Lehrstuhl für Computational Biology, Universität des Saarlandes, Saarbrücken, Germany.
OMICS. 2009 Apr;13(2):153-64. doi: 10.1089/omi.2008.0046.
CpG islands (CGIs) are generally regarded as important epigenetic regulatory elements due to their association with promoter regions. However, identification of functional CGIs is hampered by repetitive elements and species-specific particularities. Here, we compared the performance of different CGI detection programs on genomic sequences of human and mouse genes. Although mouse CGIs are shorter and G+C poorer than their human counterparts, the different tools tested in our study reliably identify CGIs in promoter regions in both species. Our study confirms that substantially fewer murine than human CGIs coincide with repetitive elements and indicates that such CGIs are subject to accelerated cytosine deamination. In addition, CpG depletion appears to anticorrelate with the epigenetic features of functional regulatory CGIs. Taking into account different deamination rates in unmethylated CGIs versus those in methylated CGIs might support the detection of functional CGIs in other species for which there is little epigenetic information available.
CpG 岛（CGIs）通常被认为是重要的表观遗传调控元件，因为它们与启动子区域有关。然而，由于重复元件和物种特异性的特殊性，功能 CGIs 的鉴定受到了阻碍。在这里，我们比较了不同 CGI 检测程序在人类和小鼠基因基因组序列上的性能。尽管小鼠 CGIs 比人类 CGIs 短且 G+C 含量较低，但我们研究中测试的不同工具可靠地识别了两种物种启动子区域中的 CGIs。我们的研究证实，与重复元件重叠的小鼠 CGI 数量明显少于人类 CGI，并表明这些 CGI 易发生胞嘧啶脱氨作用。此外，CpG 耗竭似乎与功能调节 CGI 的表观遗传特征呈负相关。考虑到未甲基化 CGIs 与甲基化 CGIs 中的脱氨率不同，可能有助于检测其他表观遗传信息较少的物种中的功能 CGIs。
