UMMS Affiliation
RNA Therapeutics Institute; Graduate School of Biomedical Sciences
Publication Date
2018-08-27
Document Type
Article
Disciplines
Computational Biology | Genetic Phenomena | Genetics and Genomics | Nucleic Acids, Nucleotides, and Nucleosides
Abstract
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.
Keywords
Introns, RNA splicing, Drosophila melanogaster, RNA sequencing, Sequence motif analysis, Gene expression, Gene ontologies, Invertebrate genomics
Rights and Permissions
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
10.1371/journal.pgen.1007588
Source
PLoS Genet. 2018 Aug 27;14(8):e1007588. doi: 10.1371/journal.pgen.1007588. eCollection 2018 Aug. Link to article on publisher's site
Journal/Book/Conference Title
PLoS genetics
Related Resources
PubMed ID
30148878
Repository Citation
Pai, Athma A.; Paggi, Joseph M.; Yan, Paul; Adelman, Karen; and Burge, Christopher B., "Numerous recursive sites contribute to accuracy of splicing in long introns in flies" (2018). Open Access Articles. 3562.
https://escholarship.umassmed.edu/oapubs/3562
Creative Commons License
This work is licensed under a Creative Commons Attribution 4.0 License.
Included in
Computational Biology Commons, Genetic Phenomena Commons, Nucleic Acids, Nucleotides, and Nucleosides Commons