Journal Article

The landscape of long noncoding RNAs in the human transcriptome

Zhao, Shuang, Poliakov, Anton, Cao, Xuhong, Evans, Joseph R, Beer, David G, Iyer, Matthew K, Barrette, Terrence R, Robinson, Dan R, Wu, Yi-Mi, Malik, Rohit, Hosono, Yasuyuki, Prensner, John R, Chinnaiyan, Arul M, Dhanasekaran, Saravana M, Sahu, Anirban, Singhal, Udit, Feng, Felix Y, Niknafs, Yashar S, Iyer, Hariharan K

2015

Overview

Arul Chinnaiyan and colleagues report the curation of 7,256 RNA sequencing libraries from tumors, normal tissues and cell lines. They find 58,648 lncRNAs, of which 79% are previously unnannotated. Long noncoding RNAs (lncRNAs) are emerging as important regulators of tissue physiology and disease processes including cancer. To delineate genome-wide lncRNA expression, we curated 7,256 RNA sequencing (RNA-seq) libraries from tumors, normal tissues and cell lines comprising over 43 Tb of sequence from 25 independent studies. We applied ab initio assembly methodology to this data set, yielding a consensus human transcriptome of 91,013 expressed genes. Over 68% (58,648) of genes were classified as lncRNAs, of which 79% were previously unannotated. About 1% (597) of the lncRNAs harbored ultraconserved elements, and 7% (3,900) overlapped disease-associated SNPs. To prioritize lineage-specific, disease-associated lncRNA expression, we employed non-parametric differential expression testing and nominated 7,942 lineage- or cancer-associated lncRNA genes. The lncRNA landscape characterized here may shed light on normal biology and cancer pathogenesis and may be valuable for future biomarker development.

• Publisher: Nature Publishing Group US,Nature Publishing Group
• Subject: 38/91 / 631/114 / Agriculture / analysis / Animal Genetics and Genomics / Bioinformatics / Biomedicine / Cancer / Cancer Research / Cell Line / Cell Line, Tumor / Data processing / Datasets / Dynamic programming / Gene Expression / Gene Function / Genetic aspects / Genomes / Genomics / Grants / Human Genetics / Humans / Molecular biology / Neoplasms - genetics / Physiological aspects / Prostate cancer / Quality control / Risk factors / RNA / RNA, Long Noncoding - genetics / Sequence Analysis, RNA - methods / Studies / Transcriptome