|Budget Amount *help
¥24,000,000 (Direct Cost : ¥24,000,000)
Fiscal Year 2004 : ¥12,000,000 (Direct Cost : ¥12,000,000)
Fiscal Year 2003 : ¥12,000,000 (Direct Cost : ¥12,000,000)
For five years, we have attempted to clarify various kinds of regularities hidden in either DNA, RNA, or amino acid sequence. In the first three years, this project belonged to the "genome information science" area while it belonged to "genome biology" in the last two years. At that second term, we also explored possibilities to collaborate with wet biologists. Two main outcomes of the project are as follows:
1. Comprehensive analyses of the transcriptional regulatory system in Bacillus subtilis
We have constructed, maintained, and updated DBTBS: database on transcription factors and promoters of B. subtilis, which is one of the most well characterized bacteria. Moreover, we have conducted a number of predictive studies based on the data in DBTBS, including prediction of regulons based on the genome comparison of related bacteria, prediction of sigma factor-dependency for each gene using microarray data, comparative analysis of the results of terminator prediction, and prediction of transcription factor-binding sites using Bayesean statistics.
2. Studies of transcriptional start sites (TSSs) and their upstream regions of human and mouse genes
Collaborating with Prof Sumio Sugano's group, we have updated the DBTSS database, which is a collection of TSSs determined by the sequences of cDNAs having the intact cap structure. Using DBTSS, a series of studies were carried out For example, we discovered that the peak of the distribution of CpG islands corresponds to the TSS of each gene statistically and that the existence of a CpG island near the TSS of a gene highly correlates with the tissue specificity of its expression. In addition, we performed a systematic prediction of so-called TOP (terminal oligo-pyrimidine-rich) genes in the human as well as mouse genomes.