Quantification of non-coding RNA target localization diversity and its application in cancers

• 来源期刊: 分子细胞生物学报（英文版）
• 年，卷（期）: 2018,（2）
• 页码范围: 130-138
• 页数: 9页
• 语种: 英文
• DOI: 10.1093/jmcb/mjy006

摘要

Subcellular localization is pivotal for RNAs and proteins to implement biological functions. The localization diversity of protein interactions has been studied as a crucial feature of proteins, considering that the protein-protein interactions take place in various subcellular locations. Nevertheless, the localization diversity of non-coding RNA (ncRNA) target proteins has not been systematically studied, especially its characteristics in cancers. In this study, we provide a new algorithm, non-coding RNA target localization coefficient (ncTALENT), to quantify the target localization diversity of ncRNAs based on the ncRNA-protein interaction and protein subcellular localization data. ncTALENT can be used to calculate the target localization coefficient of ncRNAs and measure how diversely their targets are distributed among the subcellular locations in various scenarios. We focus our study on long non-coding RNAs (IncRNAs), and our observations reveal that the target localization diversity is a primary characteristic of IncRNAs in different biotypes. Moreover, we found that IncRNAs in multiple cancers, differentially expressed cancer IncRNAs, and IncRNAs with multiple cancer target proteins are prone to have high target localization diversity. Furthermore, the analysis of gastric cancer helps us to obtain a better understanding that the target localization diversity of IncRNAs is an important feature closely related to clinical prognosis. Overall, we systematically studied the target localization diversity of the IncRNAs and uncovered its association with cancer.