The landscape of long noncoding RNAs in the human transcriptome

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

Research output: Contribution to journalArticlepeer-review

1774 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)199-208
Number of pages10
JournalNature Genetics
Volume47
Issue number3
DOIs
Publication statusPublished - Feb 25 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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