Journal
NATURE GENETICS
Volume 47, Issue 3, Pages 199-+Publisher
NATURE PORTFOLIO
DOI: 10.1038/ng.3192
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Funding
- US National Institutes of Health Prostate Specialized Program of Research Excellence [P50 CA69568]
- Early Detection Research Network [UO1 CA111275]
- US National Institutes of Health [R01 CA132874, RO1 CA154365]
- US Department of Defense [PC100171]
- Prostate Cancer Foundation
- Howard Hughes Medical Institute
- Prostate Cancer Foundation Young Investigator Award
- US Department of Defense Post-Doctoral Fellowship [W81XWH-13-1-0284]
- University of Michigan Cellular and Molecular Biology National Research Service Award Institutional Predoctoral Training Grant
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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.
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