Abstract
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.
Highlights
Circular RNAs are a mysterious type of RNA that was discovered more than 30 years ago
Common analysis methods for identifying circRNAs will truncate these short Cross-linking immunoprecipitation (CLIP)-Seq reads into even shorter segments for alignment, which could lead to ambiguous alignment to multiple places in the genome or no confident alignment at all
We tried to create a pseudo reference alignment library in which all circRNAs are represented as continuous sequences so that CLIP-Seq reads can be aligned as a whole
Summary
Circular RNAs (circRNAs) are a mysterious type of RNA that was discovered more than 30 years ago. (3) splicing factors regulate the formation of circRNAs [3,4]. (2) reverse complementary sequences in flanking introns are necessary for the formation of some circRNAs, since they can bring two discontinuous regions of RNAs close together for splicing and joining, but may not for some circRNAs [3]. In addition to their formation, the understanding of the functions of circRNAs is lacking. Conn et al and You et al reported that the expression of circRNAs is regulated during
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