ArticleNature protocols2012
The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.
Article in Nature protocols, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 852 papers.
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Who cites it
852 citing papers in PubMed, 1,357 citations in OpenAlex.
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- NASP functions in the cytoplasm to prevent histone H3 aggregation during early embryogenesis.The Journal of cell biology · 2026Article
- Human aminoacyl-tRNA synthetases as integrators of translation and cell signalling networks.Nature reviews. Molecular cell biology · 2026Review
- seq2ribo: structure-aware integration of machine learning and simulation to predict ribosome location profiles from RNA sequences.Bioinformatics (Oxford, England) · 2026Article
- Identification of unannotated microproteins involved in endothelial cell homeostasis, dysfunction, and vascular disease.Cardiovascular research · 2026Article
- Mutant KRAS-driven selective mRNA translation reveals mechanisms and therapeutic vulnerabilities in cancer.Cell reports · 2026Article
- NAT10 maintains stem cell homeostasis by mitigating mRNA decay through an acNature cell biology · 2026Article
- The use of Benzonase to produce ribosome footprints simplifies translational levels quantification by Ribo-seq.NAR genomics and bioinformatics · 2026Article
792 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Recent studies highlight the importance of translational control in determining protein abundance, underscoring the value of measuring gene expression at the level of translation. We present a protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing. This ribosome profiling approach maps the exact positions of ribosomes on transcripts by nuclease footprinting. The nuclease-protected mRNA fragments are converted into a DNA library suitable for deep sequencing using a strategy that minimizes bias. The abundance of different footprint fragments in deep sequencing data reports on the amount of translation of a gene. In addition, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, we describe an adaptation that reveals the sites of translation initiation by pretreating cells with harringtonine to immobilize initiating ribosomes. The protocol we describe requires 5-7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis require a further 4-5 days.
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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.