Abstract
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.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 1559-1563 |
| Number of pages | 5 |
| Journal | Science |
| Volume | 309 |
| Issue number | 5740 |
| DOIs | |
| State | Published - Sep 2 2005 |
ASJC Scopus subject areas
- General
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Molecular biology : The transcriptional landscape of the mammalian genome. / Carninci, P.; Kasukawa, T.; Katayama, S.; Gough, J.; Frith, M. C.; Maeda, N.; Oyama, R.; Ravasi, T.; Lenhard, B.; Wells, C.; Kodzius, R.; Shimokawa, K.; Bajic, V. B.; Brenner, S. E.; Batalov, S.; Forrest, A. R.R.; Zavolan, M.; Davis, M. J.; Wilming, L. G.; Aidinis, V.; Allen, J. E.; Ambesi-Impiombato, A.; Apweiler, R.; Aturaliya, R. N.; Bailey, T. L.; Bansal, M.; Baxter, L.; Beisel, K. W.; Bersano, T.; Bono, H.; Chalk, A. M.; Chiu, K. P.; Choudhary, V.; Christoffels, A.; Clutterbuck, D. R.; Crowe, M. L.; Dalla, E.; Dalrymple, B. P.; Bono, B.; Gatta, G. Della; Bernardo, D. Di; Down, T.; Engstrom, P.; Fagiolini, M.; Faulkner, G.; Fletcher, C. F.; Fukushima, T.; Furuno, M.; Futaki, S.; Gariboldi, M.; Georgii-Hemming, P.; Gingeras, T. R.; Gojobori, T.; Green, R. E.; Gustincich, S.; Harbers, M.; Hayashi, Y.; Hensch, T. K.; Hirokawa, N.; Hill, D.; Huminiecki, L.; Iacono, M.; Ikeo, K.; Iwama, A.; Ishikawa, T.; Jakt, M.; Kanapin, A.; Katoh, M.; Kawasawa, Y.; Kelso, J.; Kitamura, H.; Kitano, H.; Kollias, G.; Krishnan, S. P.T.; Kruger, A.; Kummerfeld, S. K.; Kurochkin, I. V.; Lareau, L. F.; Lazarevic, D.; Lipovich, L.; Liu, J.; Liuni, S.; McWilliam, S.; Babu, M. Madan; Madera, M.; Marchionni, L.; Matsuda, H.; Matsuzawa, S.; Miki, H.; Mignone, F.; Miyake, S.; Morris, K.; Mottagui-Tabar, S.; Mulder, N.; Nakano, N.; Nakauchi, H.; Ng, P.; Nilsson, R.; Nishiguchi, S.; Nishikawa, S.; Nori, F.; Ohara, O.; Okazaki, Y.; Orlando, V.; Pang, K. C.; Pavan, W. J.; Pavesi, G.; Pesole, G.; Petrovsky, N.; Piazza, S.; Reed, J.; Reid, J. F.; Ring, B. Z.; Ringwald, M.; Rost, B.; Ruan, Y.; Salzberg, S. L.; Sandelin, A.; Schneider, C.; Schönbach, C.; Sekiguchi, K.; Semple, C. A.M.; Seno, S.; Sessa, L.; Sheng, Y.; Shibata, Y.; Shimada, H.; Shimada, K.; Silva, D.; Sinclair, B.; Sperling, S.; Stupka, E.; Sugiura, K.; Sultana, R.; Takenaka, Y.; Taki, K.; Tammoja, K.; Tan, S. L.; Tang, S.; Taylor, M. S.; Tegner, J.; Teichmann, S. A.; Ueda, H. R.; Nimwegen, E.; Verardo, R.; Wei, C. L.; Yagi, K.; Yamanishi, H.; Zabarovsky, E.; Zhu, S.; Zimmer, A.; Hide, W.; Bult, C.; Grimmond, S. M.; Teasdale, R. D.; Liu, E. T.; Brusic, V.; Quackenbush, J.; Wahlestedt, C.; Mattick, J. S.; Hume, D. A.; Kai, C.; Sasaki, D.; Tomaru, Y.; Fukuda, S.; Kanamori-Katayama, M.; Suzuki, M.; Aoki, J.; Arakawa, T.; Iida, J.; Imamura, K.; Itoh, M.; Kato, T.; Kawaji, H.; Kawagashira, N.; Kawashima, T.; Kojima, M.; Kondo, S.; Konno, H.; Nakano, K.; Ninomiya, N.; Nishio, T.; Okada, M.; Plessy, C.; Shibata, K.; Shiraki, T.; Suzuki, S.; Tagami, M.; Waki, K.; Watahiki, A.; Okamura-Oho, Y.; Suzuki, H.; Kawai, J.; Hayashizaki, Y.
In: Science, Vol. 309, No. 5740, 02.09.2005, p. 1559-1563.Research output: Contribution to journal › Article › peer-review
TY - JOUR
T1 - Molecular biology
T2 - The transcriptional landscape of the mammalian genome
AU - Carninci, P.
AU - Kasukawa, T.
AU - Katayama, S.
AU - Gough, J.
AU - Frith, M. C.
AU - Maeda, N.
AU - Oyama, R.
AU - Ravasi, T.
AU - Lenhard, B.
AU - Wells, C.
AU - Kodzius, R.
AU - Shimokawa, K.
AU - Bajic, V. B.
AU - Brenner, S. E.
AU - Batalov, S.
AU - Forrest, A. R.R.
AU - Zavolan, M.
AU - Davis, M. J.
AU - Wilming, L. G.
AU - Aidinis, V.
AU - Allen, J. E.
AU - Ambesi-Impiombato, A.
