The Transcriptional Landscape of the Mammalian Genome

P. Carninci; C. Wells; S. Nishikawa; F. Nori; O. Ohara; Y. Okazaki; V. Orlando; K. C. Pang; W. J. Pavan; G. Pavesi; G. Pesole; N. Petrovsky; R. Kodzius; S. Piazza; J. Reed; J. F. Reid; B. Z. Ring; M. Ringwald; B. Rost; Y. Ruan; S. L. Salzberg; A. Sandelin; C. and Schneider; K. Shimokawa; V. B. Bajic; S. E. Brenner; S. Batalov; A. R. Forrest; M. Zavolan; M. J. Davis; L. G. Wilming; T. Kasukawa; 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; S. Katayama; 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,; J. Gough; G. Della, Gatta,; D. di, Bernardo,; T. Down; P. Engstrom; M. Fagiolini; G. Faulkner; C. F. Fletcher; T. Fukushima; M. Furuno; S. Futaki; M. C. Frith; M. Gariboldi; P. Georgii-Hemming; T. R. Gingeras; T. Gojobori; R. E. Green; S. Gustincich; M. Harbers; Y. Hayashi; T. K. Hensch; N. Hirokawa; N. Maeda; D. Hill; L. Huminiecki; M. Iacono; K. Ikeo; A. Iwama; T. Ishikawa; M. Jakt; A. Kanapin; M. Katoh; Y. Kawasawa; R. Oyama; J. Kelso; H. Kitamura; H. Kitano; G. Kollias; S. P. Krishnan; A. Kruger; S. K. Kummerfeld; I. V. Kurochkin; L. F. Lareau; D. Lazarevic; T. Ravasi; L. Lipovich; J. Liu; S. Liuni; S. McWilliam; M. Madan, Babu,; M. Madera; L. Marchionni; H. Matsuda; S. Matsuzawa; H. Miki; B. Lenhard; F. Mignone; S. Miyake; K. Morris; S. Mottagui-Tabar; N. Mulder; N. Nakano; H. Nakauchi; P. Ng; R. Nilsson; S. Nishiguchi

The Transcriptional Landscape of the Mammalian Genome

P. Carninci, C. Wells, S. Nishikawa, F. Nori, O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, G. Pesole, N. Petrovsky, R. Kodzius, S. Piazza, J. Reed, J. F. Reid, B. Z. Ring, M. Ringwald, B. Rost, Y. RuanS. L. Salzberg, A. Sandelin, C. and Schneider, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, T. Kasukawa, 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, S. Katayama, 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,, J. Gough, G. Della, Gatta,, D. di, Bernardo,, T. Down, P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, M. Furuno, S. Futaki, M. C. Frith, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, Y. Hayashi, T. K. Hensch, N. Hirokawa, N. Maeda, D. Hill, L. Huminiecki, M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. Katoh, Y. Kawasawa, R. Oyama, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. P. Krishnan, A. Kruger, S. K. Kummerfeld, I. V. Kurochkin, L. F. Lareau, D. Lazarevic, T. Ravasi, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan, Babu,, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, B. Lenhard, F. Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi

Department of Computer Science

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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.

Translated title of the contribution	The Transcriptional Landscape of the Mammalian Genome
Original language	English
Article number	1559-1563
Journal	Science
Volume	309 (5740)
Publication status	Published - 2005

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Other identifier: 1040008

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Carninci, P., Wells, C., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Kodzius, R., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., ... Nishiguchi, S. (2005). The Transcriptional Landscape of the Mammalian Genome. Science, 309 (5740), Article 1559-1563. http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040008

@article{c991dc2436754d459a74f324cb5ec599,

title = "The Transcriptional Landscape of the Mammalian Genome",

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. ",

author = "P. Carninci and C. Wells and S. Nishikawa and F. Nori and O. Ohara and Y. Okazaki and V. Orlando and Pang, {K. C.} and Pavan, {W. J.} and G. Pavesi and G. Pesole and N. Petrovsky and R. Kodzius and S. Piazza and J. Reed and Reid, {J. F.} and Ring, {B. Z.} and M. Ringwald and B. Rost and Y. Ruan and Salzberg, {S. L.} and A. Sandelin and Schneider, {C. and} and K. Shimokawa and Bajic, {V. B.} and Brenner, {S. E.} and S. Batalov and Forrest, {A. R.} and M. Zavolan and Davis, {M. J.} and Wilming, {L. G.} and T. Kasukawa and V. Aidinis and Allen, {J. E.} and A. Ambesi-Impiombato and R. Apweiler and Aturaliya, {R. N.} and Bailey, {T. L.} and M. Bansal and L. Baxter and Beisel, {K. W.} and T. Bersano and S. Katayama and H. Bono and Chalk, {A. M.} and Chiu, {K. P.} and V. Choudhary and A. Christoffels and Clutterbuck, {D. R.} and Crowe, {M. L.} and E. Dalla and Dalrymple, {B. P.} and {de, Bono,}, B. and J. Gough and {Della, Gatta,}, G. and {di, Bernardo,}, D. and T. Down and P. Engstrom and M. Fagiolini and G. Faulkner and Fletcher, {C. F.} and T. Fukushima and M. Furuno and S. Futaki and Frith, {M. C.} and M. Gariboldi and P. Georgii-Hemming and Gingeras, {T. R.} and T. Gojobori and Green, {R. E.} and S. Gustincich and M. Harbers and Y. Hayashi and Hensch, {T. K.} and N. Hirokawa and N. Maeda and D. Hill and L. Huminiecki and M. Iacono and K. Ikeo and A. Iwama and T. Ishikawa and M. Jakt and A. Kanapin and M. Katoh and Y. Kawasawa and R. Oyama and J. Kelso and H. Kitamura and H. Kitano and G. Kollias and Krishnan, {S. P.} and A. Kruger and Kummerfeld, {S. K.} and Kurochkin, {I. V.} and Lareau, {L. F.} and D. Lazarevic and T. Ravasi and L. Lipovich and J. Liu and S. Liuni and S. McWilliam and {Madan, Babu,}, M. and M. Madera and L. Marchionni and H. Matsuda and S. Matsuzawa and H. Miki and B. Lenhard and F. Mignone and S. Miyake and K. Morris and S. Mottagui-Tabar and N. Mulder and N. Nakano and H. Nakauchi and P. Ng and R. Nilsson and S. Nishiguchi",

