Discovering circRNA-microRNA Interactions from CLIP-Seq Data.

Xiao-Qin Zhang, Jian-Hua Yang
Author Information
  1. Xiao-Qin Zhang: School of Medicine, South China University of Technology, Guangzhou, People's Republic of China.
  2. Jian-Hua Yang: Key Laboratory of Gene Engineering of the Ministry of Education, Guangzhou, People's Republic of China. yangjh7@mail.sysu.edu.cn.

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

MeSH Term

Argonaute Proteins
Computational Biology
Cross-Linking Reagents
Gene Expression Regulation
Gene Regulatory Networks
High-Throughput Nucleotide Sequencing
Humans
Immunoprecipitation
MicroRNAs
RNA
RNA, Circular
Sequence Analysis, RNA
Software

Chemicals

Argonaute Proteins
Cross-Linking Reagents
MicroRNAs
RNA, Circular
RNA

Word Cloud

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