ArticleG3 (Bethesda, Md.)2014
In vivo determination of direct targets of the nonsense-mediated decay pathway in Drosophila.
Article in G3 (Bethesda, Md.), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
- Article
- mThe EMBO journal · 2021Article
- Article
- Article
- Nonsense-mediated mRNA decay: The challenge of telling right from wrong in a complex transcriptome.Wiley interdisciplinary reviews. RNA · 2019Review
- Reactivation of nonsense-mediated mRNA decay protects against C9orf72 dipeptide-repeat neurotoxicity.Brain : a journal of neurology · 2019Article
- Drosophila CrebB is a Substrate of the Nonsense-Mediated mRNA Decay Pathway that Sustains Circadian Behaviors.Molecules and cells · 2019Article
- Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes.The EMBO journal · 2018Article
- Multiple Nonsense-Mediated mRNA Processes RequireGenetics · 2018Article
- Article
- HTLV-1 Tax plugs and freezes UPF1 helicase leading to nonsense-mediated mRNA decay inhibition.Nature communications · 2018Article
- The Substrates of Nonsense-Mediated mRNA Decay inG3 (Bethesda, Md.) · 2018Article
- Stress and the nonsense-mediated RNA decay pathway.Cellular and molecular life sciences : CMLS · 2017Review
- Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease.Nucleic acids research · 2017Article
- Smooth, an hnRNP-L Homolog, Might Decrease Mitochondrial Metabolism by Post-Transcriptional Regulation of Isocitrate Dehydrogenase (Idh) and Other Metabolic Genes in the Sub-Acute Phase of Traumatic Brain Injury.Frontiers in genetics · 2017Article
- The role of nucleotide composition in premature termination codon recognition.BMC bioinformatics · 2016Article
- How cells kill a "killer" messenger.eLife · 2016Article
- Article
- Review
- Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data.G3 (Bethesda, Md.) · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) is a mRNA degradation pathway that regulates a significant portion of the transcriptome. The expression levels of numerous genes are known to be altered in NMD mutants, but it is not known which of these transcripts is a direct pathway target. Here, we present the first genome-wide analysis of direct NMD targeting in an intact animal. By using rapid reactivation of the NMD pathway in a Drosophila melanogaster NMD mutant and globally monitoring of changes in mRNA expression levels, we can distinguish between primary and secondary effects of NMD on gene expression. Using this procedure, we identified 168 candidate direct NMD targets in vivo. Remarkably, we found that 81% of direct target genes do not show increased expression levels in an NMD mutant, presumably due to feedback regulation. Because most previous studies have used up-regulation of mRNA expression as the only means to identify NMD-regulated transcripts, our results provide new directions for understanding the roles of the NMD pathway in endogenous gene regulation during animal development and physiology. For instance, we show clearly that direct target genes have longer 3' untranslated regions compared with nontargets, suggesting long 3' untranslated regions target mRNAs for NMD in vivo. In addition, we investigated the role of NMD in suppressing transcriptional noise and found that although the transposable element Copia is up-regulated in NMD mutants, this effect appears to be indirect.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.