Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

被引:192
作者
Novikova, Irina V. [1 ]
Hennelly, Scott P. [1 ]
Tung, Chang-Shung [1 ]
Sanbonmatsu, Karissa Y. [1 ]
机构
[1] Los Alamos Natl Lab, Los Alamos, NM 87545 USA
关键词
long non-coding RNA; lncRNA; lincRNA; lncRNA structure; epigenetics; CONTROLS GENE-EXPRESSION; GROUP-II INTRONS; SECONDARY STRUCTURE; CRYSTAL-STRUCTURE; X-CHROMOSOME; STRUCTURE PREDICTION; ESCHERICHIA-COLI; TELOMERASE RNA; RIBOSOME; BINDING;
D O I
10.1016/j.jmb.2013.02.030
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
070307 [化学生物学]; 071010 [生物化学与分子生物学];
摘要
Novel, profound and unexpected roles of long non-coding RNAs (lncRNAs) are emerging in critical aspects of gene regulation. Thousands of lncRNAs have been recently discovered in a wide range of mammalian systems, related to development, epigenetics, cancer, brain function and hereditary disease. The structural biology of these lncRNAs presents a brave new RNA world, which may contain a diverse zoo of new architectures and mechanisms. While structural studies of lncRNAs are in their infancy, we describe existing structural data for lncRNAs, as well as crystallographic studies of other RNA machines and their implications for lncRNAs. We also discuss the importance of dynamics in RNA machine mechanism. Determining commonalities between lncRNA systems will help elucidate the evolution and mechanistic role of lncRNAs in disease, creating a structural framework necessary to pursue lncRNA-based therapeutics. Published by Elsevier Ltd.
引用
收藏
页码:3731 / 3746
页数:16
相关论文
共 135 条
[1]
Crystal structure of a self-splicing group I intron with both exons [J].
Adams, PL ;
Stahley, MR ;
Kosek, AB ;
Wang, JM ;
Strobel, SA .
NATURE, 2004, 430 (6995) :45-50
[2]
APPELT K, 1981, J BIOL CHEM, V256, P1787
[3]
Telomeric repeat-containing RNA and RNA surveillance factors at mammalian chromosome ends [J].
Azzalin, Claus M. ;
Reichenbach, Patrick ;
Khoriauli, Lela ;
Giulotto, Elena ;
Lingner, Joachim .
SCIENCE, 2007, 318 (5851) :798-801
[4]
Long noncoding RNAs are rarely translated in two human cell lines [J].
Banfai, Balazs ;
Jia, Hui ;
Khatun, Jainab ;
Wood, Emily ;
Risk, Brian ;
Gundling, William E., Jr. ;
Kundaje, Anshul ;
Gunawardena, Harsha P. ;
Yu, Yanbao ;
Xie, Ling ;
Krajewski, Krzysztof ;
Strahl, Brian D. ;
Chen, Xian ;
Bickel, Peter ;
Giddings, Morgan C. ;
Brown, James B. ;
Lipovich, Leonard .
GENOME RESEARCH, 2012, 22 (09) :1646-1657
[5]
Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine [J].
Batey, RT ;
Gilbert, SD ;
Montange, RK .
NATURE, 2004, 432 (7015) :411-415
[6]
A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition [J].
Beltran, Manuel ;
Puig, Isabel ;
Pena, Cristina ;
Miguel Garcia, Jose ;
Belen Alvarez, Ana ;
Pena, Raul ;
Bonilla, Felix ;
Garcia de Herreros, Antonio .
GENES & DEVELOPMENT, 2008, 22 (06) :756-769
[7]
The Structure of the Eukaryotic Ribosome at 3.0 Å Resolution [J].
Ben-Shem, Adam ;
de Loubresse, Nicolas Garreau ;
Melnikov, Sergey ;
Jenner, Lasse ;
Yusupova, Gulnara ;
Yusupov, Marat .
SCIENCE, 2011, 334 (6062) :1524-1529
[8]
Distinctive structures between chimpanzee and human in a brain noncoding RNA [J].
Beniaminov, Artemy ;
Westhof, Eric ;
Krol, Alain .
RNA, 2008, 14 (07) :1270-1275
[9]
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression [J].
Bernard, Delphine ;
Prasanth, Kannanganattu V. ;
Tripathi, Vidisha ;
Colasse, Sabrina ;
Nakamura, Tetsuya ;
Xuan, Zhenyu ;
Zhang, Michael Q. ;
Sedel, Frederic ;
Jourdren, Laurent ;
Coulpier, Fanny ;
Triller, Antoine ;
Spector, David L. ;
Bessis, Alain .
EMBO JOURNAL, 2010, 29 (18) :3082-3093
[10]
RNAalifold: improved consensus structure prediction for RNA alignments [J].
Bernhart, Stephan H. ;
Hofacker, Ivo L. ;
Will, Sebastian ;
Gruber, Andreas R. ;
Stadler, Peter F. .
BMC BIOINFORMATICS, 2008, 9 (1)