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Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets
Version 1
: Received: 15 November 2019 / Approved: 17 November 2019 / Online: 17 November 2019 (11:01:25 CET)
A peer-reviewed article of this Preprint also exists.
Zhang, M.; Wang, T.; Xiao, G.; Xie, Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes 2020, 11, 54. Zhang, M.; Wang, T.; Xiao, G.; Xie, Y. Large-Scale Profiling of RBP-circRNA Interactions from Public CLIP-Seq Datasets. Genes 2020, 11, 54.
Abstract
Circular RNAs are a special type of RNAs which 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 are 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- circRNAs interactions. In conclusion, this is one of the first few studies to investigate circRNAs and their binding partners through repurposing CLIP-Seq datasets to our knowledge, and we hope our work will become a valuable resource for future studies into the biogenesis and function of circRNAs. Clirc software is available at https://github.com/Minzhe/Clirc
Keywords
Circ-RNA; CLIP-Seq; RBP
Subject
Computer Science and Mathematics, Probability and Statistics
Copyright: This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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