The landscape of long noncoding RNAs in the human transcriptome

被引：2210

作者：

Iyer, Matthew K. ^{[1
,2
]}

Niknafs, Yashar S. ^{[1
,3
]}

Malik, Rohit ^{[1
,4
]}

Singhal, Udit ^{[1
,5
]}

Sahu, Anirban ^{[1
,4
]}

Hosono, Yasuyuki ^{[1
]}

Barrette, Terrence R. ^{[1
]}

Prensner, John R. ^{[1
]}

Evans, Joseph R. ^{[1
,6
]}

Zhao, Shuang ^{[1
,6
]}

Poliakov, Anton ^{[1
]}

Cao, Xuhong ^{[1
,5
]}

Dhanasekaran, Saravana M. ^{[1
,4
]}

Wu, Yi-Mi ^{[1
]}

Robinson, Dan R. ^{[1
]}

Beer, David G. ^{[6
,7
]}

Feng, Felix Y. ^{[1
,6
,8
]}

Iyer, Hariharan K. ^{[9
]}

Chinnaiyan, Arul M. ^{[1
,2
,4
,5
,8
,10
]}

机构：

[1] Univ Michigan, Michigan Ctr Translat Pathol, Ann Arbor, MI 48109 USA

[2] Dept Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[3] Univ Michigan, Dept Cellular & Mol Biol, Ann Arbor, MI 48109 USA

[4] Univ Michigan, Dept Pathol, Ann Arbor, MI 48109 USA

[5] Univ Michigan, Howard Hughes Med Inst, Ann Arbor, MI 48109 USA

[6] Univ Michigan, Dept Radiat Oncol, Ann Arbor, MI 48109 USA

[7] Univ Michigan, Dept Surg, Thorac Surg Sect, Ann Arbor, MI 48109 USA

[8] Univ Michigan, Comprehens Canc Ctr, Ann Arbor, MI 48109 USA

[9] Colorado State Univ, Dept Stat, Ft Collins, CO 80523 USA

[10] Univ Michigan, Dept Urol, Ann Arbor, MI 48109 USA

来源：

NATURE GENETICS | 2015年 / 47卷 / 03期

基金：

美国国家卫生研究院;

关键词：

GENOME-WIDE ASSOCIATION; PROSTATE-CANCER; MUTATIONAL LANDSCAPE; GENE; REVEALS; DATABASE; EVOLUTION; SEQ; RECONSTRUCTION; SUSCEPTIBILITY;

D O I：

10.1038/ng.3192

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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.

引用

页码：199 / +

页数：13

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