Tadayuki Takeda, Yasushi Totoki, Naoki Adati, Kunihiko Takamatsu, Ritsuko Ozawa, Nagisa Nakata, Asami Maeda, Mizuki Takahashi, Hideki Noguchi, Yoko Kuroki, Atsushi Toyoda, Yoshiyuki Sakaki
RIKEN Genomic Sciences Center (GSC), 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
Comparative genomics using a variety of eukaryotic genome sequences is an extremely useful method for identification of functional regions such as exons, splicing sites and cis-regulatory elements located across an entire genome. In this study we extracted and classified the conserved sequences in human gene promoters by comparative genomics, and experimentally verified their binding capability for transcription factors (TFs). We first selected several TF genes including PAX2 and OLIG2, which are required for neurogenesis, and extracted 3kb for each promoter region upstream of the transcriptional start site. We isolated each by PCR and sequenced the syntenic regions in 12~14 primate species (e.g. Apes, Old-world monkeys, New-world monkeys and Prosimians). We identified the conserved regions by comparing the promoter sequences in primates and other mammalian genome sequences such as mouse, rat and dog with the syntenic regions in the human genome, and classified the conserved regions in terms of their specificity in primates or mammalian conservation and in terms of known or unknown elements. These conserved regions were verified for protein-DNA interaction by gel shift assay. Most of the conserved sequences located on the human TF gene promoters interact with multiple nuclear proteins, suggesting that these conserved regions include novel TF-binding sequences and primate-specific conserved regions, which may act as primate-specific transcriptional regulatory elements in the promoter.
Other abstracts in same session