Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Open accessAbstract
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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The rate of cDNA truncation at the crosslink site during reverse transcription has been reported as high as 82% for Nova and over 95% for several other RBPs.
“It has been reported that the rate of cDNA truncation at the crosslink site during reverse transcription is as high as 82% for Nova and over 95% for several other RBPs(Sugimoto et al., 2012).”
From HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism (2014) · cites this paper as Sugimoto et al., 2012
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- Authors
- Sugimoto, Y., König, J., Hussain, S., Zupan, B., Curk, T., Frye, M., & Ule, J.
- Affiliations
- MRC Laboratory of Molecular Biology (GB)
- Wellcome/MRC Cambridge Stem Cell Institute (GB)
- University of Ljubljana (SI)
- Corresponding author
- Ule, Jernej
- Venue
- Genome Biology
- Published
- 2012-08-03
- Volume
- 13
- Issue
- 8
- Pages
- R67-R67
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC4053741
- OpenAlex
- W2132803382
- Cited by
- 234
- References
- 37
- Citations by year
- 2026: 10 · 2025: 9 · 2024: 6 · 2023: 16 · 2022: 13 · 2021: 15 · 2020: 14 · 2019: 12 · 2018: 19 · 2017: 28 · 2016: 27 · 2015: 25 · 2014: 22 · 2013: 15 · 2012: 2
- FWCI
- 8.18
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository of the University of Ljubljana (University of Ljubljana) (publishedVersion, other-oa)
- Pure (University of Bath) (acceptedVersion, cc-by)
- MDC Repository (Max-Delbrueck-Center for Molecular Medicine) (acceptedVersion)
- The University of Bath Online Publications Store (The University of Bath) (submittedVersion, cc-by)
- UCL Discovery (University College London) (submittedVersion)
- Apollo (University of Cambridge) (submittedVersion, cc-by)
- Funders
- Wellcome Trust (089701)
- Javna Agencija za Raziskovalno Dejavnost RS (P2-0209, Z7-3665)
- Medical Research Council
- FP7 Ideas: European Research Council (206726)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- CLIP, iCLIP, RNA-protein interactions, UV crosslinking, nova, RNA-binding protein binding sites, binding specificity
- MeSH terms
- Neuro-Oncological Ventral Antigen, Animals, Antigens, Neoplasm, Chlorocebus aethiops, HeLa Cells, Humans, Methyltransferases, Nerve Tissue Proteins, RNA, Gene Library, RNA-Binding Proteins, Sequence Deletion, Sequence Analysis, DNA, COS Cells, Immunoprecipitation, Mice, Molecular Sequence Annotation, High-Throughput Nucleotide Sequencing
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