ArticleNature communications2024
Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Review
- Folding the message: mRNA structure as a regulatory layer of human mitochondrial gene expression.Biochimica et biophysica acta. Molecular cell research · 2026Review
- Mitochondrial translation termination, recycling, reinitiation, and rescue for in-frame and out-of-frame contexts.Nature communications · 2026Article
- Gravitational and mechanical forces shape mitochondrial translation.Nature communications · 2026Article
- Ribosomal allostery as a potential regulator of bacterial dormancy.Nature communications · 2026Article
- Nascent protein retention at polysomes reduces kinetic barriers to self-assembly.bioRxiv : the preprint server for biology · 2026Article
- Crosstalk between the ribosome quality control-associated E3 ubiquitin ligases LTN1 and RNF10.FEBS letters · 2026Article
- Bridging single-molecule and genome-wide studies of cellular mRNA translation.RNA (New York, N.Y.) · 2026Review
- Ribosome Biogenesis and Translational Control in Skeletal Muscle Atrophy and Hypertrophy: Mechanisms and Therapeutic Perspectives.Biomolecules · 2026Review
- Data-driven design of LNA-blockers for efficient contaminant removal in Ribo-Seq libraries.Scientific reports · 2026Article
- The G3BP stress-granule proteins reinforce the integrated stress response translation programme.Nature cell biology · 2026Article
- Detection and Characterization of the Eukaryotic Vacant Ribosome.International journal of molecular sciences · 2025Review
- Multi-omic assessment of mRNA translation dynamics in liver cancer cell lines.Scientific data · 2025Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- LncRNA-Encoded Micropeptides: Expression Validation, Translational Mechanisms, and Roles in Cellular Metabolism.International journal of molecular sciences · 2025Review
- All Probes Plasmids (APPs) for multicolor and long-term tracking of single-mRNA translation dynamics.Molecular biology of the cell · 2025Article
- Expanding the tagging toolbox for visualizing translation live.The Biochemical journal · 2025Review
- Selection of initiator tRNA and start codon by mammalian mitochondrial initiation factor 3 in leaderless mRNA translation.Nucleic acids research · 2025Article
- Calibrated ribosome profiling assesses the dynamics of ribosomal flux on transcripts.Nature communications · 2024Article
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Authors and funding
10 authors.
Funding
Abstract
Ribosome profiling, which is based on deep sequencing of ribosome footprints, has served as a powerful tool for elucidating the regulatory mechanism of protein synthesis. However, the current method has substantial issues: contamination by rRNAs and the lack of appropriate methods to measure ribosome numbers in transcripts. Here, we overcome these hurdles through the development of "Ribo-FilterOut", which is based on the separation of footprints from ribosome subunits by ultrafiltration, and "Ribo-Calibration", which relies on external spike-ins of stoichiometrically defined mRNA-ribosome complexes. A combination of these approaches estimates the number of ribosomes on a transcript, the translation initiation rate, and the overall number of translation events before its decay, all in a genome-wide manner. Moreover, our method reveals the allocation of ribosomes under heat shock stress, during aging, and across cell types. Our strategy of modified ribosome profiling measures kinetic and stoichiometric parameters of cellular translation across the transcriptome.
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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.