ArticleGenome biology2012
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Article in Genome biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 151 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
151 citing papers in PubMed.
- Distinct 5' and 3' coverage biases shape transcriptome interpretation in Nanopore direct RNA versus PCR-cDNA sequencing.BMC genomics · 2026Article
- OTTR-CLASH: improved biochemical and bioinformatic identification of Argonaute 2-mediated microRNA-target RNA interactions.bioRxiv : the preprint server for biology · 2026Article
- RNA-binding protein transcripts reflect composition of target mRNAs.Nucleic acids research · 2026Article
- Bridging technical innovation and computational advances in studies of RNA-protein assemblies.Nature reviews. Genetics · 2026Review
- The contribution of short tandem repeats to splicing variation in the human cortex.bioRxiv : the preprint server for biology · 2026Article
- Signal or noise? RNA-binding proteins and the challenges of binding site assignments.Nucleic acids research · 2026Review
- Novel CuCLIP-seq for in situ covalently captured protein-binding RNAs.Nature communications · 2026Article
- PARANOiD: Pipeline for Automated Read ANalysis of iCLIP Data.Bioinformatics (Oxford, England) · 2026Article
- Unnatural Amino Acid and Emerging Chemistry Approaches to Map RNA-Protein Interactions.Angewandte Chemie (International ed. in English) · 2026Review
- MUTACLASH: identifying functional small RNA target sites using crosslinking-induced mutations.RNA (New York, N.Y.) · 2026Article
- Article
- Influenza NS1 drives NEmerging microbes & infections · 2025Article
- Gene regulation through exon junction complex modularity.Nature structural & molecular biology · 2025Review
- Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.Nature communications · 2025Article
- Analysis of crosslinking sites suggestsbioRxiv : the preprint server for biology · 2025Article
- An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions.bioRxiv : the preprint server for biology · 2024Article
- The RNA-binding Selectivity of the RGG/RG Motifs of hnRNP U is Abolished by Elements Within the C-terminal Intrinsically Disordered Region.Journal of molecular biology · 2024Article
- Biospecific Chemistry for Covalent Linking of Biomacromolecules.Chemical reviews · 2024Review
- Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2).Nature protocols · 2024Review
91 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data sets to confirm that both methods identify protein-RNA cross-link sites, and to identify a slight uridine preference of UV-C-induced cross-linking. Comparing Nova CLIP and iCLIP data revealed that cDNA deletions have a preference for TTT motifs, whereas iCLIP cDNA truncations are more likely to identify clusters of YCAY motifs as the primary Nova binding sites. In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity.
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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.