AU - Apweiler, R.
AU - Aturaliya, R. N.
AU - Bailey, T. L.
AU - Bansal, M.
AU - Baxter, L.
AU - Beisel, K. W.
AU - Bersano, T.
AU - Bono, H.
AU - Chalk, A. M.
AU - Chiu, K. P.
AU - Choudhary, V.
AU - Christoffels, A.
AU - Clutterbuck, D. R.
AU - Crowe, M. L.
AU - Dalla, E.
AU - Dalrymple, B. P.
AU - Bono, B.
AU - Gatta, G. Della
AU - Bernardo, D. Di
AU - Down, T.
AU - Engstrom, P.
AU - Fagiolini, M.
AU - Faulkner, G.
AU - Fletcher, C. F.
AU - Fukushima, T.
AU - Furuno, M.
AU - Futaki, S.
AU - Gariboldi, M.
AU - Georgii-Hemming, P.
AU - Gingeras, T. R.
AU - Gojobori, T.
AU - Green, R. E.
AU - Gustincich, S.
AU - Harbers, M.
AU - Hayashi, Y.
AU - Hensch, T. K.
AU - Hirokawa, N.
AU - Hill, D.
AU - Huminiecki, L.
AU - Iacono, M.
AU - Ikeo, K.
AU - Iwama, A.
AU - Ishikawa, T.
AU - Jakt, M.
AU - Kanapin, A.
AU - Katoh, M.
AU - Kawasawa, Y.
AU - Kelso, J.
AU - Kitamura, H.
AU - Kitano, H.
AU - Kollias, G.
AU - Krishnan, S. P.T.
AU - Kruger, A.
AU - Kummerfeld, S. K.
AU - Kurochkin, I. V.
AU - Lareau, L. F.
AU - Lazarevic, D.
AU - Lipovich, L.
AU - Liu, J.
AU - Liuni, S.
AU - McWilliam, S.
AU - Babu, M. Madan
AU - Madera, M.
AU - Marchionni, L.
AU - Matsuda, H.
AU - Matsuzawa, S.
AU - Miki, H.
AU - Mignone, F.
AU - Miyake, S.
AU - Morris, K.
AU - Mottagui-Tabar, S.
AU - Mulder, N.
AU - Nakano, N.
AU - Nakauchi, H.
AU - Ng, P.
AU - Nilsson, R.
AU - Nishiguchi, S.
AU - Nishikawa, S.
AU - Nori, F.
AU - Ohara, O.
AU - Okazaki, Y.
AU - Orlando, V.
AU - Pang, K. C.
AU - Pavan, W. J.
AU - Pavesi, G.
AU - Pesole, G.
AU - Petrovsky, N.
AU - Piazza, S.
AU - Reed, J.
AU - Reid, J. F.
AU - Ring, B. Z.
AU - Ringwald, M.
AU - Rost, B.
AU - Ruan, Y.
AU - Salzberg, S. L.
AU - Sandelin, A.
AU - Schneider, C.
AU - Schönbach, C.
AU - Sekiguchi, K.
AU - Semple, C. A.M.
AU - Seno, S.
AU - Sessa, L.
AU - Sheng, Y.
AU - Shibata, Y.
AU - Shimada, H.
AU - Shimada, K.
AU - Silva, D.
AU - Sinclair, B.
AU - Sperling, S.
AU - Stupka, E.
AU - Sugiura, K.
AU - Sultana, R.
AU - Takenaka, Y.
AU - Taki, K.
AU - Tammoja, K.
AU - Tan, S. L.
AU - Tang, S.
AU - Taylor, M. S.
AU - Tegner, J.
AU - Teichmann, S. A.
AU - Ueda, H. R.
AU - Nimwegen, E.
AU - Verardo, R.
AU - Wei, C. L.
AU - Yagi, K.
AU - Yamanishi, H.
AU - Zabarovsky, E.
AU - Zhu, S.
AU - Zimmer, A.
AU - Hide, W.
AU - Bult, C.
AU - Grimmond, S. M.
AU - Teasdale, R. D.
AU - Liu, E. T.
AU - Brusic, V.
AU - Quackenbush, J.
AU - Wahlestedt, C.
AU - Mattick, J. S.
AU - Hume, D. A.
AU - Kai, C.
AU - Sasaki, D.
AU - Tomaru, Y.
AU - Fukuda, S.
AU - Kanamori-Katayama, M.
AU - Suzuki, M.
AU - Aoki, J.
AU - Arakawa, T.
AU - Iida, J.
AU - Imamura, K.
AU - Itoh, M.
AU - Kato, T.
AU - Kawaji, H.
AU - Kawagashira, N.
AU - Kawashima, T.
AU - Kojima, M.
AU - Kondo, S.
AU - Konno, H.
AU - Nakano, K.
AU - Ninomiya, N.
AU - Nishio, T.
AU - Okada, M.
AU - Plessy, C.
AU - Shibata, K.
AU - Shiraki, T.
AU - Suzuki, S.
AU - Tagami, M.
AU - Waki, K.
AU - Watahiki, A.
AU - Okamura-Oho, Y.
AU - Suzuki, H.
AU - Kawai, J.
AU - Hayashizaki, Y.
PY - 2005/9/2
Y1 - 2005/9/2
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=24644519490&partnerID=8YFLogxK
U2 - 10.1126/science.1112014
DO - 10.1126/science.1112014
M3 - Article
C2 - 16141072
AN - SCOPUS:24644519490
VL - 309
SP - 1559
EP - 1563
JO - Science (New York, N.Y.)
JF - Science (New York, N.Y.)
SN - 0036-8075
IS - 5740
ER -