ArticleNucleic acids research2022
Identifying ribosome heterogeneity using ribosome profiling.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 24 citations in OpenAlex.
- The ribosomal landscape in influenza A virus infection: from molecular mechanisms to clinical relevance.European respiratory review : an official journal of the European Respiratory Society · 2026Review
- Detecting ribosome collisions with differential rRNA fragment analysis in ribosome profiling data.NAR genomics and bioinformatics · 2025Article
- Proteomics-based characterization of ribosome heterogeneity in adult mouse organs.Cellular and molecular life sciences : CMLS · 2025Article
- High-throughput approaches for the identification of ribosome heterogeneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Emerging roles of cohesin-STAG2 in cancer.Oncogene · 2025Review
- Analyzing the role of ferroptosis in ribosome-related bone marrow failure disorders: From pathophysiology to potential pharmacological exploitation.IUBMB life · 2024Review
- Article
- Review
- RPS24 alternative splicing is a marker of cancer progression and epithelial-mesenchymal transition.Scientific reports · 2024Article
- KDM2B is required for ribosome biogenesis and its depletion unequally affects mRNA translation.bioRxiv : the preprint server for biology · 2024Article
- The Ribosome Hypothesis: Decoding Mood Disorder Complexity.International journal of molecular sciences · 2024Article
- SARS-CoV-2 infection engenders heterogeneous ribonucleoprotein interactions to impede translation elongation in the lungs.Experimental & molecular medicine · 2023Article
- Principal Component Analysis of Alternative Splicing Profiles Revealed by Long-Read ONT Sequencing in Human Liver Tissue and Hepatocyte-Derived HepG2 and Huh7 Cell Lines.International journal of molecular sciences · 2023Article
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Authors and funding
7 authors at 3 institutions in 2 countries.
Funding
Abstract
Recent studies have revealed multiple mechanisms that can lead to heterogeneity in ribosomal composition. This heterogeneity can lead to preferential translation of specific panels of mRNAs, and is defined in large part by the ribosomal protein (RP) content, amongst other things. However, it is currently unknown to what extent ribosomal composition is heterogeneous across tissues, which is compounded by a lack of tools available to study it. Here we present dripARF, a method for detecting differential RP incorporation into the ribosome using Ribosome Profiling (Ribo-seq) data. We combine the 'waste' rRNA fragment data generated in Ribo-seq with the known 3D structure of the human ribosome to predict differences in the composition of ribosomes in the material being studied. We have validated this approach using publicly available data, and have revealed a potential role for eS25/RPS25 in development. Our results indicate that ribosome heterogeneity can be detected in Ribo-seq data, providing a new method to study this phenomenon. Furthermore, with dripARF, previously published Ribo-seq data provides a wealth of new information, allowing the identification of RPs of interest in many disease and normal contexts. dripARF is available as part of the ARF R package and can be accessed through https://github.com/fallerlab/ARF.
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