note = "Other identifier: 1040008",

year = "2005",

language = "English",

volume = "309 (5740)",

journal = "Science",

issn = "1095-9203",

publisher = "American Association for the Advancement of Science",

}

Carninci, P, Wells, C, Nishikawa, S, Nori, F, Ohara, O, Okazaki, Y, Orlando, V, Pang, KC, Pavan, WJ, Pavesi, G, Pesole, G, Petrovsky, N, Kodzius, R, Piazza, S, Reed, J, Reid, JF, Ring, BZ, Ringwald, M, Rost, B, Ruan, Y, Salzberg, SL, Sandelin, A, Schneider, CA, Shimokawa, K, Bajic, VB, Brenner, SE, Batalov, S, Forrest, AR, Zavolan, M, Davis, MJ, Wilming, LG, Kasukawa, T, Aidinis, V, Allen, JE, Ambesi-Impiombato, A, Apweiler, R, Aturaliya, RN, Bailey, TL, Bansal, M, Baxter, L, Beisel, KW, Bersano, T, Katayama, S, Bono, H, Chalk, AM, Chiu, KP, Choudhary, V, Christoffels, A, Clutterbuck, DR, Crowe, ML, Dalla, E, Dalrymple, BP, de, Bono, B, Gough, J, Della, Gatta, G, di, Bernardo, D, Down, T, Engstrom, P, Fagiolini, M, Faulkner, G, Fletcher, CF, Fukushima, T, Furuno, M, Futaki, S, Frith, MC, Gariboldi, M, Georgii-Hemming, P, Gingeras, TR, Gojobori, T, Green, RE, Gustincich, S, Harbers, M, Hayashi, Y, Hensch, TK, Hirokawa, N, Maeda, N, Hill, D, Huminiecki, L, Iacono, M, Ikeo, K, Iwama, A, Ishikawa, T, Jakt, M, Kanapin, A, Katoh, M, Kawasawa, Y, Oyama, R, Kelso, J, Kitamura, H, Kitano, H, Kollias, G, Krishnan, SP, Kruger, A, Kummerfeld, SK, Kurochkin, IV, Lareau, LF, Lazarevic, D, Ravasi, T, Lipovich, L, Liu, J, Liuni, S, McWilliam, S, Madan, Babu, M, Madera, M, Marchionni, L, Matsuda, H, Matsuzawa, S, Miki, H, Lenhard, B, Mignone, F, Miyake, S, Morris, K, Mottagui-Tabar, S, Mulder, N, Nakano, N, Nakauchi, H, Ng, P, Nilsson, R & Nishiguchi, S 2005, 'The Transcriptional Landscape of the Mammalian Genome', Science, vol. 309 (5740), 1559-1563. <http://www.cs.bris.ac.uk/Publications/pub_master.jsp?id=1040008>

TY - JOUR

T1 - The Transcriptional Landscape of the Mammalian Genome

AU - Carninci, P.

AU - Wells, C.

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 - Kodzius, R.

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. and

AU - Shimokawa, K.

AU - Bajic, V. B.

AU - Brenner, S. E.

AU - Batalov, S.

AU - Forrest, A. R.

AU - Zavolan, M.

AU - Davis, M. J.

AU - Wilming, L. G.

AU - Kasukawa, T.

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 - Katayama, S.

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 - de, Bono,, B.

AU - Gough, J.

AU - Della, Gatta,, G.

AU - di, Bernardo,, D.

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 - Frith, M. C.

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 - Maeda, 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 - Oyama, R.

AU - Kelso, J.

AU - Kitamura, H.

AU - Kitano, H.

AU - Kollias, G.

AU - Krishnan, S. P.

AU - Kruger, A.

AU - Kummerfeld, S. K.

AU - Kurochkin, I. V.

AU - Lareau, L. F.

AU - Lazarevic, D.

AU - Ravasi, T.

AU - Lipovich, L.

AU - Liu, J.

AU - Liuni, S.

AU - McWilliam, S.

AU - Madan, Babu,, M.

AU - Madera, M.

AU - Marchionni, L.

AU - Matsuda, H.

AU - Matsuzawa, S.

AU - Miki, H.

AU - Lenhard, B.

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.

N1 - Other identifier: 1040008

PY - 2005

Y1 - 2005

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.

M3 - Article (Academic Journal)

SN - 1095-9203

VL - 309 (5740)

JO - Science

JF - Science

M1 - 1559-1563

ER -

The Transcriptional Landscape of the Mammalian Genome

Abstract

Bibliographical note

Access to Document

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