ArticleNature methods2023
Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 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
46 citing papers in PubMed.
- Article
- Review
- Quantitative profiling of basal and stress-induced ribosome collisions.bioRxiv : the preprint server for biology · 2026Article
- OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions.bioRxiv : the preprint server for biology · 2026Article
- tRNA mEMBO reports · 2026Article
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- iTP-seq: a scalable profiling workflow to characterize bacterial translation landscapes in vitro.Nature protocols · 2026Review
- Article
- tRNA synthetase activity is required for stress granule and P-body assembly.Genes & development · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries.Scientific reports · 2026Article
- Metabolic stress reveals widespread accumulation of cap-unmethylated RNAs.bioRxiv : the preprint server for biology · 2026Article
- Context-dependent translation inhibition as a cancer therapeutic modality.Nature communications · 2026Article
- How tailored Ribo-seq methods probe unique translation events.RNA (New York, N.Y.) · 2026Review
- Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation.Nature structural & molecular biology · 2026Article
- QuAPPro: an R shiny app for quantification and alignment of polysome profiles.BMC bioinformatics · 2026Article
- Decreased cytoplasmic crowding via inhibition of ribosome biogenesis can trigger Candida albicans filamentous growth.Nature microbiology · 2026Article
- Translational Downregulation of 5' TOP mRNAs During T Cell Exhaustion.bioRxiv : the preprint server for biology · 2025Article
- Synergistic Methods to Investigate Eukaryotic Translation and Its Quality Control.Journal of molecular biology · 2025Review
- The impact of ribosome association on lncRNA stability: a new layer of post-transcriptional control?Biochemical Society transactions · 2025Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
Abstract
Ribosome profiling has unveiled diverse regulation and perturbations of translation through a transcriptome-wide survey of ribosome occupancy, read out by sequencing of ribosome-protected messenger RNA fragments. Generation of ribosome footprints and their conversion into sequencing libraries is technically demanding and sensitive to biases that distort the representation of physiological ribosome occupancy. We address these challenges by producing ribosome footprints with P1 nuclease rather than RNase I and replacing RNA ligation with ordered two-template relay, a single-tube protocol for sequencing library preparation that incorporates adaptors by reverse transcription. Our streamlined approach reduced sequence bias and enhanced enrichment of ribosome footprints relative to ribosomal RNA. Furthermore, P1 nuclease preserved distinct juxtaposed ribosome complexes informative about yeast and human ribosome fates during translation initiation, stalling and termination. Our optimized methods for mRNA footprint generation and capture provide a richer translatome profile with low input and fewer technical challenges.
Indexed as
Identifiers
What Socratic 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 Socratic graph.