ArticleGenome research2013
Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 125 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
125 citing papers in PubMed, 189 citations in OpenAlex.
- Regulation of translation by upstream translation initiation codons of surfactant protein A1 splice variants.American journal of physiology. Lung cellular and molecular physiology · 2015Trial
- 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
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- Genetic dissection of transcription start site selection by RNA Polymerase II inbioRxiv : the preprint server for biology · 2025Article
- Transcript diversity in aging: cryptic transcription and splicing.Medical review (2021) · 2025Review
- The generation and consequences of N-terminal proteoform diversity.Cell reports · 2025Review
- Identification of translation events that drive nonsense-mediated mRNA decay reveals functional roles for noncoding RNAs.bioRxiv : the preprint server for biology · 2025Article
- The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.Developmental cell · 2025Article
- Deciphering the landscape of cis-acting sequences in natural yeast transcript leaders.Nucleic acids research · 2025Article
- Quantitative RNA pseudouridine maps reveal multilayered translation control through plant rRNA, tRNA and mRNA pseudouridylation.Nature plants · 2025Article
- Quantitative profiling of human translation initiation reveals elements that potently regulate endogenous and therapeutically modified mRNAs.Molecular cell · 2025Article
- Swi/Snf chromatin remodeling regulates transcriptional interference and gene repression.Molecular cell · 2024Article
- Deciphering thebioRxiv : the preprint server for biology · 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
- Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms.Life science alliance · 2024Article
- Article
- Review
- Article
- The regulatory landscape of 5' UTRs in translational control during zebrafish embryogenesis.bioRxiv : the preprint server for biology · 2023Article
65 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
2 authors at 1 institution in 1 country.
Funding
Abstract
Transcript leaders (TLs) can have profound effects on mRNA translation and stability. To map TL boundaries genome-wide, we developed TL-sequencing (TL-seq), a technique combining enzymatic capture of m(7)G-capped mRNA 5' ends with high-throughput sequencing. TL-seq identified mRNA start sites for the majority of yeast genes and revealed many examples of intragenic TL heterogeneity. Surprisingly, TL-seq identified transcription initiation sites within 6% of protein-coding regions, and these sites were concentrated near the 5' ends of ORFs. Furthermore, ribosome density analysis showed these truncated mRNAs are translated. Translation-associated TL-seq (TATL-seq), which combines TL-seq with polysome fractionation, enabled annotation of TLs, and simultaneously assayed their function in translation. Using TATL-seq to address relationships between TL features and translation of the downstream ORF, we observed that upstream AUGs (uAUGs), and no other upstream codons, were associated with poor translation and nonsense-mediated mRNA decay (NMD). We also identified hundreds of genes with very short TLs, and demonstrated that short TLs were associated with poor translation initiation at the annotated start codon and increased initiation at downstream AUGs. This frequently resulted in out-of-frame translation and subsequent termination at premature termination codons, culminating in NMD of the transcript. Unlike previous approaches, our technique enabled observation of alternative TL variants for hundreds of genes and revealed significant differences in translation in genes with distinct TL isoforms. TL-seq and TATL-seq are useful tools for annotation and functional characterization of TLs, and can be applied to any eukaryotic system to investigate TL-mediated regulation of gene expression.
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.