ArticleNucleic acids research2015
Assessing the translational landscape of myogenic differentiation by ribosome profiling.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 52 citations in OpenAlex.
- Calorie restriction and rapamycin distinctly restore non-canonical ORF translation in the muscles of aging mice.NPJ Regenerative medicine · 2024Article
- Targeting N4-acetylcytidine suppresses hepatocellular carcinoma progression by repressing eEF2-mediated HMGB2 mRNA translation.Cancer communications (London, England) · 2024Article
- LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2'-O-methylation.Nature communications · 2023Article
- Ribosome biogenesis and function in development and disease.Development (Cambridge, England) · 2023Review
- Translational control of stem cell function.Nature reviews. Molecular cell biology · 2021Review
- Widespread translational control regulates retinal development in mouse.Nucleic acids research · 2021Article
- RiboDiPA: a novel tool for differential pattern analysis in Ribo-seq data.Nucleic acids research · 2020Article
- Fermented Feed Modulates Meat Quality and Promotes the Growth ofAnimals : an open access journal from MDPI · 2020Article
- RiboMiner: a toolset for mining multi-dimensional features of the translatome with ribosome profiling data.BMC bioinformatics · 2020Article
- RNA Sequencing in Comparison to Immunohistochemistry for Measuring Cancer Biomarkers in Breast Cancer and Lung Cancer Specimens.Biomedicines · 2020Article
- Article
- Heterogeneity and specialized functions of translation machinery: from genes to organisms.Nature reviews. Genetics · 2018Review
- Csde1 binds transcripts involved in protein homeostasis and controls their expression in an erythroid cell line.Scientific reports · 2018Article
- GWIPS-viz: 2018 update.Nucleic acids research · 2018Article
- Ribosome profiling uncovers selective mRNA translation associated with eIF2 phosphorylation in erythroid progenitors.PloS one · 2018Article
- Article
- Translation of CircRNAs.Molecular cell · 2017Article
- Extensive translational regulation during seed germination revealed by polysomal profiling.The New phytologist · 2017Article
- Proteomic Analysis of Chicken Skeletal Muscle during Embryonic Development.Frontiers in physiology · 2017Article
- Decoding sORF translation - from small proteins to gene regulation.RNA biology · 2016Review
Corrections and comments
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Authors and funding
8 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The formation of skeletal muscles is associated with drastic changes in protein requirements known to be safeguarded by tight control of gene transcription and mRNA processing. The contribution of regulation of mRNA translation during myogenesis has not been studied so far. We monitored translation during myogenic differentiation of C2C12 myoblasts, using a simplified protocol for ribosome footprint profiling. Comparison of ribosome footprints to total RNA showed that gene expression is mostly regulated at the transcriptional level. However, a subset of transcripts, enriched for mRNAs encoding for ribosomal proteins, was regulated at the level of translation. Enrichment was also found for specific pathways known to regulate muscle biology. We developed a dedicated pipeline to identify translation initiation sites (TISs) and discovered 5333 unannotated TISs, providing a catalog of upstream and alternative open reading frames used during myogenesis. We identified 298 transcripts with a significant switch in TIS usage during myogenesis, which was not explained by alternative promoter usage, as profiled by DeepCAGE. Also these transcripts were enriched for ribosomal protein genes. This study demonstrates that differential mRNA translation controls protein expression of specific subsets of genes during myogenesis. Experimental protocols, analytical workflows, tools and data are available through public repositories (http://lumc.github.io/ribosome-profiling-analysis-framework/).
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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.