Profiling ascidian promoters as the primordial type of vertebrate promoter

Kohji Okamura, Riu Yamashita, Noriko Takimoto, Koki Nishitsuji, Yutaka Suzuki, Takehiro G. Kusakabe, Kenta Nakai

Research output: Contribution to conferencePaperpeer-review

6 Citations (Scopus)

Abstract

Background: 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 largescale analysis of their promoters. Results: 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. Conclusions: 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.

Original languageEnglish
DOIs
Publication statusPublished - 2011
Event10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Computational Biology, InCoB 2011/ISCB-Asia 2011 - Kuala Lumpur, Malaysia
Duration: 2011 Nov 302011 Dec 2

Other

Other10th International Conference on Bioinformatics and 1st ISCB Asia Joint Conference 2011: Computational Biology, InCoB 2011/ISCB-Asia 2011
CountryMalaysia
CityKuala Lumpur
Period11/11/3011/12/2

ASJC Scopus subject areas

  • Agricultural and Biological Sciences (miscellaneous)
  • Artificial Intelligence
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Software
  • Biotechnology
  • Genetics

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