The 10th International Conference on Bioinformatics
Renaissance Kuala Lumpur Hotel, Kuala Lumpur, Malaysia
November 30, 2011
6.1 (6. Sequence analysis and evolution II)
Oral presentation

Profiling ascidian promoters as the primordial type of vertebrate promoter
Kohji Okamura1,2, Riu Yamashita1, Noriko Takimoto3, Koki Nishitsuji3,4, Yutaka Suzuki5, Takehiro G. Kusakabe4, and Kenta Nakai1
1Hum. Genome Ctr., Inst. Med. Sci., Univ. Tokyo, Japan, 2Ctr. Inf. Biol., Ochanomizu Univ., Japan, 3Dept. Life Sci., Grad. Sch. Life Sci., Univ. Hyogo, Japan, 4Dept. Biol., Fac. Sci. Eng., Konan Univ., Japan, 5Dept. Med. Genome Sci., Grad. Sch. Frontier Sci., Univ. Tokyo, Japan
CpG islands are observed in mammals and other vertebrates, generally escape DNA methylation, and tend to occur in the promoters of widely expressed genes. Another class of promoter has lower G+C and CpG contents, and is thought to be involved in the spatiotemporal regulation of gene expression. Non-vertebrate deuterostomes are reported to have a single class of promoter with high-frequency CpG dinucleotides, suggesting that this is the original type of promoter. However, the limited annotation of these genes has impeded the large-scale analysis of their promoters. To determine the origins of the two classes of vertebrate promoters, we chose Ciona intestinalis, an invertebrate that is evolutionarily close to the vertebrates, and identified its transcription start sites genome-wide using a next-generation sequencer. We indeed observed a high CpG content around the transcription start sites, but their levels in the promoters and background sequences differed much less than in mammals. The CpG-rich stretches were also fairly restricted, so they appeared more similar to mammalian CpG-poor promoters. From these data, we infer that CpG islands are not sufficiently ancient to be found in invertebrates. They probably appeared early in vertebrate evolution via some active mechanism and have since been maintained as part of vertebrate promoters.