The Reality of Pervasive Transcription

被引:329
作者
Clark, Michael B. [1 ]
Amaral, Paulo P. [1 ]
Schlesinger, Felix J. [2 ]
Dinger, Marcel E. [1 ]
Taft, Ryan J. [1 ]
Rinn, John L. [3 ]
Ponting, Chris P. [4 ]
Stadler, Peter F. [5 ]
Morris, Kevin V. [6 ]
Morillon, Antonin [7 ]
Rozowsky, Joel S. [8 ]
Gerstein, Mark B. [8 ]
Wahlestedt, Claes [9 ]
Hayashizaki, Yoshihide [10 ]
Carninci, Piero [10 ]
Gingeras, Thomas R. [2 ]
Mattick, John S. [1 ]
机构
[1] Univ Queensland, Inst Mol Biosci, Brisbane, Qld, Australia
[2] Cold Spring Harbor Lab, Watson Sch Biol Sci, Cold Spring Harbor, NY 11724 USA
[3] Broad Inst, Cambridge, MA USA
[4] Univ Oxford, Dept Physiol Anat & Genet, MRC Funct Genom Unit, Oxford, England
[5] Univ Leipzig, Dept Comp Sci, Leipzig, Germany
[6] Scripps Res Inst, Dept Mol & Expt Med, La Jolla, CA 92037 USA
[7] Inst Curie, UMR3244, Paris, France
[8] Yale Univ, New Haven, CT USA
[9] Univ Miami, Miami, FL USA
[10] RIKEN Yokohama Inst, Omics Sci Ctr, Tsurumi Ku, Kanagawa, Japan
基金
英国医学研究理事会; 英国生物技术与生命科学研究理事会; 澳大利亚研究理事会;
关键词
LONG NONCODING RNAS; GENOME; EXPRESSION; REVEAL; IDENTIFICATION; ARCHITECTURE; NUMBERS; MAPS; SEQ;
D O I
10.1371/journal.pbio.1000625
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
[No abstract available]
引用
收藏
页数:6
相关论文
共 44 条
  • [1] Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays
    Agarwal, Ashish
    Koppstein, David
    Rozowsky, Joel
    Sboner, Andrea
    Habegger, Lukas
    Hillier, LaDeana W.
    Sasidharan, Rajkumar
    Reinke, Valerie
    Waterston, Robert H.
    Gerstein, Mark
    [J]. BMC GENOMICS, 2010, 11
  • [2] Noncoding RNA in development
    Amaral, Paulo P.
    Mattick, John S.
    [J]. MAMMALIAN GENOME, 2008, 19 (7-8) : 454 - 492
  • [3] Armour CD, 2009, NAT METHODS, V6, P647, DOI [10.1038/NMETH.1360, 10.1038/nmeth.1360]
  • [4] Equal Numbers of Neuronal and Nonneuronal Cells Make the Human Brain an Isometrically Scaled-Up Primate Brain
    Azevedo, Frederico A. C.
    Carvalho, Ludmila R. B.
    Grinberg, Lea T.
    Farfel, Jose Marcelo
    Ferretti, Renata E. L.
    Leite, Renata E. P.
    Jacob Filho, Wilson
    Lent, Roberto
    Herculano-Houzel, Suzana
    [J]. JOURNAL OF COMPARATIVE NEUROLOGY, 2009, 513 (05) : 532 - 541
  • [5] Pervasive transcription constitutes a new level of eukaryotic genome regulation
    Berretta, Julia
    Morillon, Antonin
    [J]. EMBO REPORTS, 2009, 10 (09) : 973 - 982
  • [6] Global identification of human transcribed sequences with genome tiling arrays
    Bertone, P
    Stolc, V
    Royce, TE
    Rozowsky, JS
    Urban, AE
    Zhu, XW
    Rinn, JL
    Tongprasit, W
    Samanta, M
    Weissman, S
    Gerstein, M
    Snyder, M
    [J]. SCIENCE, 2004, 306 (5705) : 2242 - 2246
  • [7] Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
    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
    [J]. NATURE, 2007, 447 (7146) : 799 - 816
  • [8] Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia
    Carninci, P
    Waki, K
    Shiraki, T
    Konno, H
    Shibata, K
    Itoh, M
    Aizawa, K
    Arakawa, T
    Ishii, Y
    Sasaki, D
    Bono, H
    Kondo, S
    Sugahara, Y
    Saito, R
    Osato, N
    Fukuda, S
    Sato, K
    Watahiki, A
    Hirozane-Kishikawa, T
    Nakamura, M
    Shibata, Y
    Yasunishi, A
    Kikuchi, N
    Yoshiki, A
    Kusakabe, M
    Gustincich, S
    Beisel, K
    Pavan, W
    Aidinis, V
    Nakagawara, A
    Held, WA
    Iwata, H
    Kono, T
    Nakauchi, H
    Lyons, P
    Wells, C
    Hume, DA
    Fagiolini, M
    Hensch, TK
    Brinkmeier, M
    Camper, S
    Hirota, J
    Mombaerts, P
    Muramatsu, M
    Okazaki, Y
    Kawai, J
    Hayashizaki, Y
    [J]. GENOME RESEARCH, 2003, 13 (6B) : 1273 - 1289
  • [9] The transcriptional landscape of the mammalian genome
    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
    [J]. SCIENCE, 2005, 309 (5740) : 1559 - 1563
  • [10] Genome-wide analysis of mammalian promoter architecture and evolution
    Carninci, Piero
    Sandelin, Albin
    Lenhard, Boris
    Katayama, Shintaro
    Shimokawa, Kazuro
    Ponjavic, Jasmina
    Semple, Colin A. M.
    Taylor, Martin S.
    Engström, Par G.
    Frith, Martin C.
    Forrest, Alistair R. R.
    Alkema, Wynand B.
    Tan, Sin Lam
    Plessy, Charles
    Kodzius, Rimantas
    Ravasi, Timothy
    Kasukawa, Takeya
    Fukuda, Shiro
    Kanamori-Katayama, Mutsumi
    Kitazume, Yayoi
    Kawaji, Hideya
    Kai, Chikatoshi
    Nakamura, Mari
    Konno, Hideaki
    Nakano, Kenji
    Mottagui-Tabar, Salim
    Arner, Peter
    Chesi, Alessandra
    Gustincich, Stefano
    Persichetti, Francesca
    Suzuki, Harukazu
    Grimmond, Sean M.
    Wells, Christine A.
    Orlando, Valerio
    Wahlestedt, Claes
    Liu, Edison T.
    Harbers, Matthias
    Kawai, Jun
    Bajic, Vladimir B.
    Hume, David A.
    Hayashizaki, Yoshihide
    [J]. NATURE GENETICS, 2006, 38 (06) : 626 - 635