Homologous Block Structure in the Promoter Regions

Comparative sequence analysis was carried out for the regions adjacent (1kb) to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. Within the homologous blocks, the sequence identity was uniformly 65% regardless of their length. About 90% of the previously characterized transcription factor binding sites were located within those blocks. In 46% of the blocks, the 5' ends were bounded by interspersed repetitive elements, some of which may have nucleated the genomic rearrangements. The length of the blocks was shortest in the promoters of genes encoding transcription factors and of genes whose expression patterns are brain specific, which suggests that the evolutional diversifications in the transcriptional modulations should be the most marked in these populations of genes. [PMID: 15342556]