Genome-wide analysis of alternative splicing in Caenorhabditis elegans
- Arun K. Ramani1,2,5,6,
- John A. Calarco1,2,3,5,6,
- Qun Pan1,
- Sepand Mavandadi1,
- Ying Wang3,
- Andrew C. Nelson4,
- Leo J. Lee1,
- Quaid Morris1,2,
- Benjamin J. Blencowe1,2,
- Mei Zhen2,3,6 and
- Andrew G. Fraser1,2,6
- 1 Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Ontario M5S 3E1, Canada;
- 2 Department of Molecular Genetics, University of Toronto, Ontario M5S 1A8, Canada;
- 3 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada;
- 4 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3DY, United Kingdom
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↵5 These authors contributed equally to this work.
Abstract
Alternative splicing (AS) plays a crucial role in the diversification of gene function and regulation. Consequently, the systematic identification and characterization of temporally regulated splice variants is of critical importance to understanding animal development. We have used high-throughput RNA sequencing and microarray profiling to analyze AS in C. elegans across various stages of development. This analysis identified thousands of novel splicing events, including hundreds of developmentally regulated AS events. To make these data easily accessible and informative, we constructed the C. elegans Splice Browser, a web resource in which researchers can mine AS events of interest and retrieve information about their relative levels and regulation across development. The data presented in this study, along with the Splice Browser, provide the most comprehensive set of annotated splice variants in C. elegans to date, and are therefore expected to facilitate focused, high resolution in vivo functional assays of AS function.
Footnotes
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↵6 Corresponding authors.
E-mail andyfraser.utoronto{at}gmail.com.
E-mail john.calarco{at}utoronto.ca.
E-mail ramaniak{at}gmail.com.
E-mail zhen{at}lunenfeld.ca.
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[Supplemental material is available for this article. The sequence data from this study have been submitted to the NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi) under accession no. SRA009279. The microarray data from this study have been submitted to the NCBI Gene Expression Omnibus (http://www.ncbi.nlm.nih.gov/geo) under accession no. GSE25927.]
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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.114645.110.
- Received September 1, 2010.
- Accepted December 7, 2010.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
Freely available online through the Genome Research Open Access option.
