ArticleGenome biology2009
High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers, 1 of them a synthesis that pooled it.
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Who cites it
70 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Quantitative RNA-seq meta-analysis of alternative exon usage inGenome research · 2017Pooled it
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- Endonucleolytic cleavage is the primary mechanism of decay elicited byGenome research · 2025Article
- The Functional Meaning of 5'UTR in Protein-Coding Genes.International journal of molecular sciences · 2023Review
- mThe EMBO journal · 2021Article
- SMG5-SMG7 authorize nonsense-mediated mRNA decay by enabling SMG6 endonucleolytic activity.Nature communications · 2021Article
- Poly(U)-specific endoribonuclease ENDOU promotes translation of human CHOP mRNA by releasing uORF element-mediated inhibition.The EMBO journal · 2021Article
- Nonsense suppression therapies in human genetic diseases.Cellular and molecular life sciences : CMLS · 2021Review
- Long noncoding RNAMolecular therapy. Nucleic acids · 2021Article
- Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.Molecular biology and evolution · 2021Article
- Exploring the Diverse Functional and Regulatory Consequences of Alternative Splicing in Development and Disease.Frontiers in genetics · 2021Review
- Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge.Scientific reports · 2020Article
- Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.Scientific reports · 2020Article
- Murine Long Noncoding RNA Morrbid Contributes in the Regulation of NRAS Splicing in Hepatocytes In Vitro.International journal of molecular sciences · 2020Article
- Pervasive changes of mRNA splicing inProceedings of the National Academy of Sciences of the United States of America · 2020Article
- mRNA Editing, Processing and Quality Control inGenetics · 2020Review
- Gene expression dynamics are a proxy for selective pressures on alternatively polyadenylated isoforms.Nucleic acids research · 2020Article
- Defining nonsense-mediated mRNA decay intermediates in human cells.Methods (San Diego, Calif.) · 2019Review
- Selective profiling of ribosomes associated with yeast Upf proteins.Methods (San Diego, Calif.) · 2019Article
- A Upf3b-mutant mouse model with behavioral and neurogenesis defects.Molecular psychiatry · 2018Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile 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.
resultsWe 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.
conclusionsWe 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.
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