Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung1,3,4,
- Phaedra Agius2,3,
- Jakub O. Westholm1,
- Michael Chen1,
- Katsutomo Okamura1,
- Nicolas Robine1,
- Christina S. Leslie2 and
- Eric C. Lai1,5
- 1 Sloan-Kettering Institute, Department of Developmental Biology, 1017 Rockefeller Research Laboratories, New York, New York 10065,USA;
- 2 Sloan-Kettering Institute, Computational Biology Program, New York, New York 10065, USA
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↵3 These authors contributed equally to this work.
Abstract
Mirtrons are intronic hairpin substrates of the dicing machinery that generate functional microRNAs. In this study, we describe experimental assays that defined the essential requirements for entry of introns into the mirtron pathway. These data informed a bioinformatic screen that effectively identified functional mirtrons from the Drosophila melanogaster transcriptome. These included 17 known and six confident novel mirtrons among the top 51 candidates, and additional candidates had limited read evidence in available small RNA data. Our computational model also proved effective on Caenorhabditis elegans, for which the identification of 14 cloned mirtrons among the top 22 candidates more than tripled the number of validated mirtrons in this species. A few low-scoring introns generated mirtron-like read patterns from atypical RNA structures, but their paucity suggests that relatively few such loci were not captured by our model. Unexpectedly, we uncovered examples of clustered mirtrons in both fly and worm genomes, including a <8-kb region in C. elegans harboring eight distinct mirtrons. Altogether, we demonstrate that discovery of functional mirtrons, unlike canonical miRNAs, is amenable to computational methods independent of evolutionary constraint.
Footnotes
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↵5 Corresponding author.
E-mail laie{at}mskcc.org; fax (212) 717-3604.
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[Supplemental material is available for this article. Small RNA data have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo/). A full list of accession numbers can be found in Supplemental Table S1.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.113050.110.
- Received July 19, 2010.
- Accepted November 10, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.
