Discovering circRNA-microRNA Interactions from CLIP-Seq Data

Abstract

Circular RNAs (circRNAs) represent an abundant group of noncoding RNAs in eukaryotes and are emerging as important regulatory molecules in physiological and pathological processes. However, the precise mechanisms and functions of most of circRNAs remain largely unknown. In this chapter, we describe how to identify circRNA-microRNA interactions from Argonaute (AGO) cross-linking and immunoprecipitation followed by sequencing (CLIP-Seq) and RNA-Seq data using starBase platform and software. We developed three stand-alone computational software, including circSeeker, circAnno, and clipSearch, to identify and annotate circRNAs and their interactions with microRNAs (miRNAs). In addition, we developed interactive Web applications to evaluate circRNA-miRNA interactions identified from CLIP-Seq data and discover the miRNA-sponge circRNAs. starBase platform provides a genome browser to comparatively analyze these interactions at multiple levels. As a means of comprehensively integrating CLIP-Seq and RNA-Seq data, starBase platform is expected to reveal the regulatory networks involving miRNAs and circRNAs. The software and platform are available at http://starbase.sysu.edu.cn/circTools.php.

Keywords: CLIP-Seq; Interactome; RNA-Seq; circRNA; miRNA sponge; microRNA.