ArticleNature methods2021
Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle.RNA biology · 2025Review
- Comparative CRISPRi screens reveal a human stem cell dependence on mRNA translation-coupled quality control.Nature structural & molecular biology · 2025Article
- Expanding and improving analyses of nucleotide recoding RNA-seq experiments with the EZbakR suite.PLoS computational biology · 2025Article
- Advances in ribosome profiling technologies.Biochemical Society transactions · 2025Review
- Transcriptome and Temporal Transcriptome Analyses in Single Cells.International journal of molecular sciences · 2024Review
- Metabolic RNA Labeling and Translating Ribosome Affinity Purification for Measurement of Nascent RNA Translation.Bio-protocol · 2024Article
- Genome-wide quantification of RNA flow across subcellular compartments reveals determinants of the mammalian transcript life cycle.Molecular cell · 2024Article
- Correcting 4sU induced quantification bias in nucleotide conversion RNA-seq data.Nucleic acids research · 2024Article
- Control of cell state transitions by post-transcriptional regulation.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Distinct hypoxia-induced translational profiles of embryonic and adult-derived macrophages.iScience · 2023Article
- Stress-induced nuclear speckle reorganization is linked to activation of immediate early gene splicing.The Journal of cell biology · 2023Article
- Simultaneous measurement of nascent transcriptome and translatome using 4-thiouridine metabolic RNA labeling and translating ribosome affinity purification.Nucleic acids research · 2023Article
- RiboGalaxy: A Galaxy-based Web Platform for Ribosome Profiling Data Processing - 2023 Update.Journal of molecular biology · 2023Article
- grandR: a comprehensive package for nucleotide conversion RNA-seq data analysis.Nature communications · 2023Article
- Short open reading frame genes in innate immunity: from discovery to characterization.Trends in immunology · 2022Review
- Preferential translation of p53 target genes.RNA biology · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way.
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