title: Profiling ascidian promoters as the primordial type of vertebrate promoter.
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 large-scale 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.
authors.affiliation: Human Genome Centre, Institute of Medical Science, University of Tokyo, Tokyo, Japan.
authors.forename: Kohji
authors.initials: K
authors.lastname: Okamura
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Noriko
authors.initials: N
authors.lastname: Takimoto
authors.forename: Koki
authors.initials: K
authors.lastname: Nishitsuji
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Takehiro G
authors.initials: TG
authors.lastname: Kusakabe
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D000818:Animals; D005075:Biological Evolution; D018899:CpG Islands; D005787:Gene Frequency; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site; D014561:Urochordata / Q000235:genetics*; D014714:Vertebrates / Q000235:genetics*