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High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

Arun K Ramani12, Andrew C Nelson23, Philipp Kapranov45, Ian Bell4, Thomas R Gingeras46* and Andrew G Fraser12*

Author Affiliations

1 Donnelly CCBR, College Street, University of Toronto, Toronto, M5S 3E1, Canada

2 The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK

3 Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 3DY, UK

4 Affymetrix, Inc., Central Expressway, Santa Clara, CA 95051, USA

5 Helicos Biosciences Corporation, Cambridge, MA 02139, USA

6 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA

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Genome Biology 2009, 10:R101  doi:10.1186/gb-2009-10-9-r101

Published: 24 September 2009

Abstract

Background

While many genome sequences are complete, transcriptomes are less well characterized. We used both genome-scale tiling arrays and massively parallel sequencing to map the Caenorhabditis elegans transcriptome across development. We utilized this framework to identify transcriptome changes in animals lacking the nonsense-mediated decay (NMD) pathway.

Results

We find that while the majority of detectable transcripts map to known gene structures, >5% of transcribed regions fall outside current gene annotations. We show that >40% of these are novel exons. Using both technologies to assess isoform complexity, we estimate that >17% of genes change isoform across development. Next we examined how the transcriptome is perturbed in animals lacking NMD. NMD prevents expression of truncated proteins by degrading transcripts containing premature termination codons. We find that approximately 20% of genes produce transcripts that appear to be NMD targets. While most of these arise from splicing errors, NMD targets are enriched for transcripts containing open reading frames upstream of the predicted translational start (uORFs). We identify a relationship between the Kozak consensus surrounding the true start codon and the degree to which uORF-containing transcripts are targeted by NMD and speculate that translational efficiency may be coupled to transcript turnover via the NMD pathway for some transcripts.

Conclusions

We generated a high-resolution transcriptome map for C. elegans and used it to identify endogenous targets of NMD. We find that these transcripts arise principally through splicing errors, strengthening the prevailing view that splicing and NMD are highly interlinked processes.