Discovery of Proteinâ€“lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets

Jun-Hao Li,Wen-Ju Sun,Hui Zhou,Liang-Hu Qu,Shun Liu,Jie Wu,Jian-Hua Yang,Ling-Ling Zheng,Ze-Lin Wang

doi:10.3389/fbioe.2014.00088

Jun-Hao Li, Wen-Ju Sun + Show 7 more

Open Access

https://doi.org/10.3389/fbioe.2014.00088

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Abstract

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, physiological, and pathological processes. However, the precise mechanism and functions of most of lncRNAs remain largely unknown. Recent advances in high-throughput sequencing of immunoprecipitated RNAs after cross-linking (CLIP-Seq) provide powerful ways to identify biologically relevant protein–lncRNA interactions. In this study, by analyzing millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies, we identified 22,735 RBP–lncRNA regulatory relationships. We found that one single lncRNA will generally be bound and regulated by one or multiple RBPs, the combination of which may coordinately regulate gene expression. We also revealed the expression correlation of these interaction networks by mining expression profiles of over 6000 normal and tumor samples from 14 cancer types. Our combined analysis of CLIP-Seq data and genome-wide association studies data discovered hundreds of disease-related single nucleotide polymorphisms resided in the RBP binding sites of lncRNAs. Finally, we developed interactive web implementations to provide visualization, analysis, and downloading of the aforementioned large-scale datasets. Our study represented an important step in identification and analysis of RBP–lncRNA interactions and showed that these interactions may play crucial roles in cancer and genetic diseases.

Highlights

Despite that the majority of RNA-binding proteins (RBPs) binding sites were mapped to protein-coding genes, on average 1.1% of RBP binding sites lay within exons of human long non-coding RNAs (lncRNAs)
By analyzing a large set of RBP binding sites derived from all available CLIP-Seq experimental techniques (PAR-CLIP, HITS-CLIP, iCLIP, CLASH), we have shown extensive and complex RBP–lncRNA interaction networks (Figure 1)
RBP–lncRNA interactions identified by low stringent immunoprecipitation of non-cross-linked RNA–protein complexes, such as RIP-Chip and RIP-Seq, may contain indirect binding relationships (Konig et al, 2011)

Summary

Introduction

Mammalian genomes encode thousands of long non-coding RNAs (lncRNAs) (Wang and Chang, 2011; Guttman and Rinn, 2012). lncRNAs play important roles in a variety of biological processes that have been implicated in regulating tumorigenesis through interaction with RNA-binding proteins (RBPs) (Konig et al, 2011; Wang and Chang, 2011; Guttman and Rinn, 2012; Ulitsky and Bartel, 2013). LncRNAs play important roles in a variety of biological processes that have been implicated in regulating tumorigenesis through interaction with RNA-binding proteins (RBPs) (Konig et al, 2011; Wang and Chang, 2011; Guttman and Rinn, 2012; Ulitsky and Bartel, 2013). Increasing evidence suggests that many RBP–lncRNA interactions play important roles in correct transcriptional regulation (Konig et al, 2011; Wang and Chang, 2011; Guttman and Rinn, 2012; Ulitsky and Bartel, 2013). Deciphering the interactions between hundreds of RBPs and thousands of lncRNAs remains a daunting challenge

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