Title |
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
|
---|---|
Published in |
Genome Biology, August 2012
|
DOI | 10.1186/gb-2012-13-8-r67 |
Pubmed ID | |
Authors |
Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule |
Abstract |
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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Geographical breakdown
Country | Count | As % |
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United States | 2 | 29% |
France | 1 | 14% |
United Kingdom | 1 | 14% |
Unknown | 3 | 43% |
Demographic breakdown
Type | Count | As % |
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Scientists | 3 | 43% |
Members of the public | 3 | 43% |
Science communicators (journalists, bloggers, editors) | 1 | 14% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 6 | 2% |
Germany | 4 | 1% |
Austria | 3 | <1% |
United Kingdom | 2 | <1% |
Czechia | 1 | <1% |
Switzerland | 1 | <1% |
France | 1 | <1% |
Poland | 1 | <1% |
Unknown | 335 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Ph. D. Student | 106 | 30% |
Researcher | 73 | 21% |
Student > Master | 40 | 11% |
Student > Bachelor | 32 | 9% |
Professor | 19 | 5% |
Other | 43 | 12% |
Unknown | 41 | 12% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 153 | 43% |
Biochemistry, Genetics and Molecular Biology | 99 | 28% |
Computer Science | 12 | 3% |
Immunology and Microbiology | 10 | 3% |
Chemistry | 10 | 3% |
Other | 25 | 7% |
Unknown | 45 | 13% |