Is sequencing enlightenment ending the dark age of the transcriptome?

被引：23

作者：

Carninci, Piero ^{[1
]}

机构：

[1] RIKEN Yokohama Inst, Omics Sci Ctr, Kanagawa, Japan

来源：

NATURE METHODS | 2009年 / 6卷 / 10期

关键词：

HUMAN GENOME; RNA-SEQ; DISCOVERY; CELL;

D O I：

10.1038/nmeth1009-711

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Sequencing-based technologies for RNA discovery are playing a key role in deciphering the transcriptome and hold the potential to provide us with a census of RNAs and their functions.

引用

页码：711 / 713

页数：3

共 17 条

[1] 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

[2] Targeting a complex transcriptome: The construction of the mouse full-length cDNA encyclopedia [J].

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 .

GENOME RESEARCH, 2003, 13 (6B) :1273-1289

[3] 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

[4] Genome-wide analysis of mammalian promoter architecture and evolution [J].

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 .

NATURE GENETICS, 2006, 38 (06) :626-635

[5] Stem cell transcriptome profiling via massive-scale mRNA sequencing [J].

Cloonan, Nicole ;

Forrest, Alistair R. R. ;

Kolle, Gabriel ;

Gardiner, Brooke B. A. ;

Faulkner, Geoffrey J. ;

Brown, Mellissa K. ;

Taylor, Darrin F. ;

Steptoe, Anita L. ;

Wani, Shivangi ;

Bethel, Graeme ;

Robertson, Alan J. ;

Perkins, Andrew C. ;

Bruce, Stephen J. ;

Lee, Clarence C. ;

Ranade, Swati S. ;

Peckham, Heather E. ;

Manning, Jonathan M. ;

McKernan, Kevin J. ;

Grimmond, Sean M. .

NATURE METHODS, 2008, 5 (07) :613-619

[6] Efficient targeted transcript discovery via array-based normalization of RACE libraries [J].

Djebali, Sarah ;

Kapranov, Philipp ;

Foissac, Sylvain ;

Lagarde, Julien ;

Reymond, Alexandre ;

Ucla, Catherine ;

Wyss, Carine ;

Drenkow, Jorg ;

Dumais, Erica ;

Murray, Ryan R. ;

Lin, Chenwei ;

Szeto, David ;

Denoeud, France ;

Calvo, Miquel ;

Frankish, Adam ;

Harrow, Jennifer ;

Makrythanasis, Periklis ;

Vidal, Marc ;

Salehi-Ashtiani, Kourosh ;

Antonarakis, Stylianos E. ;

Gingeras, Thomas R. ;

Guigo, Roderic .

NATURE METHODS, 2008, 5 (07) :629-635

[7] The regulated retrotransposon transcriptome of mammalian cells [J].

Faulkner, Geoffrey J. ;

Kimura, Yasumasa ;

Daub, Carsten O. ;

Wani, Shivangi ;

Plessy, Charles ;

Irvine, Katharine M. ;

Schroder, Kate ;

Cloonan, Nicole ;

Steptoe, Anita L. ;

Lassmann, Timo ;

Waki, Kazunori ;

Hornig, Nadine ;

Arakawa, Takahiro ;

Takahashi, Hazuki ;

Kawai, Jun ;

Forrest, Alistair R. R. ;

Suzuki, Harukazu ;

Hayashizaki, Yoshihide ;

Hume, David A. ;

Orlando, Valerio ;

Grimmond, Sean M. ;

Carninci, Piero .

NATURE GENETICS, 2009, 41 (05) :563-571

[8] Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs [J].

Fejes-Toth, Katalin ;

Sotirova, Vihra ;

Sachidanandam, Ravi ;

Assaf, Gordon ;

Hannon, Gregory J. ;

Kapranov, Philipp ;

Foissac, Sylvain ;

Willingham, Aarron T. ;

Duttagupta, Radha ;

Dumais, Erica ;

Gingeras, Thomas R. .

NATURE, 2009, 457 (7232) :1028-1032

[9] Tag-based approaches for transcriptome research and genome annotation [J].

Harbers, M ;

Carninci, P .

NATURE METHODS, 2005, 2 (07) :495-502

[10] RNA maps reveal new RNA classes and a possible function for pervasive transcription [J].

Kapranov, Philipp ;

Cheng, Jill ;

Dike, Sujit ;

Nix, David A. ;

Duttagupta, Radharani ;

Willingham, Aarron T. ;

Stadler, Peter F. ;

Hertel, Jana ;

Hackermueller, Joerg ;

Hofacker, Ivo L. ;

Bell, Ian ;

Cheung, Evelyn ;

Drenkow, Jorg ;

Dumais, Erica ;

Patel, Sandeep ;

Helt, Gregg ;

Ganesh, Madhavan ;

Ghosh, Srinka ;

Piccolboni, Antonio ;

Sementchenko, Victor ;

Tammana, Hari ;

Gingeras, Thomas R. .

SCIENCE, 2007, 316 (5830) :1484-1488

← 1 2 →