Human Cancer Long Non-Coding RNA Transcriptomes

被引：306

作者：

Gibb, Ewan A. ^{[1
,2
]}

Vucic, Emily A. ^{[1
,2
]}

Enfield, Katey S. S. ^{[1
,3
]}

Stewart, Greg L. ^{[1
,3
]}

Lonergan, Kim M. ^{[1
]}

Kennett, Jennifer Y. ^{[1
,2
]}

Becker-Santos, Daiana D. ^{[1
,3
]}

MacAulay, Calum E. ^{[1
,2
,3
]}

Lam, Stephen ^{[1
]}

Brown, Carolyn J. ^{[1
,4
]}

Lam, Wan L. ^{[1
,2
,3
]}

机构：

[1] British Columbia Canc Agcy, Res Ctr, Vancouver, BC V5Z 4E6, Canada

[2] Univ British Columbia, Dept Pathol & Lab Med, Vancouver, BC V5Z 1M9, Canada

[3] Univ British Columbia, Interdisciplinary Oncol Program, Vancouver, BC V5Z 1M9, Canada

[4] Univ British Columbia, Dept Med Genet, Vancouver, BC V5Z 1M9, Canada

来源：

PLOS ONE | 2011年 / 6卷 / 10期

基金：

美国国家卫生研究院;

关键词：

HOUSEKEEPING GENES; FUNCTIONAL-ROLE; CELL; EXPRESSION; IDENTIFICATION; INACTIVATION; CHROMATIN; MEG3; ASSOCIATION; CARCINOMA;

D O I：

10.1371/journal.pone.0025915

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];

摘要：

Once thought to be a part of the 'dark matter' of the genome, long non-coding RNAs (lncRNAs) are emerging as an integral functional component of the mammalian transcriptome. LncRNAs are a novel class of mRNA-like transcripts which, despite no known protein-coding potential, demonstrate a wide range of structural and functional roles in cellular biology. However, the magnitude of the contribution of lncRNA expression to normal human tissues and cancers has not been investigated in a comprehensive manner. In this study, we compiled 272 human serial analysis of gene expression (SAGE) libraries to delineate lncRNA transcription patterns across a broad spectrum of normal human tissues and cancers. Using a novel lncRNA discovery pipeline we parsed over 24 million SAGE tags and report lncRNA expression profiles across a panel of 26 different normal human tissues and 19 human cancers. Our findings show extensive, tissue-specific lncRNA expression in normal tissues and highly aberrant lncRNA expression in human cancers. Here, we present a first generation atlas for lncRNA profiling in cancer.

引用

页数：10

共 71 条

[1]

Regulation of X-chromosome inactivation by the X-inactivation centre [J].

Augui, Sandrine ;

Nora, Elphege P. ;

Heard, Edith .

NATURE REVIEWS GENETICS, 2011, 12 (06) :429-442

[2]

NCBI GEO: archive for functional genomics data sets-10 years on [J].

Barrett, Tanya ;

Troup, Dennis B. ;

Wilhite, Stephen E. ;

Ledoux, Pierre ;

Evangelista, Carlos ;

Kim, Irene F. ;

Tomashevsky, Maxim ;

Marshall, Kimberly A. ;

Phillippy, Katherine H. ;

Sherman, Patti M. ;

Muertter, Rolf N. ;

Holko, Michelle ;

Ayanbule, Oluwabukunmi ;

Yefanov, Andrey ;

Soboleva, Alexandra .

NUCLEIC ACIDS RESEARCH, 2011, 39 :D1005-D1010

[3]

Benetatos L, 2011, INT J CANC

[4]

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project [J].

