to generate a comprehensive profile of splicing events in Schizosaccharomyces pombe, amongst the simplest organisms that possess mammalian-like splice site degeneracy. We reveal an unprecedented level of alternative splicing, including alternative splice site selection for over half of all annotated introns, hundreds of novel exon-skipping events, and thousands of novel introns. Moreover, the frequency of these events is far higher than previous estimates, with alternative splice sites on average activated at ∼3% the rate of canonical sites. Although a subset of alternative sites are conserved in related species, implying functional potential, the majority are not detectably conserved. Interestingly, the rate of aberrant splicing is inversely related to expression level, with lowly expressed genes more prone to erroneous splicing. Although we validate many events with RNAseq, the proportion of alternative splicing discovered with lariat sequencing is far greater, a difference we attribute to preferential decay of aberrantly spliced transcripts. Together, these data suggest the spliceosome possesses far lower fidelity than previously appreciated, highlighting the potential contributions of alternative splicing in generating novel gene structures.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Nicholas
N
Stepankiw
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Madhura
M
Raghavan
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
Elizabeth A
EA
Fogarty
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA agrimson@cornell.edu.
Andrew
A
Grimson
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA jpleiss@cornell.edu.
Jeffrey A
JA
Pleiss
D017398:Alternative Splicing; D015966:Gene Expression Regulation, Fungal; D007438:Introns; D022821:RNA Splice Sites; D012568:Schizosaccharomyces / Q000235:genetics*; D017423:Sequence Analysis, RNA
D022821:RNA Splice Sites