The characteristic landscape of lncRNAs classified by RBP–lncRNA interactions across 10 cancers

Abstract

RNA-binding proteins (RBPs) are key regulators of gene expression. Some long non-coding RNAs (lncRNAs) affect gene expression by interacting with RBPs. However, whether this influences the biological characteristics of lncRNAs in diseases still remains unknown. Here, we classify lncRNAs into two categories, using the interaction information between lncRNAs and RBPs: the lncRNAs that interact with RBPs (Rlncs) and the lncRNAs that do not interact with RBPs (NRlncs). Then we systematically analyze the basic attributes and functions of the two categories of lncRNAs across 10 cancers. By comparing the two categories, we find that the attributes of Rlncs are significantly higher than those of NRlncs in different aspects such as expression level, protein-coding potential, and evolutionary conservation. Furthermore, functional enrichment analysis reveals that the two categories of lncRNAs are involved in different functions and biological pathways. Finally, the prognostic analysis results suggest that the two categories of lncRNAs affect the overall survival of patients through participating in different functions. Our systematic characterization of Rlncs and NRlncs provides a new perspective for understanding the role of lncRNAs, and improves knowledge of cancer biology.