ArticleGenome research2015
Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 1 of them a synthesis that pooled it.
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Who cites it
116 citing papers in PubMed, 1 synthesis or guideline pooled it, 177 citations in OpenAlex.
- Guidelines for Genome-Scale Analysis of Biological Rhythms.Journal of biological rhythms · 2017Guideline
- Allele-specific expression is associated with lower translational efficiency in mouse embryos and stem cells.bioRxiv : the preprint server for biology · 2026Article
- Time to rethink circadian rhythms beyond the transcriptome.Journal of biochemistry · 2026Review
- Mechanism of RACK1-dependent ZAKα activation at stalled and collided ribosomes.Molecular cell · 2026Article
- Myostatin Exhibits an Evolutionarily Conserved Circadian Pattern in Skeletal Muscles.Journal of cachexia, sarcopenia and muscle · 2025Article
- Loss of non-canonical translation initiation factors impairs perinatal cardiac function in mice.Experimental animals · 2025Article
- Daily liver rhythms: Coupling morphological and molecular oscillations.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Upstream open reading frames dynamically modulate CLOCK protein translation to regulate circadian rhythms and sleep.PLoS biology · 2025Article
- Circadian Control of Protein Synthesis.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025Review
- MCTS2 and distinct eIF2D roles in uORF-dependent translation regulation revealed by in vitro re-initiation assays.The EMBO journal · 2025Article
- Circadian de(regulation) in physiology: implications for disease and treatment.Genes & development · 2024Review
- Temporal dynamics of membrane contact sites.Nature cell biology · 2024Article
- Circadian period is compensated for repressor protein turnover rates in single cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Circadian regulation of macromolecular complex turnover and proteome renewal.The EMBO journal · 2024Article
- Diurnal control of iron responsive element containing mRNAs through iron regulatory proteins IRP1 and IRP2 is mediated by feeding rhythms.Genome biology · 2024Article
- Interorgan rhythmicity as a feature of healthful metabolism.Cell metabolism · 2024Review
- Circadian Regulation of Cardiac Arrhythmias and Electrophysiology.Circulation research · 2024Review
- Regulation of protein O-GlcNAcylation by circadian, metabolic, and cellular signals.The Journal of biological chemistry · 2024Review
- Circadian regulation of translation.RNA biology · 2024Review
- Circadian regulation of liver function: from molecular mechanisms to disease pathophysiology.Nature reviews. Gastroenterology & hepatology · 2023Review
56 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.
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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.