Identifying and functionally characterizing tissue-specific and ubiquitously expressed human lncRNAs

Abstract

// Chunjie Jiang 1, * , Yongsheng Li 1, * , Zheng Zhao 1, * , Jianping Lu 1 , Hong Chen 1 , Na Ding 1 , Guangjuan Wang 1 , Juan Xu 1 , Xia Li 1 1 College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China * These authors have contributed equally to this work Correspondence to: Xia Li, e-mail: lixia@hrbmu.edu.cn Juan Xu, e-mail: xujuanbiocc@ems.hrbmu.edu.cn Keywords: ubiquitously expressed lncRNAs, tissue-specific lncRNAs, genomic structure, epigenetic regulation, functional prediction Received: August 25, 2015     Accepted: December 26, 2015     Published: January 09, 2016 ABSTRACT Recent advances in transcriptome sequencing have made it possible to distinguish ubiquitously expressed long non-coding RNAs (UE lncRNAs) from tissue-specific lncRNAs (TS lncRNAs), thereby providing clues to their cellular functions. Here, we assembled and functionally characterized a consensus lncRNA transcriptome by curating hundreds of RNA-seq datasets across normal human tissues from 16 independent studies. In total, 1,184 UE and 2,583 TS lncRNAs were identified. These different lncRNA populations had several distinct features. Specifically, UE lncRNAs were associated with genomic compaction and highly conserved exons and promoter regions. We found that UE lncRNAs are regulated at the transcriptional level (with especially strong regulation of enhancers) and are associated with epigenetic modifications and post-transcriptional regulation. Based on these observations we propose a novel way to predict the functions of UE and TS lncRNAs through analysis of their genomic location and similarities in epigenetic modifications. Our characterization of UE and TS lncRNAs may provide a foundation for lncRNA genomics and the delineation of complex disease mechanisms.