ArticleeLife2015
Quality control of transcription start site selection by nonsense-mediated-mRNA decay.
Article in eLife, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 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
84 citing papers in PubMed, 141 citations in OpenAlex.
- Signatures of nonsense-mediated mRNA decay but no evidence for transcriptional adaptation associated with protein-truncating variants in wild yeast diploids.Molecular biology and evolution · 2026Article
- Context-dependent interplay of Swi-Snf and Tup1-Cyc8 influences chromatin and transcription at antagonistically regulated genes.Nature communications · 2026Article
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
- Nonsense mutations can increase mRNA levels.Biology open · 2026Article
- Genetic dissection of transcription start site selection by RNA polymerase II in Saccharomyces cerevisiae.Genetics · 2026Article
- Mapping and quantifying nascent transcript start sites using TT-TSS-seq.Genome research · 2026Article
- Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.RNA biology · 2025Review
- The impact of ribosome association on lncRNA stability: a new layer of post-transcriptional control?Biochemical Society transactions · 2025Review
- Genetic dissection of transcription start site selection by RNA Polymerase II inbioRxiv : the preprint server for biology · 2025Article
- Identification and Functions of lncRNAs in Fungi.Non-coding RNA · 2025Review
- Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for noncoding RNAs.bioRxiv : the preprint server for biology · 2025Article
- Global effect of copper excess and deficiency in Saccharomyces cerevisiae proficient or deficient in nonsense-mediated mRNA decay.Genomics · 2025Article
- RNA anchoring of Upf1 facilitates recruitment of Dcp2 in the NMD decapping complex.Nucleic acids research · 2025Article
- Predicting and comparing transcription start sites in single cell populations.PLoS computational biology · 2025Article
- RNA 3'end tailing safeguards cells against products of pervasive transcription termination.Nature communications · 2024Article
- Splicing the Difference: Harnessing the Complexity of the Transcriptome in Hematopoiesis.Experimental hematology · 2024Review
- RNA degradation triggered by decapping is largely independent of initial deadenylation.The EMBO journal · 2024Article
- Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1.PLoS biology · 2024Article
24 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. Moreover, we found that the low specificity of RNA polymerase II TSSs selection generates, for 47% of the expressed genes, NMD-sensitive transcript isoforms carrying uORFs or starting downstream of the ATG START codon. Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.
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.