Ciona intestinalis transcriptome project. Ciona intestinalis

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 in mid-tailbud-stage embryos 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.

在哺乳动物中，CpG岛（CpG island）是优良的基因标记物，因其常与启动子区域相关联。在哺乳动物及其他脊椎动物中，可观察到富含G+C碱基与CpG二核苷酸（CpG dinucleotide）的基因组片段，不过不同物种间的碱基组成差异显著。CpG岛通常可规避DNA甲基化修饰，且多存在于广泛表达基因的启动子区域。另一类启动子的G+C与CpG含量较低，被认为参与基因表达的时空特异性调控。据报道，无脊椎动物仅具有一类富含CpG二核苷酸的启动子，这提示该类启动子是原始的启动子类型。然而，无脊椎动物基因的注释信息有限，阻碍了对其启动子的大规模分析。为探究脊椎动物两类启动子的起源，我们选取了与脊椎动物演化关系相近的无脊椎动物——柄海鞘（Ciona intestinalis），并利用下一代测序仪（next-generation sequencer）技术在其尾芽中期胚胎中完成了全基因组范围的转录起始位点（transcription start site）鉴定。我们在转录起始位点周围检测到较高的G+C与CpG含量，但启动子区域与背景序列间的该成分差异远小于哺乳动物。富含CpG的基因组片段同样较为局限，因此这类片段与哺乳动物的低CpG启动子的相似性高于CpG岛启动子。基于上述数据，我们推断CpG岛的演化历史并不足够久远，无法在无脊椎动物中被发现。这类结构可能通过某种主动机制在脊椎动物演化早期出现，并自此作为脊椎动物启动子的组成部分被保留下来。