Abstract
Comparative genomics is widely used in identification of exon-inton boundaries and noncoding regulatory elements. This strategy has been successfully used in human-mouse comparison. However, the 75 million years of separation from their last common ancestor will cause the recent changes in DNA which account for uniquely primate biological traits. Therefore, in order to investigate primate-specific regulatory element, we compare the promoter sequence of human and their nearest primate relatives. Currently, only 223 sequences belonging to 61 primate genes of 19 species have been identified in NCBI. Thus, we purified genomic DNAs from cell cultures of Lemur, Erythrocebus, Pongo, Macaca, Saimiri, Pan, and Gorilla, and cloned the promoter region of several genes of interest. All sequences were analyzed via TRANSPLORER®, GenomeNet, and promoter cluster motif classification (PCMC) program. We analyzed promoter sequences of genes whose expression profiles differ significantly between human and chimpanzee brains. Some transcription factor binding sites were only predicted uniquely in human or chimpanzee promoters. We amplified 19 set of promoter sequences. Of which the promoters of somatostatin receptor 2 (sstr2) and the promoters of src family associated phosphoprotein 2 (scap2) were obtained. Prediction of transcription binding sites revealed that some binding sites, such as CCAAT box, and FOXJ2, were important in regulation of scap2 mRNA expression. We have also obtained sequences from the upstream regions of primate rnase2 and rnase3 which was emerged from a gene duplication event after divergence of Old World monkeys from New World monkeys. We have found a 34-nucleotide difference containing a potential binding site for Hand1/E47 in rnase2 promoter. According to maximum parsimony method, we suggested that two mechanisms may cause difference of the 34 gap sequence. One was that an insertion of 34 nucleotides arose after gene duplication, and then a deletion of the gap sequence occurred in the lineage of hominoids. The other was that two deletions occurred in the lineage of hominoids and prosimians.