RNA Therapeutics Institute; Graduate School of Biomedical Sciences
Computational Biology | Genetic Phenomena | Genetics and Genomics | Nucleic Acids, Nucleotides, and Nucleosides
Recursive splicing, a process by which a single intron is removed from pre-mRNA transcripts in multiple distinct segments, has been observed in a small subset of Drosophila melanogaster introns. However, detection of recursive splicing requires observation of splicing intermediates that are inherently unstable, making it difficult to study. Here we developed new computational approaches to identify recursively spliced introns and applied them, in combination with existing methods, to nascent RNA sequencing data from Drosophila S2 cells. These approaches identified hundreds of novel sites of recursive splicing, expanding the catalog of recursively spliced fly introns by 4-fold. A subset of recursive sites were validated by RT-PCR and sequencing. Recursive sites occur in most very long ( > 40 kb) fly introns, including many genes involved in morphogenesis and development, and tend to occur near the midpoints of introns. Suggesting a possible function for recursive splicing, we observe that fly introns with recursive sites are spliced more accurately than comparably sized non-recursive introns.
Introns, RNA splicing, Drosophila melanogaster, RNA sequencing, Sequence motif analysis, Gene expression, Gene ontologies, Invertebrate genomics
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Copyright: © 2018 Pai et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI of Published Version
PLoS Genet. 2018 Aug 27;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug. Link to article on publisher's site
Pai AA, Paggi JM, Yan P, Adelman K, Burge CB. (2018). Numerous recursive sites contribute to accuracy of splicing in long introns in flies. Open Access Publications by UMMS Authors. https://doi.org/10.1371/journal.pgen.1007588. Retrieved from https://escholarship.umassmed.edu/oapubs/3562
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