The 5th International Tunicate Meeting

Okinawa Industry Support Center, Okinawa, Japan

June 22, 2009

Oral 6-4 (Session 6: Gene network and genomics)

Oral presentation

Characterization and definition of promoter-associated CpG islands in ascidian genomes

Kohji Okamura1, Riu Yamashita1, Noriko Takimoto2, Koki Nishitsuji2,3, Yutaka Suzuki4, Takehiro G. Kusakabe3, and Kenta Nakai1,5 1Hum. Genome Ctr., Inst. Med. Sci., Univ. Tokyo, Japan, 2Dept. Life Sci., Grad. Sch. Life Sci., Univ. Hyogo, Japan, 3Dept. Biol., Fac. Sci. Eng., Konan Univ., Japan, 4Dept. Med. Genome Sci., Grad. Sch. Frontier Sci., Univ. Tokyo, Japan, 5BIRD, JST, Japan

In mammals, CpG islands are a good marker to find some classes of genes because they are often linked to a promoter. Such genomic stretches with a high G+C content and a high frequency of the CpG dinucleotide are observed not only in mammals but also in other vertebrates, even though the G+C and CpG contents vary considerably among these species. In most cases, CpG islands escape DNA methylation, which is related to gene repression in general. Hence, CpG islands tend to be promoters of broadly expressed genes. On the other hand, existence of CpG islands in invertebrate animals is unclear. Since there is a striking difference in DNA methylation pattern between vertebrates and invertebrates, which show global and fractional methylation, respectively, the function of DNA methylation per se in the latter group is also elusive. To address these questions in invertebrates, we performed determination of transcription start sites of ascidian genes by combination of the oligo-capping method and massive-scale cDNA sequencing. As a first step, we focused on genes expressed in tailbud embryos of Ciona intestinalis and treated them with or without 5-aza-2'-deoxycytidine to investigate some effects of undermethylation. As a result of excluding trans-spliced genes from the sequence analysis, for which accurate positions of transcription start sites cannot be determined, we found characteristic features of ascidian core promoters. Like vertebrates, they tend to be G+C- and CpG-rich, but over a narrower range around the transcription start sites. We also found asymmetric distribution of deaminated dinucleotides, suggesting a role of methylation in transcription and the existence of determinant of orientation of transcription. Furthermore, almost all promoters fall into the same category, whereas vertebrate promoters are divided into two classes in terms of CpG. Comparison of the experimental result with the genome of another ascidian Ciona savignyi also supported our finding, leading to the first definition of promoter-associated CpG islands in invertebrate organisms.