ArticleeLife2022
Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.
Article in eLife, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
What it found
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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
27 citing papers in PubMed, 43 citations in OpenAlex.
- The MODNAP benchmark set for modeling ribose-based modified nucleic acid and nucleic acid-protein complexes: a case study with AlphaFold 3.Nucleic acids research · 2026Article
- 2'-O-Methylation maintains ribosome structural and translation integrity.Molecular cell · 2026Article
- Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.Nature communications · 2026Article
- Ribosomal modifications are associated with mesenchymal fate selection in the neural crest lineage.Nature communications · 2026Article
- Ribosome heterogeneity and specialization in musculoskeletal physiology and pathology.JBMR plus · 2026Article
- Review
- Structural insights into cauliflower mitoribosome in translation state and in association with a late assembly factor.Nature communications · 2025Article
- A reference-guided iterative approach to polish the nanopore sequencing basecalling for therapeutic RNA quality control.Communications biology · 2025Article
- Review
- Specialized ribosomes: integrating new insights and current challenges.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- High-throughput approaches for the identification of ribosome heterogeneity.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- The dual life of disordered lysine-rich domains of snoRNPs in rRNA modification and nucleolar compaction.Nature communications · 2024Article
- Combining Nanopore direct RNA sequencing with genetics and mass spectrometry for analysis of T-loop base modifications across 42 yeast tRNA isoacceptors.Nucleic acids research · 2024Article
- RNA modifying enzymes shape tRNA biogenesis and function.The Journal of biological chemistry · 2024Review
- Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster.Nucleic acids research · 2024Article
- Review
- GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.Nucleic acids research · 2024Article
- Detection of queuosine and queuosine precursors in tRNAs by direct RNA sequencing.Nucleic acids research · 2023Article
- Ribonucleic Acid-Mediated Control of Protein Translation Under Stress.Antioxidants & redox signaling · 2023Review
- Nanopore sequencing of internal 2'-PORNA (New York, N.Y.) · 2023Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Nucleotides in RNA and DNA are chemically modified by numerous enzymes that alter their function. Eukaryotic ribosomal RNA (rRNA) is modified at more than 100 locations, particularly at highly conserved and functionally important nucleotides. During ribosome biogenesis, modifications are added at various stages of assembly. The existence of differently modified classes of ribosomes in normal cells is unknown because no method exists to simultaneously evaluate the modification status at all sites within a single rRNA molecule. Using a combination of yeast genetics and nanopore direct RNA sequencing, we developed a reliable method to track the modification status of single rRNA molecules at 37 sites in 18 S rRNA and 73 sites in 25 S rRNA. We use our method to characterize patterns of modification heterogeneity and identify concerted modification of nucleotides found near functional centers of the ribosome. Distinct, undermodified subpopulations of rRNAs accumulate upon loss of Dbp3 or Prp43 RNA helicases, suggesting overlapping roles in ribosome biogenesis. Modification profiles are surprisingly resistant to change in response to many genetic and acute environmental conditions that affect translation, ribosome biogenesis, and pre-mRNA splicing. The ability to capture single-molecule RNA modification profiles provides new insights into the roles of nucleotide modifications in RNA function.
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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.