This article is part of the supplement: Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Computational Biology

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Profiling ascidian promoters as the primordial type of vertebrate promoter

Kohji Okamura12, Riu Yamashita1, Noriko Takimoto3, Koki Nishitsuji34, Yutaka Suzuki5, Takehiro G Kusakabe4 and Kenta Nakai1*

Author affiliations

1 Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan

2 Centre for Informational Biology, Ochanomizu University, Tokyo, Japan

3 Department of Life Science, Graduate School of Life Science, University of Hyogo, Hyogo, Japan

4 Department of Biology, Faculty of Science and Engineering, Konan University, Kobe, Japan

5 Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan

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Citation and License

BMC Genomics 2011, 12(Suppl 3):S7  doi:10.1186/1471-2164-12-S3-S7

Published: 30 November 2011



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.