Modular regulatory principles of large non-coding RNAs

被引:1911
作者
Guttman, Mitchell [1 ,2 ]
Rinn, John L. [1 ,3 ]
机构
[1] Broad Inst MIT & Harvard, Cambridge, MA 02142 USA
[2] MIT, Dept Biol, Cambridge, MA 02139 USA
[3] Harvard Univ, Cambridge, MA 02138 USA
关键词
X-CHROMOSOME INACTIVATION; OPEN READING FRAMES; XIST RNA; TRANSCRIPTIONAL ACTIVITY; CHROMATIN STATE; GENE-EXPRESSION; HUMAN GENOME; STEM-CELLS; INTERGENIC TRANSCRIPTION; HISTONE MODIFICATION;
D O I
10.1038/nature10887
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
07 ; 0710 ; 09 ;
摘要
It is clear that RNA has a diverse set of functions and is more than just a messenger between gene and protein. The mammalian genome is extensively transcribed, giving rise to thousands of non-coding transcripts. Whether all of these transcripts are functional is debated, but it is evident that there are many functional large non-coding RNAs (ncRNAs). Recent studies have begun to explore the functional diversity and mechanistic role of these large ncRNAs. Here we synthesize these studies to provide an emerging model whereby large ncRNAs might achieve regulatory specificity through modularity, assembling diverse combinations of proteins and possibly RNA and DNA interactions.
引用
收藏
页码:339 / 346
页数:8
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[1]   High-resolution profiling of histone methylations in the human genome [J].
Barski, Artern ;
Cuddapah, Suresh ;
Cui, Kairong ;
Roh, Tae-Young ;
Schones, Dustin E. ;
Wang, Zhibin ;
Wei, Gang ;
Chepelev, Iouri ;
Zhao, Keji .
CELL, 2007, 129 (04) :823-837
[2]   MicroRNAs: Target Recognition and Regulatory Functions [J].
Bartel, David P. .
CELL, 2009, 136 (02) :215-233
[3]   Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin [J].
Bernstein, E ;
Duncan, EM ;
Masui, O ;
Gil, J ;
Heard, E ;
Allis, CD .
MOLECULAR AND CELLULAR BIOLOGY, 2006, 26 (07) :2560-2569
[4]   RETRACTED: The Noncoding RNA Mistral Activates Hoxa6 and Hoxa7 Expression and Stem Cell Differentiation by Recruiting MLL1 to Chromatin (Retracted Article) [J].
Bertani, Stephane ;
Sauer, Silvia ;
Bolotin, Eugene ;
Sauer, Frank .
MOLECULAR CELL, 2011, 43 (06) :1040-1046
[5]   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
[6]   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
[7]   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
[8]   THE PRODUCT OF THE MOUSE XIST GENE IS A 15 KB INACTIVE X-SPECIFIC TRANSCRIPT CONTAINING NO CONSERVED ORF AND LOCATED IN THE NUCLEUS [J].
BROCKDORFF, N ;
ASHWORTH, A ;
KAY, GF ;
MCCABE, VM ;
NORRIS, DP ;
COOPER, PJ ;
SWIFT, S ;
RASTAN, S .
CELL, 1992, 71 (03) :515-526
[9]   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
[10]   Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses [J].
Cabili, Moran N. ;
Trapnell, Cole ;
Goff, Loyal ;
Koziol, Magdalena ;
Tazon-Vega, Barbara ;
Regev, Aviv ;
Rinn, John L. .
GENES & DEVELOPMENT, 2011, 25 (18) :1915-1927