PRJDA46247 TSS Seq of Ascidian Embryos In mammals, CpG islands are good markers of genes because they are often linked to promoters. Genomic stretches with high frequencies of G+C and the CpG dinucleotide are observed in mammals and other vertebrates, although their contents vary considerably among species. CpG islands 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. Invertebrates 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 invertebrate 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 genomewide using a next-generation sequencer. We observed high G+C and CpG contents 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 were more similar to mammalian CpG-poor promoters than to CpG island 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. cintailb bioproject PRJDA46247 PRJDA46247 true genomeprj 46247 46247 false See above (STUDY_ABSTRACT) Linked publication http://dx.doi.org/10.1186/1471-2164-12-S3-S7