Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.
AAAS Promotion

Site Tools

  • AAAS
  • Subscribe
  • Feedback

Site Search

Search Advanced

Science 2 September 2005:
Vol. 309. no. 5740, pp. 1559 - 1563
DOI: 10.1126/science.1112014
Prev | Table of Contents | Next

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

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Redundant Roles of Tead1 and Tead2 in Notochord Development and the Regulation of Cell Proliferation and Survival.
A. Sawada, H. Kiyonari, K. Ukita, N. Nishioka, Y. Imuta, and H. Sasaki (2008)
Mol. Cell. Biol. 28, 3177-3189
   Abstract »    Full Text »    PDF »
From the Cover: Estimating the size of the human interactome.
M. P. H. Stumpf, T. Thorne, E. de Silva, R. Stewart, H. J. An, M. Lappe, and C. Wiuf (2008)
PNAS 105, 6959-6964
   Abstract »    Full Text »    PDF »
The Protein Dendrite Arborization and Synapse Maturation 1 (Dasm-1) Is Dispensable for Dendrite Arborization.
A. Mishra, B. Knerr, S. Paixao, E. R. Kramer, and R. Klein (2008)
Mol. Cell. Biol. 28, 2782-2791
   Abstract »    Full Text »    PDF »
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets.
H. Wei, P. F. Kuan, S. Tian, C. Yang, J. Nie, S. Sengupta, V. Ruotti, G. A. Jonsdottir, S. Keles, J. A. Thomson, et al. (2008)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Computational Analysis of Full-length cDNAs Reveals Frequent Coupling Between Transcriptional and Splicing Programs.
T.-M. Chern, N. Paul, E. van Nimwegen, and M. Zavolan (2008)
DNA Res 15, 63-72
   Abstract »    Full Text »    PDF »
Alternative Splicing at NAGNAG Acceptor Sites Shares Common Properties in Land Plants and Mammals.
K. Iida, M. Shionyu, and Y. Suso (2008)
Mol. Biol. Evol. 25, 709-718
   Abstract »    Full Text »    PDF »
The Eukaryotic Genome as an RNA Machine.
P. P. Amaral, M. E. Dinger, T. R. Mercer, and J. S. Mattick (2008)
Science 319, 1787-1789
   Abstract »    Full Text »    PDF »
Long, abundantly expressed non-coding transcripts are altered in cancer.
D. S. Perez, T. R. Hoage, J. R. Pritchett, A. L. Ducharme-Smith, M. L. Halling, S. C. Ganapathiraju, P. S. Streng, and D. I. Smith (2008)
Hum. Mol. Genet. 17, 642-655
   Abstract »    Full Text »    PDF »
Noncoding RNA and DNA as Biomarkers: Toward an Epigenetic Fetal Barcode for Use in Maternal Plasma.
C. B. M. Oudejans (2008)
Clin. Chem. 54, 456-457
   Full Text »    PDF »
Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.
A. Rada-Iglesias, A. Ameur, P. Kapranov, S. Enroth, J. Komorowski, T. R. Gingeras, and C. Wadelius (2008)
Genome Res. 18, 380-392
   Abstract »    Full Text »    PDF »
Primary Ciliary Dyskinesia in Mice Lacking the Novel Ciliary Protein Pcdp1.
L. Lee, D. R. Campagna, J. L. Pinkus, H. Mulhern, T. A. Wyatt, J. H. Sisson, J. A. Pavlik, G. S. Pinkus, and M. D. Fleming (2008)
Mol. Cell. Biol. 28, 949-957
   Abstract »    Full Text »    PDF »
Rfold: an exact algorithm for computing local base pairing probabilities.
H. Kiryu, T. Kin, and K. Asai (2008)
Bioinformatics 24, 367-373
   Abstract »    Full Text »    PDF »
Specific expression of long noncoding RNAs in the mouse brain.
T. R. Mercer, M. E. Dinger, S. M. Sunkin, M. F. Mehler, and J. S. Mattick (2008)
PNAS 105, 716-721
   Abstract »    Full Text »    PDF »
SnoReport: computational identification of snoRNAs with unknown targets.
J. Hertel, I. L. Hofacker, and P. F. Stadler (2008)
Bioinformatics 24, 158-164
   Abstract »    Full Text »    PDF »
DBTSS: database of transcription start sites, progress report 2008.
H. Wakaguri, R. Yamashita, Y. Suzuki, S. Sugano, and K. Nakai (2008)
Nucleic Acids Res. 36, D97-D101
   Abstract »    Full Text »    PDF »
UTRome.org: a platform for 3'UTR biology in C. elegans.
M. Mangone, P. MacMenamin, C. Zegar, F. Piano, and K. C. Gunsalus (2008)
Nucleic Acids Res. 36, D57-D62
   Abstract »    Full Text »    PDF »
The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.
G. Roma, M. Sardiello, G. Cobellis, P. Cruz, G. Lago, R. Sanges, and E. Stupka (2008)
Nucleic Acids Res. 36, D741-D746
   Abstract »    Full Text »    PDF »
LOCATE: a mammalian protein subcellular localization database.
J. Sprenger, J. Lynn Fink, S. Karunaratne, K. Hanson, N. A. Hamilton, and R. D. Teasdale (2008)
Nucleic Acids Res. 36, D230-D233
   Abstract »    Full Text »    PDF »
Ensembl 2008.
P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, et al. (2008)
Nucleic Acids Res. 36, D707-D714
   Abstract »    Full Text »    PDF »
NONCODE v2.0: decoding the non-coding.
S. He, C. Liu, G. Skogerbo, H. Zhao, J. Wang, T. Liu, B. Bai, Y. Zhao, and R. Chen (2008)
Nucleic Acids Res. 36, D170-D172
   Abstract »    Full Text »    PDF »
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update.
J. C. Bryne, E. Valen, M.-H. E. Tang, T. Marstrand, O. Winther, I. da Piedade, A. Krogh, B. Lenhard, and A. Sandelin (2008)
Nucleic Acids Res. 36, D102-D106
   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 »
From the Cover: Distinguishing protein-coding and noncoding genes in the human genome.
M. Clamp, B. Fry, M. Kamal, X. Xie, J. Cuff, M. F. Lin, M. Kellis, K. Lindblad-Toh, and E. S. Lander (2007)
PNAS 104, 19428-19433
   Abstract »    Full Text »    PDF »
Targeted discovery of novel human exons by comparative genomics.
A. Siepel, M. Diekhans, B. Brejova, L. Langton, M. Stevens, C. L.G. Comstock, C. Davis, B. Ewing, S. Oommen, C. Lau, et al. (2007)
Genome Res. 17, 1763-1773
   Abstract »    Full Text »    PDF »