The Transcriptional Landscape of the Mammalian Genome

  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},
  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.



Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution

The transcribed portions of the human genome are predominantly composed of interlaced networks of both poly A+ and poly A– annotated transcripts and unannotated transcripts of unknown function, which has important implications for interpreting genotype-phenotype associations, regulation of gene expression, and the definition of a gene.

Global Identification of Human Transcribed Sequences with Genome Tiling Arrays

This work constructed a series of high-density oligonucleotide tiling arrays representing sense and antisense strands of the entire nonrepetitive sequence of the human genome and found 10,595 transcribed sequences not detected by other methods.

Antisense Transcription in the Mammalian Transcriptome

Experimental evidence that perturbation of an antisense RNA can alter the expression of sense messenger RNAs is presented, suggesting that antisense transcription contributes to control of transcriptional outputs in mammals.

Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage

By analyzing four libraries (brain, cortex, hippocampus, and cerebellum), this work redefined more accurately the TSPs of 11-27% of the analyzed transcriptional units that were hit.

Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.

The argument for a re-evaluation of the total number of human genes and an alternative term for "gene" to encompass these growing, novel classes of RNA transcripts in the human genome is strongly supported.

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project, which also include non-protein-coding RNAs, and the lower gene number estimation of genome annotations.

A Guide to the Mammalian Genome

The RIKEN Mouse Gene Encyclopedia Project has provided a model for eukaryotic transcriptome projects and developed new approaches to production of full-length cDNAs that required (1) a novel reverse transcriptase reaction (to enable effective complete firststrand synthesis), (2) novel 5 end capture technology, and (3) novel approaches to normalization and subtraction of cDNA libraries.

Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation

GIS analysis, in which 5′ and 3′ signatures of full-length cDNAs are accurately extracted into paired-end ditags (PETs) that are concatenated for efficient sequencing and mapped to genome sequences to demarcate the transcription boundaries of every gene, is developed.