ArticleCurrent protocols in molecular biology2013
Genome-wide annotation and quantitation of translation by ribosome profiling.
Article in Current protocols in molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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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.
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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.
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Who cites it
46 citing papers in PubMed, 75 citations in OpenAlex.
- RNA variation as the driver of genomic efficiency and phenotypic complexity.International journal of biological sciences · 2026Review
- The impact of ribosome association on lncRNA stability: a new layer of post-transcriptional control?Biochemical Society transactions · 2025Review
- Translation dysregulation in cancer as a source for targetable antigens.Cancer cell · 2025Article
- Unlocking the secrets of the immunopeptidome: MHC molecules, ncRNA peptides, and vesicles in immune response.Frontiers in immunology · 2025Review
- MIWI N-terminal arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis.Nucleic acids research · 2024Article
- The MYCN 5' UTR as a therapeutic target in neuroblastoma.Cell reports · 2024Article
- Ribosome profiling reveals downregulation of UMP biosynthesis as the major early response to phage infection.Microbiology spectrum · 2024Article
- It's a competitive business.eLife · 2024Article
- MIWI arginines orchestrate generation of functional pachytene piRNAs and spermiogenesis.bioRxiv : the preprint server for biology · 2024Article
- The Helix-Loop-Helix motif of human EIF3A regulates translation of proliferative cellular mRNAs.PloS one · 2023Article
- Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.Genome biology · 2022Article
- Using DMS-MaPseq to uncover the roles of DEAD-box proteins in ribosome assembly.Methods (San Diego, Calif.) · 2022Article
- Cytoplasmic long noncoding RNAs are differentially regulated and translated during human neuronal differentiation.RNA (New York, N.Y.) · 2021Article
- Optimization of Ribosome Footprinting Conditions for Ribo-Seq in Human andFrontiers in molecular biosciences · 2021Article
- Protein Stability Buffers the Cost of Translation Attenuation following eIF2α Phosphorylation.Cell reports · 2020Article
- mTORC1 signalling is not essential for the maintenance of muscle mass and function in adult sedentary mice.Journal of cachexia, sarcopenia and muscle · 2020Article
- Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence.Molecular cell · 2019Article
- mTOR and other effector kinase signals that impact T cell function and activity.Immunological reviews · 2019Review
- Proteogenomic Annotation of Chinese Hamsters Reveals Extensive Novel Translation Events and Endogenous Retroviral Elements.Journal of proteome research · 2019Article
- Active Tonic mTORC1 Signals Shape Baseline Translation in Naive T Cells.Cell reports · 2019Article
Corrections and comments
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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. A protocol for genome-wide, quantitative analysis of in vivo translation by deep sequencing is presented here. 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. Additionally, footprints reveal the exact regions of the transcriptome that are translated. To better define translated reading frames, an adaptation that reveals the sites of translation initiation by pre-treating cells with harringtonine to immobilize initiating ribosomes is described. The protocol described requires 5 to 7 days to generate a completed ribosome profiling sequencing library. Sequencing and data analysis requires an additional 4 to 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.