The Transcriptional Landscape of the Mammalian Genome

@article{Carninci2005TheTL,
  title={The Transcriptional Landscape of the Mammalian Genome},
  author={Piero Carninci and Takeya Kasukawa and Shintaro Katayama and Julian Gough and Martin C. Frith and Norihiro Maeda and Rieko Oyama and Timothy Ravasi and Boris Lenhard and Christine A. Wells and Rimantas Kodzius and Keiko Shimokawa and Vladimir B. Bajic and Steven E. Brenner and Sergei Batalov and Alistair R. R. Forrest and Mihaela Zavolan and M. J. Davis and Laurens G. Wilming and Vassilis Aidinis and J. Allen and Alberto Ambesi-Impiombato and Rolf Apweiler and Rajith N. Aturaliya and Timothy L. Bailey and Mukesh Bansal and Laura Baxter and Kirk W. Beisel and Thomas M. Bersano and Hidemasa Bono and Alistair M. Chalk and Kuo Ping Chiu and Vidhu Choudhary and Alan Christoffels and Daniel R. Clutterbuck and Mark L. Crowe and Emiliano Dalla and Brian P. Dalrymple and Bernard de Bono and Giusy Della Gatta and Diego di Bernardo and Thomas A. Down and Peter Engstrom and Michela Fagiolini and Geoffrey J. Faulkner and Colin F. Fletcher and Takahiro Fukushima and Masaaki Furuno and Shiroh Futaki and Manuela Gariboldi and Patrik Georgii‐Hemming and Thomas R. Gingeras and Takashi Gojobori and Richard E. Green and Stefano Gustincich and Matthias Harbers and Y. Hayashi and Takao K. Hensch and Nobutaka Hirokawa and David P. Hill and Lukasz Huminiecki and Michele Iacono and Kazuho Ikeo and Atsushi Iwama and Takashi Ishikawa and Martin L. Jakt and Alexander Kanapin and Masahiro Katoh and Yuka Imamura Kawasawa and John Kelso and Hidemitsu Kitamura and Hiroako Kitano and George Kollias and S. P. T. Krishnan and Ad{\'e}le Kruger and Sarah K. Kummerfeld and Igor Kurochkin and Liana F. Lareau and Dejan Lazarevi{\'c} and Leonard Lipovich and J. Liu and Sabino Liuni and S. M. McWilliam and M. Madan Babu and Martin Madera and Luigi Marchionni and Hideo Matsuda and S Matsuzawa and H. Miki and Flavio Mignone and S. Miyake and Ken A. Morris and Salim Mottagui-Tabar and N Mulder and N Nakano and Hiromitsu Nakauchi and Patrick C. Ng and Roland Nilsson and Seiji Nishiguchi and S Nishikawa and F Nori and Osamu Ohara and Yasushi Okazaki and Valerio Orlando and Ken C. Pang and William J. Pavan and Giulio Pavesi and Graziano Pesole and Nikolai Petrovsky and Stefano Piazza and Jake Reed and James Francis Reid and Brian Z. Ring and Martin Ringwald and Burkhard Rost and Yuxuan Ruan and Steven L. Salzberg and Albin Sandelin and Claudio Schneider and Christian Sch{\"o}nbach and K Sekiguchi and Colin A. Semple and Shigeto Seno and Luca Sessa and Y. Sheng and Y Shibata and Hiroshi Shimada and Kaori Shimada and D Silva and Bella Sinclair and Sebastian Sperling and Elia Stupka and Koji Sugiura and Razvan Sultana and Yoichi Takenaka and K Taki and Kairi Tammoja and S. L. Tan and S. H. Tang and M. S. Taylor and Jesper N. Tegner and Sarah A. Teichmann and Hiroki R. Ueda and Erik van Nimwegen and Roberto Verardo and C. L. Wei and K. Yagi and Hiroshi Yamanishi and Eugene R. Zabarovsky and S. M. Zhu and Andreas D. Zimmer and Winston A Hide and Carol J. Bult and Sean M. Grimmond and Rohan D. Teasdale and Edison T. Liu and Vladimir Brusic and John Quackenbush and Claes Wahlestedt and John S. A. Mattick and David A. Hume and Chikatoshi Kai and Daisuke Sasaki and Yasuhiro Tomaru and Shiro Fukuda and Mutsumi Kanamori-Katayama and M. Suzuki and J Aoki and Takahiro Arakawa and Jun Iida and Kengo Imamura and Masayoshi Itoh and T. Kato and Hideya Kawaji and Nobuyuki Kawagashira and Tsugumi Kawashima and M Kojima and Shinji Kondo and Hideaki Konno and Kazumi Nakano and Noriko Ninomiya and Takeshi Nishio and M Okada and Charles Plessy and Kazuhiro Shibata and Toshiyuki Shiraki and S. Suzuki and Michihira Tagami and Kazunori Waki and Akira Watahiki and Yuko Okamura-Oho and H. Suzuki and Jun Kawai and Yoshihide Hayashizaki},
  journal={Science},
  year={2005},
  volume={309},
  pages={1559 - 1563}
}
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… 

The transcriptional landscape.

The application of new and less biased methods to study the transcriptional output from genomes, such as tiling arrays and deep sequencing, has revealed that most of the genome is transcribed and

The gateway to transcription: identifying, characterizing and understanding promoters in the eukaryotic genome

Recent experimental and computational advances that have enabled the identification and analysis of transcriptional promoters on an unprecedented scale are reviewed, laying a foundation for systematic determination of the transcriptional regulatory networks in eukaryotic cells.

A paired-end sequencing strategy to map the complex landscape of transcription initiation

A paired- end sequencing strategy is described, which enables more robust mapping and characterization of capped transcripts and demonstrated paired-end TSS analysis to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes.

Our evolving knowledge of the transcriptional landscape

The development of a genome-scale approach to identification of the 5′ ends of capped mRNAs (CAGE) has given new insights into many aspects of mammalian RNApolII transcription control. They include

The regulated retrotransposon transcriptome of mammalian cells

It is reported that 6–30% of cap-selected mouse and human RNA transcripts initiate within repetitive elements, and it is concluded that retrotransposon transcription has a key influence upon the transcriptional output of the mammalian genome.

Tagging mammalian transcription complexity.

Transcriptional landscape of the human and fly genomes: nonlinear and multifunctional modular model of transcriptomes.

An interlaced model of the genome in which many regions serve multifunctional purposes and are highly modular in their utilization is illustrated, illustrating the underappreciated organizational complexity ofThe genome and one of the functional roles of transcription from unannotated portions of the genomes.

Genome-wide analysis of mammalian promoter architecture and evolution

These tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini.

Noncoding transcription at enhancers: general principles and functional models.

The possibility that enhancer transcription and the resulting enhancer RNAs may, in some cases, have functional roles, rather than represent mere transcriptional noise at accessible genomic regions, is supported by an increasing amount of experimental data.

A high-resolution map of transcription in the yeast genome.

By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts.
...

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