The functions and unique features of long intergenic non-coding RNA

被引:1077
作者
Ransohoff, Julia D. [1 ]
Wei, Yuning [1 ]
Khavari, Paul A. [1 ,2 ]
机构
[1] Stanford Univ, Sch Med, Program Epithelial Biol, Stanford, CA 94305 USA
[2] Vet Affairs Palo Alto Healthcare Syst, Palo Alto, CA 94304 USA
基金
美国国家卫生研究院;
关键词
X-CHROMOSOME INACTIVATION; GENOME-WIDE ANALYSIS; EMBRYONIC STEM-CELLS; OPEN READING FRAMES; GENE-EXPRESSION; MESSENGER-RNA; TRANSCRIPTIONAL ACTIVITY; XIST RNA; BINDING PROTEINS; ACTIVE CHROMATIN;
D O I
10.1038/nrm.2017.104
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Long intergenic non-coding RNA (lincRNA) 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. Some genes currently annotated as encoding lincRNAs include small open reading frames (smORFs) and encode functional peptides and thus may be more properly classified as coding RNAs. lincRNAs may broadly serve to fine-tune the expression of neighbouring genes with remarkable tissue specificity through a diversity of mechanisms, highlighting our rapidly evolving understanding of the non-coding genome.
引用
收藏
页码:143 / 157
页数:15
相关论文
共 166 条
[21]   Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions [J].
Chu, Ci ;
Qu, Kun ;
Zhong, Franklin L. ;
Artandi, Steven E. ;
Chang, Howard Y. .
MOLECULAR CELL, 2011, 44 (04) :667-678
[22]   Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse [J].
Church, Deanna M. ;
Goodstadt, Leo ;
Hillier, LaDeana W. ;
Zody, Michael C. ;
Goldstein, Steve ;
She, Xinwe ;
Bult, Carol J. ;
Agarwala, Richa ;
Cherry, Joshua L. ;
DiCuccio, Michael ;
Hlavina, Wratko ;
Kapustin, Yuri ;
Meric, Peter ;
Maglott, Donna ;
Birtle, Zoe ;
Marques, Ana C. ;
Graves, Tina ;
Zhou, Shiguo ;
Teague, Brian ;
Potamousis, Konstantinos ;
Churas, Christopher ;
Place, Michael ;
Herschleb, Jill ;
Runnheim, Ron ;
Forrest, Daniel ;
Amos-Landgraf, James ;
Schwartz, David C. ;
Cheng, Ze ;
Lindblad-Toh, Kerstin ;
Eichler, Evan E. ;
Ponting, Chris P. .
PLOS BIOLOGY, 2009, 7 (05)
[23]   Genome-wide analysis of long noncoding RNA stability [J].
Clark, Michael B. ;
Johnston, Rebecca L. ;
Inostroza-Ponta, Mario ;
Fox, Archa H. ;
Fortini, Ellen ;
Moscato, Pablo ;
Dinger, Marcel E. ;
Mattick, John S. .
GENOME RESEARCH, 2012, 22 (05) :885-898
[24]   Classification and function of small open reading frames [J].
Couso, Juan-Pablo ;
Patraquim, Pedro .
NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2017, 18 (09) :575-589
[25]  
D'Lima NG, 2017, NAT CHEM BIOL, V13, P174, DOI [10.1038/NCHEMBIO.2249, 10.1038/nchembio.2249]
[26]   Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture [J].
Darrow, Emily M. ;
Huntley, Miriam H. ;
Dudchenko, Olga ;
Stamenova, Elena K. ;
Durand, Neva C. ;
Sun, Zhuo ;
Huang, Su-Chen ;
Sanborn, Adrian L. ;
Machol, Ido ;
Shamim, Muhammad ;
Seberg, Andrew P. ;
Lander, Eric S. ;
Chadwick, Brian P. ;
Aiden, Erez Lieberman .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (31) :E4504-E4512
[27]   The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression [J].
Derrien, Thomas ;
Johnson, Rory ;
Bussotti, Giovanni ;
Tanzer, Andrea ;
Djebali, Sarah ;
Tilgner, Hagen ;
Guernec, Gregory ;
Martin, David ;
Merkel, Angelika ;
Knowles, David G. ;
Lagarde, Julien ;
Veeravalli, Lavanya ;
Ruan, Xiaoan ;
Ruan, Yijun ;
Lassmann, Timo ;
Carninci, Piero ;
Brown, James B. ;
Lipovich, Leonard ;
Gonzalez, Jose M. ;
Thomas, Mark ;
Davis, Carrie A. ;
Shiekhattar, Ramin ;
Gingeras, Thomas R. ;
Hubbard, Tim J. ;
Notredame, Cedric ;
Harrow, Jennifer ;
Guigo, Roderic .
GENOME RESEARCH, 2012, 22 (09) :1775-1789
[28]   Tyrosine phosphorylation of RNA Polymerase II CTD is associated with antisense promoter transcription and active enhancers in mammalian cells [J].
Descostes, Nicolas ;
Heidemann, Martin ;
Spinelli, Lionel ;
Schueller, Roland ;
Maqbool, Muhammad Ahmad ;
Fenouil, Romain ;
Koch, Frederic ;
Innocenti, Charlene ;
Gut, Marta ;
Gut, Ivo ;
Eick, Dirk ;
Andrau, Jean-Christophe .
ELIFE, 2014, 3
[29]   The four dimensions of noncoding RNA conservation [J].
Diederichs, Sven .
TRENDS IN GENETICS, 2014, 30 (04) :121-123
[30]   LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint [J].
Dimitrova, Nadya ;
Zamudio, Jesse R. ;
Jong, Robyn M. ;
Soukup, Dylan ;
Resnick, Rebecca ;
Sarma, Kavitha ;
Ward, Amanda J. ;
Raj, Arjun ;
Lee, Jeannie T. ;
Sharp, Phillip A. ;
Jacks, Tyler .
MOLECULAR CELL, 2014, 54 (05) :777-790