ArticleNAR genomics and bioinformatics2021
Deep conservation of ribosome stall sites across RNA processing genes.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 39 citations in OpenAlex.
- Differential regulation of translational stress responses by herpesvirus ubiquitin deconjugases.The FEBS journal · 2026Article
- Translational landscape during seed germination revealed by ribosome profiling.The Plant journal : for cell and molecular biology · 2026Article
- Conditional deep learning model reveals translation elongation determinants during amino acid deprivation.Communications biology · 2025Article
- Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control.Nature structural & molecular biology · 2025Article
- Are Bacterial Processes Dependent on Global Ribosome Pausing Affected by tRNA Modification Defects?Journal of molecular biology · 2025Review
- Interpreting ribosome dynamics during mRNA translation.The Journal of biological chemistry · 2025Review
- Human CCR4 deadenylase homolog Angel1 is a non-stop mRNA decay factor.RNA (New York, N.Y.) · 2025Article
- Landscape and regulation of mRNA translation in the early C. elegans embryo.Cell reports · 2025Article
- The translational landscape of HIV-1 infected cells reveals key gene regulatory principles.Nature structural & molecular biology · 2025Article
- Landscape and regulation of mRNA translation in the earlybioRxiv : the preprint server for biology · 2025Article
- Conserved GTPase OLA1 promotes efficient translation on D/E-rich mRNA.Nature communications · 2025Article
- DNA methylation orchestrates secondary metabolite biosynthesis and transport in Papaver somniferum.PloS one · 2025Article
- A review of Ribosome profiling and tools used in Ribo-seq data analysis.Computational and structural biotechnology journal · 2024Review
- A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.Science advances · 2024Article
- Translation in Bacillus subtilis is spatially and temporally coordinated during sporulation.Nature communications · 2024Article
- Translation Rates and Protein Folding.Journal of molecular biology · 2024Review
- Divergent proteomic profiles of opium poppy cultivars.Turkish journal of biology = Turk biyoloji dergisi · 2024Article
- Pyruvate Kinase M (PKM) binds ribosomes in a poly-ADP ribosylation dependent manner to induce translational stalling.Nucleic acids research · 2023Article
- Implications of tRNA abundance on translation elongation across bovine tissues.Frontiers in genetics · 2023Article
- A nascent peptide code for translational control of mRNA stability in human cells.Nature communications · 2022Article
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 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rate of translation can vary depending on the mRNA template. During the elongation phase the ribosome can transiently pause or permanently stall. A pause can provide the nascent protein with the time to fold or be transported, while stalling can serve as quality control and trigger degradation of aberrant mRNA and peptide. Ribosome profiling has allowed for the genome-wide detection of such pauses and stalls, but due to library-specific biases, these predictions are often unreliable. Here, we take advantage of the deep conservation of protein synthesis machinery, hypothesizing that similar conservation could exist for functionally important locations of ribosome slowdown, here collectively called stall sites. We analyze multiple ribosome profiling datasets from phylogenetically diverse eukaryotes: yeast, fruit fly, zebrafish, mouse and human to identify conserved stall sites. We find thousands of stall sites across multiple species, with the enrichment of proline, glycine and negatively charged amino acids around conserved stalling. Many of the sites are found in RNA processing genes, suggesting that stalling might have a conserved role in RNA metabolism. In summary, our results provide a rich resource for the study of conserved stalling and indicate possible roles of stalling in gene regulation.
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.