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Published online before print April 11, 2001, 10.1101/gr.GR-1640R
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Vol. 11, Issue 5, 677-684, May 2001

REPORTS
Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

Yutaka Suzuki,1,2,3,9 Tatsuhiko Tsunoda,2,3 Jun Sese,4 Hirotoshi Taira,5 Junko Mizushima-Sugano,1,2 Hiroko Hata,1 Toshio Ota,6 Takao Isogai,6 Toshihiro Tanaka,2 Yusuke Nakamura,2 Akira Suyama,7 Yoshiyuki Sakaki,2,3 Shinichi Morishita,4 Kousaku Okubo,8 and Sumio Sugano1,2

1 Department of Virology and 2 Human Genome Center, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 108-8639, Japan; 3 Genome Science Center, Institute of Physical and Chemical Research (RIKEN); Wakoshi, Saitama 351-0106, Japan; 4 Department of Complexity Science and Engineering Graduate School of Frontier Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan; 5 Intelligent Communication Laboratory, Nippon Telegraph and Telephone Communication Science Laboratories, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan; 6 Helix Research Institute, Kisarazushi, Chiba 292-0812, Japan; 7 Department of Life Sciences, University of Tokyo, Meguro-ku, Tokyo 153-0041, Japan; 8 The Institute of Molecular and Cell Biology, Osaka University, Suita-shi, Osaka 565-0871, Japan

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the "oligo-capping" method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+ PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and the TM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.

[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos. AU098358-AU100608.]

9 Corresponding author.

11:677-684 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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