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- Title
Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.
- Authors
Hu, Xihao; Wong, Thomas K. F.; Lu, Zhi John; Chan, Ting Fung; Lau, Terrence Chi Kong; Yiu, Siu Ming; Yip, Kevin Y.
- Abstract
Motivation: High-throughput sequencing has been used to probe RNA structures, by treating RNAs with reagents that preferentially cleave or mark certain nucleotides according to their local structures, followed by sequencing of the resulting fragments. The data produced contain valuable information for studying various RNA properties.Results: We developed methods for statistically modeling these structure-probing data and extracting structural features from them. We show that the extracted features can be used to predict RNA ‘zipcodes’ in yeast, regions bound by the She complex in asymmetric localization. The prediction accuracy was better than using raw RNA probing data or sequence features. We further demonstrate the use of the extracted features in identifying binding sites of RNA binding proteins from whole-transcriptome global photoactivatable-ribonucleoside-enhanced cross-linking and immunopurification (gPAR-CLIP) data.Availability: The source code of our implemented methods is available at http://yiplab.cse.cuhk.edu.hk/probrna/.Contact: kevinyip@cse.cuhk.edu.hkSupplementary information: Supplementary data are available at Bioinformatics online.
- Subjects
MOLECULAR structure of RNA; PROTEIN binding; BINDING sites; PROTEIN crosslinking; NUCLEOTIDE sequence
- Publication
Bioinformatics, 2014, Vol 30, Issue 8, p1049
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btt757