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Science 2 September 2005:
Vol. 309. no. 5740, pp. 1559 - 1563
DOI: 10.1126/science.1112014
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Reports

The Transcriptional Landscape of the Mammalian Genome

The FANTOM Consortium: * P. Carninci,{dagger} T. Kasukawa, S. Katayama, J. Gough,{dagger} M. C. Frith,{dagger} N. Maeda, R. Oyama, T. Ravasi,{dagger} B. Lenhard,{dagger} C. Wells,{dagger} R. Kodzius, K. Shimokawa, V. B. Bajic,{dagger} S. E. Brenner, S. Batalov, A. R. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. E. Allen, A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. Bansal, L. Baxter, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. T. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. Ruan, S. L. Salzberg, A. Sandelin, C. Schneider, C. Schönbach, K. Sekiguchi, C. A. M. Semple, S. Seno, L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, D. Silva, B. Sinclair, S. Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, H. R. Ueda, E. van Nimwegen, R. Verardo, C. L. Wei, K. Yagi, H. Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult,{dagger} S. M. Grimmond, R. D. Teasdale, E. T. Liu,{dagger} V. Brusic, J. Quackenbush,{dagger} C. Wahlestedt,{dagger} J. S. Mattick,{dagger} D. A. Hume,{dagger} RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group)* C. Kai, D. Sasaki, Y. Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki,{dagger} J. Aoki, T. Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. Suzuki, M. Tagami, K. Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. Kawai, Y. Hayashizaki{dagger}{ddagger}

This study describes comprehensive polling of transcription start and termination sites and analysis of previously unidentified full-length complementary DNAs derived from the mouse genome. We identify the 5' and 3' boundaries of 181,047 transcripts with extensive variation in transcripts arising from alternative promoter usage, splicing, and polyadenylation. There are 16,247 new mouse protein-coding transcripts, including 5154 encoding previously unidentified proteins. Genomic mapping of the transcriptome reveals transcriptional forests, with overlapping transcription on both strands, separated by deserts in which few transcripts are observed. The data provide a comprehensive platform for the comparative analysis of mammalian transcriptional regulation in differentiation and development.

* Affiliations can be found on Science Online (available at www.sciencemag.org/cgi/content/full/309/5740/1559/DC1).

{dagger} These authors are core authorship members.

{ddagger} To whom correspondence should be addressed. E-mail: yosihide{at}gsc.riken.jp

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   Abstract »    Full Text »    PDF »
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invit (2008)
Nucleic Acids Res. 36, D793-D799
   Abstract »    Full Text »    PDF »
Synthetic antibodies for specific recognition and crystallization of structured RNA.
J.-D. Ye, V. Tereshko, J. K. Frederiksen, A. Koide, F. A. Fellouse, S. S. Sidhu, S. Koide, A. A. Kossiakoff, and J. A. Piccirilli (2008)
PNAS 105, 82-87
   Abstract »    Full Text »    PDF »
A code for transcription initiation in mammalian genomes.
M. C. Frith, E. Valen, A. Krogh, Y. Hayashizaki, P. Carninci, and A. Sandelin (2008)
Genome Res. 18, 1-12
   Abstract »    Full Text »    PDF »
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs.
L. O. Barrera, Z. Li, A. D. Smith, K. C. Arden, W. K. Cavenee, M. Q. Zhang, R. D. Green, and B. Ren (2008)
Genome Res. 18, 46-59
   Abstract »    Full Text »    PDF »
Conservation and Diversification of Msx Protein in Metazoan Evolution.
H. Takahashi, A. Kamiya, A. Ishiguro, A. C. Suzuki, N. Saitou, A. Toyoda, and J. Aruga (2008)
Mol. Biol. Evol. 25, 69-82
   Abstract »    Full Text »    PDF »


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