ArticleProceedings of the National Academy of Sciences of the United States of America2009
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 227 papers.
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Who cites it
227 citing papers in PubMed, 372 citations in OpenAlex.
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- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Nonsense-mediated mRNA decay factors target short poly(A)-tailed mRNAs lacking a premature termination codon.Nature communications · 2026Article
- A bifunctional H/ACA snoRNP mediates both pseudouridylation and rRNA scaffolding during ribosome assembly.bioRxiv : the preprint server for biology · 2026Article
- RAPseq enables large-scale identification of RBP-RNA interactions and reveals essentials of post-transcriptional gene regulation.Nucleic acids research · 2026Article
- Ribosomal RNA synthesis by RNA polymerase I is subject to premature termination of transcription.eLife · 2026Article
- Sni445 recruits box C/D snoRNPs snR4 and snR45 to guide ribosomal RNA acetylation by Kre33.Nucleic acids research · 2026Article
- Yeast elongation factor homolog New1 protects a subset of mRNAs from degradation by no-go decay.Nucleic acids research · 2026Article
- A transcription termination mechanism for maintaining homogeneous protein expression.Nucleic acids research · 2025Article
- Rapid remodeling of NTP levels enables immediate translational adaptation to energy stress in yeast.Molecular cell · 2025Article
- Integrative proteogenomic characterization reveals therapeutic targets in poorly differentiated and anaplastic thyroid cancers.Nature communications · 2025Article
- The snoRNP chaperone snR190 and the Npa1 complex form a macromolecular assembly required for 60S ribosomal subunit maturation.Nucleic acids research · 2025Article
- Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability.RNA (New York, N.Y.) · 2025Article
- Differential impact of divalent metals on native elongating transcript sequencing (NET-seq) protocols for RNA polymerases I and II.PloS one · 2025Article
- reCRAC: A Stringent Method for Precise Mapping of Protein-RNA Interactions in Yeast.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.Microbial genomics · 2024Article
- GPATCH4 regulates rRNA and snRNA 2'-O-methylation in both DHX15-dependent and DHX15-independent manners.Nucleic acids research · 2024Article
- The Efg1-Bud22 dimer associates with the U14 snoRNP contacting the 5' rRNA domain of an early 90S pre-ribosomal particle.Nucleic acids research · 2024Article
- YLR419W is the homolog of the mammalian translation initiation factormicroPublication biology · 2024Article
167 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
Abstract
The U3 small nucleolar ribonucleoprotein (snoRNP) plays an essential role in ribosome biogenesis but, like many RNA-protein complexes, its architecture is poorly understood. To address this problem, binding sites for the snoRNP proteins Nop1, Nop56, Nop58, and Rrp9 were mapped by UV cross-linking and analysis of cDNAs. Cross-linked protein-RNA complexes were purified under highly-denaturing conditions, ensuring that only direct interactions were detected. Recovered RNA fragments were amplified after linker ligation and cDNA synthesis. Cross-linking was successfully performed either in vitro on purified complexes or in vivo in living cells. Cross-linking sites were precisely mapped either by Sanger sequencing of multiple cloned fragments or direct, high-throughput Solexa sequencing. Analysis of RNAs associated with the snoRNP proteins revealed remarkably high signal-to-noise ratios and identified specific binding sites for each of these proteins on the U3 RNA. The results were consistent with previous data, demonstrating the reliability of the method, but also provided insights into the architecture of the U3 snoRNP. The snoRNP proteins were also cross-linked to pre-rRNA fragments, with preferential association at known sites of box C/D snoRNA function. This finding demonstrates that the snoRNP proteins directly contact the pre-rRNA substrate, suggesting roles in snoRNA recruitment. The techniques reported here should be widely applicable to analyses of RNA-protein interactions.
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