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Open AccessArticle

Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets

by Minzhe Zhang 1, Tao Wang 1,2,3, Guanghua Xiao 1,2,4 and Yang Xie 1,2,4,*
1
Quantitative Biomedical Research Center, Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
2
Harold C. Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX 75390, USA
3
Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
4
Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
*
Author to whom correspondence should be addressed.
Genes 2020, 11(1), 54; https://doi.org/10.3390/genes11010054
Received: 15 November 2019 / Revised: 26 December 2019 / Accepted: 29 December 2019 / Published: 3 January 2020
(This article belongs to the Section Technologies and Resources for Genetics)
Circular RNAs are a special type of RNA that has recently attracted a lot of research interest in studying its formation and function. RNA binding proteins (RBPs) that bind circRNAs are important in these processes, but have been relatively less studied. CLIP-Seq technology has been invented and applied to profile RBP-RNA interactions on the genome-wide scale. While mRNAs are usually the focus of CLIP-Seq experiments, RBP-circRNA interactions could also be identified through specialized analysis of CLIP-Seq datasets. However, many technical difficulties are involved in this process, such as the usually short read length of CLIP-Seq reads. In this study, we created a pipeline called Clirc specialized for profiling circRNAs in CLIP-Seq data and analyzing the characteristics of RBP-circRNA interactions. In conclusion, to our knowledge, this is one of the first studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs. View Full-Text
Keywords: Circ-RNA; CLIP-Seq; RBP Circ-RNA; CLIP-Seq; RBP
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Zhang, M.; Wang, T.; Xiao, G.; Xie, Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes 2020, 11, 54.

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