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Nat Genet. 2015 Mar;47(3):199-208. doi: 10.1038/ng.3192. Epub 2015 Jan 19.

The landscape of long noncoding RNAs in the human transcriptome.

Author information

1
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan, USA.
2
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan, USA.
3
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA.
4
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA.
5
Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA.
6
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA.
7
1] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA. [2] Section of Thoracic Surgery, Department of Surgery, University of Michigan, Ann Arbor, Michigan, USA.
8
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Radiation Oncology, University of Michigan, Ann Arbor, Michigan, USA. [3] Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA.
9
Department of Statistics, Colorado State University, Fort Collins, Colorado, USA.
10
1] Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, Michigan, USA. [2] Department of Computational Medicine and Bioinformatics, Ann Arbor, Michigan, USA. [3] Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA. [4] Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan, USA. [5] Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan, USA. [6] Department of Urology, University of Michigan, Ann Arbor, Michigan, USA.

Abstract

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.

PMID:
25599403
PMCID:
PMC4417758
DOI:
10.1038/ng.3192
[Indexed for MEDLINE]
Free PMC Article

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