Birney, Ewan ;

Stamatoyannopoulos, John A. ;

Dutta, Anindya ;

Guigo, Roderic ;

Gingeras, Thomas R. ;

Margulies, Elliott H. ;

Weng, Zhiping ;

Snyder, Michael ;

Dermitzakis, Emmanouil T. ;

Stamatoyannopoulos, John A. ;

Thurman, Robert E. ;

Kuehn, Michael S. ;

Taylor, Christopher M. ;

Neph, Shane ;

Koch, Christoph M. ;

Asthana, Saurabh ;

Malhotra, Ankit ;

Adzhubei, Ivan ;

Greenbaum, Jason A. ;

Andrews, Robert M. ;

Flicek, Paul ;

Boyle, Patrick J. ;

Cao, Hua ;

Carter, Nigel P. ;

Clelland, Gayle K. ;

Davis, Sean ;

Day, Nathan ;

Dhami, Pawandeep ;

Dillon, Shane C. ;

Dorschner, Michael O. ;

Fiegler, Heike ;

Giresi, Paul G. ;

Goldy, Jeff ;

Hawrylycz, Michael ;

Haydock, Andrew ;

Humbert, Richard ;

James, Keith D. ;

Johnson, Brett E. ;

Johnson, Ericka M. ;

Frum, Tristan T. ;

Rosenzweig, Elizabeth R. ;

Karnani, Neerja ;

Lee, Kirsten ;

Lefebvre, Gregory C. ;

Navas, Patrick A. ;

Neri, Fidencio ;

Parker, Stephen C. J. ;

Sabo, Peter J. ;

Sandstrom, Richard ;

Shafer, Anthony .

NATURE, 2007, 447 (7146) :799-816

[5]

THE PRODUCT OF THE H19 GENE MAY FUNCTION AS AN RNA [J].

BRANNAN, CI ;

DEES, EC ;

INGRAM, RS ;

TILGHMAN, SM .

MOLECULAR AND CELLULAR BIOLOGY, 1990, 10 (01) :28-36

[6]

The long and the short of noncoding RNAs [J].

Brosnan, Christopher A. ;

Voinnet, Olivier .

CURRENT OPINION IN CELL BIOLOGY, 2009, 21 (03) :416-425

[7]

A GENE FROM THE REGION OF THE HUMAN X-INACTIVATION CENTER IS EXPRESSED EXCLUSIVELY FROM THE INACTIVE X-CHROMOSOME [J].

BROWN, CJ ;

BALLABIO, A ;

RUPERT, JL ;

LAFRENIERE, RG ;

GROMPE, M ;

TONLORENZI, R ;

WILLARD, HF .

NATURE, 1991, 349 (6304) :38-44

[8]

Büschges R, 1999, BRAIN PATHOL, V9, P435

[9]

Long Noncoding RNAs, Chromatin, and Development [J].

Caley, Daniel P. ;

Pink, Ryan C. ;

Trujillano, Daniel ;

Carter, David R. F. .

THESCIENTIFICWORLDJOURNAL, 2010, 10 :90-102

[10]

The transcriptional landscape of the mammalian genome [J].

Carninci, P ;

Kasukawa, T ;

Katayama, S ;

Gough, J ;

Frith, MC ;

Maeda, N ;

Oyama, R ;

Ravasi, T ;

Lenhard, B ;

Wells, C ;

Kodzius, R ;

Shimokawa, K ;

Bajic, VB ;

Brenner, SE ;

Batalov, S ;

Forrest, ARR ;

Zavolan, M ;

Davis, MJ ;

Wilming, LG ;

Aidinis, V ;

Allen, JE ;

Ambesi-Impiombato, X ;

Apweiler, R ;

Aturaliya, RN ;

Bailey, TL ;

Bansal, M ;

Baxter, L ;

Beisel, KW ;

Bersano, T ;

Bono, H ;

Chalk, AM ;

Chiu, KP ;

Choudhary, V ;

Christoffels, A ;

Clutterbuck, DR ;

Crowe, ML ;

Dalla, E ;

Dalrymple, BP ;

de Bono, B ;

Della Gatta, G ;

di Bernardo, D ;

Down, T ;

Engstrom, P ;

Fagiolini, M ;

Faulkner, G ;

Fletcher, CF ;

Fukushima, T ;

Furuno, M ;

Futaki, S ;

Gariboldi, M .

SCIENCE, 2005, 309 (5740) :1559-1563

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