Long non-coding RNAs in stem cell pluripotency

被引:20
作者
Ng, Shi-Yan [1 ]
Stanton, Lawrence W. [1 ,2 ,3 ]
机构
[1] Genome Inst Singapore, Stem Cell & Dev Biol Grp, Singapore, Singapore
[2] Natl Univ Singapore, Dept Biol Sci, Singapore 117548, Singapore
[3] Nanyang Technol Univ, Sch Biol Sci, Singapore, Singapore
关键词
GENE-EXPRESSION; MESSENGER-RNAS; ANTISENSE RNA; SELF-RENEWAL; DIFFERENTIATION; CHROMATIN; MOUSE; TSIX; TRANSCRIPTION; GENOME;
D O I
10.1002/wrna.1146
中图分类号
Q2 [细胞生物学];
学科分类号
071009 ; 090102 ;
摘要
Pluripotency refers to the self-renewal of undifferentiated embryonic stem cells (ESCs), and is maintained by a tightly regulated gene regulatory network involving an intricate interplay between transcription factors and their genomic targets, as well as epigenetic processes that influence gene expression. Long non-coding RNAs (lncRNAs) are newly discovered members of gene regulatory networks that govern a variety of cell functions. Defined as RNA transcripts larger than 200 nucleotides, lncRNAs have little or no protein-coding capacity and have been shown to act via various mechanisms, and are important in a variety of biological functions. Recent reports have described the discovery of pluripotent lncRNAs involved in the maintenance and induction of stem cell pluripotency. Here, we discuss how lncRNAs may integrate into the pluripotency network, as well as prominent questions in this emerging field. WIREs RNA 2013, 4:121128. doi: 10.1002/wrna.1146 For further resources related to this article, please visit the WIREs website. Conflict of interest: The authors declare no conflict of interest.
引用
收藏
页码:121 / 128
页数:8
相关论文
共 59 条
[1]   Complex architecture and regulated expression of the Sox2ot locus during vertebrate development [J].
Amaral, Paulo P. ;
Neyt, Christine ;
Wilkins, Simon J. ;
Askarian-Amiri, Marjan E. ;
Sunkin, Susan M. ;
Perkins, Andrew C. ;
Mattick, John S. .
RNA, 2009, 15 (11) :2013-2027
[2]   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
[3]   Dicer is essential for mouse development [J].
Bernstein, E ;
Kim, SY ;
Carmell, MA ;
Murchison, EP ;
Alcorn, H ;
Li, MZ ;
Mills, AA ;
Elledge, SJ ;
Anderson, KV ;
Hannon, GJ .
NATURE GENETICS, 2003, 35 (03) :215-217
[4]   Global identification of human transcribed sequences with genome tiling arrays [J].
Bertone, P ;
Stolc, V ;
Royce, TE ;
Rozowsky, JS ;
Urban, AE ;
Zhu, XW ;
Rinn, JL ;
Tongprasit, W ;
Samanta, M ;
Weissman, S ;
Gerstein, M ;
Snyder, M .
SCIENCE, 2004, 306 (5705) :2242-2246
[5]   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
[6]   Changing Nuclear Landscape and Unique PML Structures During Early Epigenetic Transitions of Human Embryonic Stem Cells [J].
Butler, John T. ;
Hall, Lisa L. ;
Smith, Kelly P. ;
Lawrence, Jeanne B. .
JOURNAL OF CELLULAR BIOCHEMISTRY, 2009, 107 (04) :609-621
[7]   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
[8]   A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA [J].
Cesana, Marcella ;
Cacchiarelli, Davide ;
Legnini, Ivano ;
Santini, Tiziana ;
Sthandier, Olga ;
Chinappi, Mauro ;
Tramontano, Anna ;
Bozzoni, Irene .
CELL, 2011, 147 (02) :358-369
[9]  
Chakraborty D, 2012, NAT METHODS, V9, P360, DOI [10.1038/nmeth.1894, 10.1038/NMETH.1894]
[10]   Comparative Analysis of Human Protein-Coding and Noncoding RNAs between Brain and 10 Mixed Cell Lines by RNA-Seq [J].
Chen, Geng ;
Yin, Kangping ;
Shi, Leming ;
Fang, Yuanzhang ;
Qi, Ya ;
Li, Peng ;
Luo, Jian ;
He, Bing ;
Liu, Mingyao ;
Shi, Tieliu .
PLOS ONE, 2011, 6 (11)