The Transcriptional Landscape of the Mammalian Genome
Piero Carninci(Online Technologies (United States)), Takeya Kasukawa(Online Technologies (United States)), Shintaro Katayama(Online Technologies (United States)), Julian Gough(Online Technologies (United States)), Martin C. Frith(The University of Queensland), Norihiro Maeda(Online Technologies (United States)), Rieko Oyama(Online Technologies (United States)), Timothy Ravasi(Online Technologies (United States)), Boris Lenhard(Karolinska Institutet), Christine A. Wells(Griffith University), Rimantas Kodzius(Online Technologies (United States)), Koya Shimokawa(Online Technologies (United States)), Vladimir B. Bajić(Online Technologies (United States)), Steven E. Brenner(Online Technologies (United States)), Serge Batalov(Online Technologies (United States)), Alistair R. R. Forrest(The University of Queensland), Mihaela Zavolan(University of Basel), Melissa J. Davis(The University of Queensland), Laurens Wilming(Online Technologies (United States)), Vassilis Aidinis(Online Technologies (United States)), Jonathan Allen(J. Craig Venter Institute), Alberto Ambesi‐Impiombato(Online Technologies (United States)), Rolf Apweiler(Online Technologies (United States)), Rajith Aturaliya(The University of Queensland), Timothy L. Bailey(The University of Queensland), Mukul S. Bansal(Online Technologies (United States)), Laura L. Baxter(National Institutes of Health), Kirk W. Beisel(Online Technologies (United States)), Tom Bersano(Online Technologies (United States)), Hidemasa Bono(Online Technologies (United States)), Alistair M. Chalk(Karolinska Institutet), Kuo Ping Chiu(Agency for Science, Technology and Research), Vijayata Choudhary(Agency for Science, Technology and Research), Alan Christoffels(National University of Singapore), D. R. Clutterbuck(Online Technologies (United States)), Mark L. Crowe(The University of Queensland), Emiliano Dalla(Online Technologies (United States)), Brian P. Dalrymple(Commonwealth Scientific and Industrial Research Organisation), Bernard de Bono(Online Technologies (United States)), Giusy Della Gatta(Online Technologies (United States)), Diego di Bernardo(Online Technologies (United States)), Thomas A. Down(Online Technologies (United States)), Pär G. Engström(Karolinska Institutet), Michela Fagiolini(Online Technologies (United States)), Geoffrey J. Faulkner(The University of Queensland), Colin Fletcher(Online Technologies (United States)), Tatsuya Fukushima(Online Technologies (United States)), Masaaki Furuno(Online Technologies (United States)), Sugiko Futaki(Aichi Medical University), Manuela Gariboldi(Online Technologies (United States)), Patrik Georgii‐Hemming(Karolinska Institutet), T Gingeras(Online Technologies (United States)), Takashi Gojobori(Online Technologies (United States)), Richard E. Green(Online Technologies (United States)), Stefano Gustincich(Online Technologies (United States)), Matthias Harbers(Online Technologies (United States)), Yoshitaka Hayashi(Aichi Medical University), Takao K. Hensch(Online Technologies (United States)), Nobutaka Hirokawa(Online Technologies (United States)), David E. Hill(Online Technologies (United States)), Łukasz Huminiecki(Karolinska Institutet), Michele Iacono(University of Milan), Kazuho Ikeo(Online Technologies (United States)), Atsushi Iwama(Online Technologies (United States)), Takanori Ishikawa(Online Technologies (United States)), Lars Martin Jakt(Online Technologies (United States)), Alexander Kanapin(Online Technologies (United States)), Masaru Katoh(Online Technologies (United States)), Yuka Imamura Kawasawa(Online Technologies (United States)), Janet Kelso(Online Technologies (United States)), Hiroshi Kitamura(Online Technologies (United States)), Hiroaki Kitano(Online Technologies (United States)), George Kollias(Online Technologies (United States)), Sivanand Krishnan(Agency for Science, Technology and Research), Adéle Kruger(Online Technologies (United States)), Sarah Kummerfeld(Online Technologies (United States)), Igor V. Kurochkin(Online Technologies (United States)), Liana F. Lareau(Online Technologies (United States)), Dejan Lazarević(Online Technologies (United States)), Leonard Lipovich(Agency for Science, Technology and Research), Jinfeng Liu(Online Technologies (United States)), Sabino Liuni(Online Technologies (United States)), Sean McWilliam(Commonwealth Scientific and Industrial Research Organisation), M. Madan Babu(Online Technologies (United States)), Martin Madera(Online Technologies (United States)), Luigi Marchionni(Online Technologies (United States)), Hideo Matsuda(Online Technologies (United States)), Shu‐ichi Matsuzawa(Online Technologies (United States)), Hiroaki Miki(Online Technologies (United States)), Flavio Mignone(University of Milan), S. Miyake(Online Technologies (United States)), Ken A. Morris(Creighton University), Salim Mottagui‐Tabar(Scripps Research Institute), Nicola Mulder(Online Technologies (United States)), Norio Nakano(Online Technologies (United States)), Hiromitsu Nakauchi(Online Technologies (United States)), Patrick Ng(Agency for Science, Technology and Research), Roland Nilsson(Online Technologies (United States)), Seiji Nishiguchi(Online Technologies (United States)), Shigemichi Nishikawa(Online Technologies (United States)), Franco Nori(Online Technologies (United States)), Osamu Ohara(Online Technologies (United States)), Yasushi Okazaki(Online Technologies (United States)), Valerio Orlando(Online Technologies (United States)), Ken C. Pang(The University of Melbourne), William J. Pavan(National Institutes of Health), Giulio Pavesi(University of Milan), Graziano Pesole(University of Milan), Nikolai Petrovsky(Flinders University), Silvano Piazza(Online Technologies (United States)), James Reed(Online Technologies (United States)), James F. Reid(Online Technologies (United States)), Brian Z. Ring(Online Technologies (United States)), Martin Ringwald(Online Technologies (United States)), Burkhard Rost(Online Technologies (United States)), Yijun Ruan(Agency for Science, Technology and Research), Steven L. Salzberg(J. Craig Venter Institute), Albin Sandelin(Karolinska Institutet), C. Schneider(Online Technologies (United States)), Christian Schönbach(Online Technologies (United States)), Kiyotoshi Sekiguchi(Aichi Medical University), Colin A. Semple(Online Technologies (United States)), Shigeto Seno(Online Technologies (United States)), Luca Sessa(Online Technologies (United States)), Ying Sheng(Online Technologies (United States)), Yûkô Shibata(Online Technologies (United States)), Hiroshi Shimada(Online Technologies (United States)), Kiyo Shimada(Online Technologies (United States)), D. Silva(National Institutes of Health), Bella Sinclair(Online Technologies (United States)), Silke Sperling(Max Planck Society), Elia Stupka(Online Technologies (United States)), Koji Sugiura(Online Technologies (United States)), Răzvan Sultana(J. Craig Venter Institute), Yasuhiro Takenaka(Online Technologies (United States)), Kohei Taki(Online Technologies (United States)), Kairi Tammoja(Karolinska Institutet), Sin Lam Tan(Agency for Science, Technology and Research), S. Tang(Agency for Science, Technology and Research), Martin S. Taylor(University of Oxford), Jesper Tegnér(Online Technologies (United States)), Sarah A. Teichmann(Online Technologies (United States)), Hiroki R. Ueda(Online Technologies (United States)), Erik van Nimwegen(University of Basel), Roberto Verardo(Online Technologies (United States)), Chia Lin Wei(Agency for Science, Technology and Research), Ken Yagi(Online Technologies (United States)), Hiromichi Yamanishi(Online Technologies (United States)), Eugene R. Zabarovsky(Karolinska Institutet), Shanshan Zhu(Online Technologies (United States)), Andreas Zimmer(University of Bonn), W. Hide(Online Technologies (United States)), Carol J. Bult(Online Technologies (United States)), Sean M. Grimmond(The University of Queensland), Rohan D. Teasdale(The University of Queensland), E. T. Liu(Agency for Science, Technology and Research), Vladimir Brusić(Agency for Science, Technology and Research), John Quackenbush(J. Craig Venter Institute), Claes Wahlestedt(Scripps Research Institute), John S. Mattick(The University of Queensland), David Hume(The University of Queensland), C. Kai(Online Technologies (United States)), Daisuke Sasaki(Online Technologies (United States)), Yuji Tomaru(Online Technologies (United States)), Shiro Fukuda(Online Technologies (United States)), Mutsumi Kanamori-Katayama(Online Technologies (United States)), Masanori Suzuki(Online Technologies (United States)), Juliana Ide Aoki(Online Technologies (United States)), Takahiro Arakawa(Online Technologies (United States)), Juri Iida(Online Technologies (United States)), K. Imamura(Online Technologies (United States)), Masayoshi Itoh(Online Technologies (United States)), Tomomi Kato(Online Technologies (United States)), Hideya Kawaji(Online Technologies (United States)), Nobuyuki Kawagashira(Online Technologies (United States)), Tsugumi Kawashima(Online Technologies (United States)), Miki Kojima(Online Technologies (United States)), Shinji Kondo(Online Technologies (United States)), Hiroyuki Konno(Online Technologies (United States)), Kenji Nakano(Online Technologies (United States)), N. Ninomiya(Online Technologies (United States)), T. Nishio(Online Technologies (United States)), Mitsuhiro Okada(Online Technologies (United States)), Charles Plessy(Online Technologies (United States)), Kazuhiro Shibata(Online Technologies (United States)), Toshiyuki Shiraki(Online Technologies (United States)), Satoru Suzuki(Online Technologies (United States)), Michihira Tagami(Online Technologies (United States)), Kazunori Waki(Online Technologies (United States)), Akira Watahiki(University of Tsukuba), Yuko Okamura-Oho(Online Technologies (United States)), Harukazu Suzuki(Online Technologies (United States)), Jun Kawai(Online Technologies (United States)), Yoshihide Hayashizaki(University of Tsukuba)
Cited by 3,589
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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