The time-resolved transcriptome of C. elegans
- Max E. Boeck1,2,
- Chau Huynh1,
- Lou Gevirtzman1,
- Owen A. Thompson1,
- Guilin Wang3,
- Dionna M. Kasper3,
- Valerie Reinke3,
- LaDeana W. Hillier1 and
- Robert H. Waterston1
- 1Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, USA;
- 2Department of Biology, Regis University, Denver, Colorado 80221, USA;
- 3Department of Genetics, School of Medicine, Yale University, New Haven, Connecticut 06520, USA
- Corresponding author: waterston{at}gs.washington.edu
Abstract
We generated detailed RNA-seq data for the nematode Caenorhabditis elegans with high temporal resolution in the embryo as well as representative samples from post-embryonic stages across the life cycle. The data reveal that early and late embryogenesis is accompanied by large numbers of genes changing expression, whereas fewer genes are changing in mid-embryogenesis. This lull in genes changing expression correlates with a period during which histone mRNAs produce almost 40% of the RNA-seq reads. We find evidence for many more splice junctions than are annotated in WormBase, with many of these suggesting alternative splice forms, often with differential usage over the life cycle. We annotated internal promoter usage in operons using SL1 and SL2 data. We also uncovered correlated transcriptional programs that span >80 kb. These data provide detailed annotation of the C. elegans transcriptome.
Footnotes
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[Supplemental material is available for this article.]
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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.202663.115.
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Freely available online through the Genome Research Open Access option.
- Received December 2, 2015.
- Accepted August 15, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
