@article{32e46936793643c992745a874fcaddf0,
title = "Genome-wide analysis of mammalian promoter architecture and evolution",
abstract = "Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our 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. Among the TSSs, we identified new start sites associated with the majority of exons and with 3′ UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.",
author = "Piero Carninci and Albin Sandelin and Boris Lenhard and Shintaro Katayama and Kazuro Shimokawa and Jasmina Ponjavic and Semple, \{Colin A.M.\} and Taylor, \{Martin S.\} and Engstr{\"o}m, \{P{\"a}r G.\} and Frith, \{Martin C.\} and Forrest, \{Alistair R.R.\} and Alkema, \{Wynand B.\} and Tan, \{Sin Lam\} and Charles Plessy and Rimantas Kodzius and Timothy Ravasi and Takeya Kasukawa and Shiro Fukuda and Mutsumi Kanamori-Katayama and Yayoi Kitazume and Hideya Kawaji and Chikatoshi Kai and Mari Nakamura and Hideaki Konno and Kenji Nakano and Salim Mottagui-Tabar and Peter Arner and Alessandra Chesi and Stefano Gustincich and Francesca Persichetti and Harukazu Suzuki and Grimmond, \{Sean M.\} and Wells, \{Christine A.\} and Valerio Orlando and Claes Wahlestedt and Liu, \{Edison T.\} and Matthias Harbers and Jun Kawai and Bajic, \{Vladimir B.\} and Hume, \{David A.\} and Yoshihide Hayashizaki",
note = "Funding Information: We thank the following individuals for discussion, encouragement and technical assistance: H. Atsui, A. Hasegawa, K. Hayashida, H. Himei, F. Hori, C. Kawazu, M. Kojima, K. Waki, M. Aoki, K Murakami, M. Murata, M. Nishikawa, H. Nishiyori, K. Nomura, M. Ohno, H. Sato, Y. Shigemoto, N. Suzuki, Y. Takeda and K. Yoshida. We especially thank A. Wada, T. Ogawa, M. Muramatsu, A. Kira and all the members of RIKEN Yokohama Research Promotion Division for supporting and encouraging the project. We also thank the Laboratory of Genome Exploration Research Group for secretarial and technical assistance, and Yokohama City University, who provided human samples and computational resources of the RIKEN Super Combined Cluster (RSCC). This work was mainly supported by Research Grant for the Genome Network Project from the Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT), the RIKEN Genome Exploration Research Project from the Japanese Ministry of Education, Culture, Sports, Science and Technology of the Japanese Government (to Y.H.), Advanced and Innovational Research Program in Life Science (to Y.H.), National Project on Protein Structural and Functional Analysis from MEXT (to Y.H.), Presidential Research Grant for Intersystem Collaboration of RIKEN (to P.C. and Y.H.) and a grant from the Six Framework Program from the European Commission (to P.C.).",
year = "2006",
month = jun,
doi = "10.1038/ng1789",
language = "English",
volume = "38",
pages = "626--635",
journal = "Nature Genetics",
issn = "1061-4036",
publisher = "Nature Research",
number = "6",
}