Large-Scale Collection and Characterization of Promoters of Human and Mouse Genes

Article type: Research Article

Authors: Suzuki, Yutaka | Yamashita, Riu | Shirota, Matsuyuki | Sakakibara, Yuta^; | Chiba, Joe | Mizushima-Sugano, Junko | Kel, Alexander E. | Arakawa, Takahiro | Carninci, Piero^; | Kawai, Jun^; | Hayashizaki, Yoshihide^; | Takagi, Toshihisa | Nakai, Kenta | Sugano, Sumio

Affiliations: Human Genome Center, The Institute of Medical Science, The University of Tokyo: 4-6-1 Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan | Department of Biological Science and Technology, Science University of Tokyo, 2641 Yamazaki, Noda-shi, Chiba, 278-8510, Japan | BIOBASE GmbH, Halchtersche Str. 33, D-38304 Wolfenbüttel, Germany | Genome Science Laboratory, Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan | Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan

Note: [] Corresponding author. Tel.: +81 3 5449 5343; Fax: +81 3 5449 5416; E-mail: [email protected]

Abstract: We report the generation and initial characterization of a large-scale collection of sequences of putative promoter regions (PPRs) of human and mouse genes. Based on our unique collection of 400,225 and 580,209 human and mouse full-length cDNAs, we determined exact transcriptional start sites (TSSs). Using positional information of the TSSs, we could retrieve adjacent sequences as PPRs for 8,793 and 6,875 human and mouse genes, respectively. The positions of the PPRs were 4 kb upstream to previously reported 5'-ends of cDNAs on average, demonstrating that full-length cDNA information is indispensable for this purpose. Among those PPRs supported by experimentally validated TSSs, 3,324 could be paired as mutually homologous genes between human and mouse and were used for the comprehensive comparative studies. The sequence identities in the proximal regions of the TSSs were 45% on average, and 22,794 putative transcription factor binding sites that are conserved between human and mouse were identified. The data resource created in the present work and the results of the sequences' initial characterization should lay the firm foundation for deciphering the transcriptional modulations of human genes. All the data were deposited and made available through a database for comparative studies, DBTSS.

Keywords: full-length cDNA, promoter, comparative genomics, transcriptional start sites

Journal: In Silico Biology, vol. 4, no. 4, pp. 429-444, 2004