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The Transcriptional Landscape of the Mammalian Genome

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Authors

Piero Carninci,Takeya Kasukawa

Shintaro Katayama,Julian Gough,Martin Frith,Norihiro Maeda,Rieko Oyama,Timothy Ravasi,Boris Lenhard,Christine Wells,Rimantas Kodzius,Koya Shimokawa,Vladimir Bajić,Steven Brenner,Serge Batalov,Alistair Forrest,Mihaela Zavolan,Melissa Davis,Marcelo Soares,Vassilis Aidinis,Jonathan Allen,Alberto Ambesi‐Impiombato,Rolf Apweiler,Rajith Aturaliya,Timothy Bailey,Mukul Bansal,Laura Baxter,Kirk Beisel,Tom Bersano,Hidemasa Bono,Alistair Chalk,Kuo Chiu,Vijayata Choudhary,Alan Christoffels,D. Clutterbuck,Mark Crowe,Emiliano Dalla,Brian Dalrymple,Bernard Bono,Giusy Gatta,Diego Bernardo,Thomas Down,Pär Engström,Michela Fagiolini,Geoffrey Faulkner,Colin Fletcher,Tatsuya Fukushima,Masaaki Furuno,Sugiko Futaki,Manuela Gariboldi,Patrik Georgii‐Hemming,T Gingeras,Takashi Gojobori,Edward Green,Stefano Gustincich,Matthias Harbers,Yoshitaka Hayashi,Takao Hensch,Nobutaka Hirokawa,David Hill,Łukasz Huminiecki,Michele Iacono,Kazuho Ikeo,Atsushi Iwama,Takanori Ishikawa,Lars Jakt,Alexander Kanapin,Masaru Katoh,Yuka Kawasawa,Janet Kelso,Hiroshi Kitamura,Hiroaki Kitano,George Kollias,Sivanand Krishnan,Adéle Kruger,Sarah Kummerfeld,Igor Kurochkin,Liana Lareau,Dejan Lazarević,Leonard Lipovich,Jinfeng Liu,Sabino Liuni,Sean McWilliam,M. Babu,Martin Madera,Luigi Marchionni,Hideo Matsuda,Shu‐ichi Matsuzawa,Hiroaki Miki,Flavio Mignone,S. Miyake,Ken Morris,Salim Mottagui‐Tabar,Nicola Mulder,Norio Nakano,Hiromitsu Nakauchi,Patrick Duriez,Roland Nilsson,Seiji Nishiguchi,Shigemichi Nishikawa,Franco Nori,Osamu Ohara,Yasushi Okazaki,Valerio Orlando,Ken Pang,William Pavan,Giulio Pavesi,Graziano Pesole,Nikolai Petrovsky,Silvano Piazza,James Reed,James Reid,Brian Ring,Martin Ringwald,Burkhard Rost,Yijun Ruan,Steven Salzberg,Albin Sandelin,C. Schneider,Christian Schönbach,Kiyotoshi Sekiguchi,Colin Semple,Shigeto Seno,Luca Sessa,Ying Sheng,Yûkô Shibata,Hiroshi Shimada,Kiyo Shimada,D. Silva,Bella Sinclair,Silke Sperling,Elia Stupka,Koji Sugiura,Răzvan Sultana,Yasuhiro Takenaka,Kohei Taki,Kairi Koort,Sin Tan,Tang Suisheng,Martin Taylor,Jesper Tegnér,Sarah Teichmann,Hiroki Ueda,Erik Nimwegen,Roberto Verardo,Chia‐Lin Wei,Ken Yagi,Hiromichi Yamanishi,Eugene Zabarovsky,Shanshan Zhu,Andreas Zimmer,Winston Hide,Carol Bult,Sean Grimmond,Rohan Teasdale,E. Liu,Vladimir Brusić,John Quackenbush,Claes Wahlestedt,John Mattick,David Hume,Kai Cui,Daisuke Sasaki,Yuji Tomaru,Shiro Fukuda,Mutsumi Kanamori-Katayama,Masanori Suzuki,Juliana Aoki,Takahiro Arakawa,Juri Iida,Masayoshi Itoh,Tomomi Kato,Hideya Kawaji,Nobuyuki Kawagashira,Tsugumi Kawashima,Miki Kojima,Shinji Kondo,Hiroyuki Konno,Kenji Nakano,Noriko Ninomiya,Tomoaki Nishio,Mitsuhiro Okada,Charles Plessy,Kazuhiro Shibata,Toshiyuki Shiraki,Satoru Suzuki,Michihira Tagami,Kazunori Waki,Akira Watahiki,Yuko Okamura-Oho,Harukazu Suzuki,Jun Kawai,Yoshihide Hayashizaki,S. Krishnan,Kuniyasu Shimokawa,Vladimir Bajic,Ranajit Chakraborty,Joke Allemeersch,Dejan Lazarevic

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Journal

Published

Sep 1, 2005

DOI

10.1126/science.1112014

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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.

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