Discovering circRNA-microRNA interactions from CLIP-Seq and RNA-Seq data

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, researchers from the South China University of Technology 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. They developed three stand-alone computational software, including circSeeker, circAnno, and clipSearch, to identify and annotate circRNAs and their interactions with microRNAs (miRNAs). In addition, the researchers 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.

 Basic framework for identifying circRNA-miRNA interactions from CLIP-Seq and RNA-Seq data

rna-seq

Stand-alone software for identifying the circRNAs and their interactions with miRNAs are provided in starBase platform. All results generated by this framework are displayed in the visual browser and web page

Availability  – The software and platform are available at – http://starbase.sysu.edu.cn/circTools.php

Zhang XQ, Yang JH. (2018) Discovering circRNA-microRNA Interactions from CLIP-Seq Data. Methods Mol Biol 1724:193-207. [abstract]

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