Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers
Xiaohui Yan,Xiaohui Yan,Zhongyi Hu,Yi Feng,Xiaowen Hu,Jiao Yuan,Sihai Dave Zhao,Youyou Zhang,Lu Yang,Lu Yang,Weiwei Shan,Weiwei Shan,Qun He,Lingling Fan,Lingling Fan,Lana E. Kandalaft,Lana E. Kandalaft,Janos L. Tanyi,Chunsheng Li,Chao-Xing Yuan,Dongmei Zhang,Dongmei Zhang,Huiqing Yuan,Keqin Hua,Yiling Lu,Dionyssios Katsaros,Qihong Huang,Kathleen T. Montone,Yi Fan,George Coukos,Jeff Boyd,Anil K. Sood,Timothy R. Rebbeck,Gordon B. Mills,Chi V. Dang,Lin Zhang +35 more
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TLDR
A comprehensive analysis of lncRNA alterations at transcriptional, genomic, and epigenetic levels in 5,037 human tumor specimens across 13 cancer types from The Cancer Genome Atlas suggests that the expression and dysregulation of lNCRNAs are highly cancer type specific compared with protein-coding genes.About:
This article is published in Cancer Cell.The article was published on 2015-10-12 and is currently open access. It has received 559 citations till now.read more
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Journal ArticleDOI
Long Noncoding RNAs in Cancer Pathways
Adam M. Schmitt,Howard Y. Chang +1 more
TL;DR: It is understood that lncRNAs drive many important cancer phenotypes through their interactions with other cellular macromolecules including DNA, protein, and RNA, making these molecules attractive targets for therapeutic intervention in the fight against cancer.
Journal ArticleDOI
Functional Classification and Experimental Dissection of Long Noncoding RNAs
Florian Kopp,Joshua T. Mendell +1 more
TL;DR: This review categorizes lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and proposes an experimental approach to dissect lncRNAs activity based on these classifications.
Journal ArticleDOI
Long Noncoding RNA and Cancer: A New Paradigm.
TL;DR: The emerging functions and association of lncRNAs in different types of cancer and their potential implications in cancer diagnosis and therapy are reviewed.
A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response
Maite Huarte,Mitchell Guttman,Mitchell Guttman,David M. Feldser,Manuel Garber,Magdalena J. Koziol,Magdalena J. Koziol,Daniela Kenzelmann-Broz,Ahmad M. Khalil,Ahmad M. Khalil,Or Zuk,Ido Amit,Michal Rabani,Laura D. Attardi,Aviv Regev,Aviv Regev,Eric S. Lander,Eric S. Lander,Eric S. Lander,Tyler Jacks,John L. Rinn,John L. Rinn +21 more
TL;DR: In this paper, the identification of lincRNAs (lincRNA-p21) that serve as a repressor in p53-dependent transcriptional responses was reported, and the observed transcriptional repression was mediated through the physical association with hnRNP-K at repressed genes and regulation of p53 mediates apoptosis.
Journal ArticleDOI
The functions and unique features of long intergenic non-coding RNA.
TL;DR: Long intergenic non-coding RNA genes have diverse features that distinguish them from mRNA-encoding genes and exercise functions such as remodelling chromatin and genome architecture, RNA stabilization and transcription regulation, including enhancer-associated activity.
References
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Journal ArticleDOI
Long non-coding RNAs: insights into functions
TL;DR: The rapidly advancing field of long ncRNAs is reviewed, describing their conservation, their organization in the genome and their roles in gene regulation, and the medical implications.
Journal ArticleDOI
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien,Rory Johnson,Giovanni Bussotti,Andrea Tanzer,Sarah Djebali,Hagen Tilgner,Gregory Guernec,David C. Martin,Angelika Merkel,David G. Knowles,Julien Lagarde,Lavanya Veeravalli,Xiaoan Ruan,Yijun Ruan,Timo Lassmann,Piero Carninci,James B. Brown,Leonard Lipovich,José M. González,Mark G. Thomas,Carrie A. Davis,Ramin Shiekhattar,Thomas R. Gingeras,Tim Hubbard,Cedric Notredame,Jennifer Harrow,Roderic Guigó +26 more
TL;DR: The most complete human lncRNA annotation to date is presented, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts, and expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes.
Journal ArticleDOI
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
Mitchell Guttman,Ido Amit,Manuel Garber,Courtney French,Michael F. Lin,David M. Feldser,Maite Huarte,Maite Huarte,Or Zuk,Bryce W. Carey,John P. Cassady,Moran N. Cabili,Rudolf Jaenisch,Tarjei S. Mikkelsen,Tyler Jacks,Nir Hacohen,Bradley E. Bernstein,Bradley E. Bernstein,Manolis Kellis,Manolis Kellis,Aviv Regev,John L. Rinn,John L. Rinn,John L. Rinn,Eric S. Lander +24 more
TL;DR: It is demonstrated that specific lincRNAs are transcriptionally regulated by key transcription factors in these processes such as p53, NFκB, Sox2, Oct4 (also known as Pou5f1) and Nanog, defining a unique collection of functional linc RNAs that are highly conserved and implicated in diverse biological processes.
Journal ArticleDOI
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
Moran N. Cabili,Cole Trapnell,Cole Trapnell,Loyal A. Goff,Magdalena J. Koziol,Magdalena J. Koziol,Barbara Tazon-Vega,Barbara Tazon-Vega,Aviv Regev,John L. Rinn,John L. Rinn +10 more
TL;DR: It is found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that l incRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes.
Journal ArticleDOI
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Philipp Kapranov,Jill Cheng,Sujit Dike,David A. Nix,Radharani Duttagupta,Aarron T. Willingham,Peter F. Stadler,Jana Hertel,Jörg Hackermüller,Ivo L. Hofacker,Ian Bell,Evelyn Cheung,Jorg Drenkow,Erica Dumais,Sandeep Patel,Gregg Helt,Madhavan Ganesh,Srinka Ghosh,Antonio Piccolboni,Victor Sementchenko,Hari Tammana,Thomas R. Gingeras +21 more
TL;DR: Three potentially functional classes of RNAs have been identified, two of which are syntenically conserved and correlate with the expression state of protein-coding genes and support a highly interleaved organization of the human transcriptome.
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