Integrating Large-Scale RNA-Seq and CLIP-Seq Datasets Enables Study of lncRNA

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, researchers at Sun Yat-sen University analyzed millions of RNA-binding protein (RBP) binding sites from 117 CLIP-Seq datasets generated by 50 independent studies and identified 22,735 RBP-lncRNA regulatory relationships.

rna-seq

The GWAS-associated SNPs and binding sites of three RBPs in the locus of PVT1

The researchers 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. They 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, the researchers developed interactive web implementations to provide visualization, analysis, and downloading of the aforementioned large-scale datasets.

Availability – StarBase V2.0 is available at: http://starbase.sysu.edu.cn/rbpLncRNA.php

Li JH, Liu S, Zheng LL, Wu J, Sun WJ, Wang ZL, Zhou H, Qu LH, Yang JH. (2015) Discovery of Protein-lncRNA Interactions by Integrating Large-Scale CLIP-Seq and RNA-Seq Datasets. Front Bioeng Biotechnol 2:88. [article]

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