Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae
Analysis of similarity within 142 pairs of orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae
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DOI：
10.1093/nar/30.5.1233
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发表时间：
2002-03-01
影响因子：
14.9
通讯作者：
Kondrashov, AS
中科院分区：
文献类型：
--
作者：
Webb, CT;Shabalina, SA;Kondrashov, AS
相关物种基因组之间的相似性模式反映了 DNA 内选择性约束的分布。我们分析了秀丽隐杆线虫和布里格斯隐杆线虫的 142 个直系同源基因间区域的比对，发现了一种镶嵌模式，其中高度相似性的区域（系统发育足迹）散布着不可比对的序列。足迹覆盖了大约 20% 的基因间区域，通常成簇出现，在 5' UTR 内很少见，但在 3' UTR 内常见。足迹的转换与颠换比率高于随机预期，GC 含量也高于基因间区域的其余部分。当基因定向使得它们的5'端形成基因间区域的边界时，基因间区域内的足迹数量和足迹的GC含量更高。总的来说，这里确定的模式和特征以及其他比较和实验研究表明，许多足迹具有调节功能，尽管其他类型的功能也是可能的。这些结论可能在真核生物中相当普遍，并且通过基因组比较确定的保守调控元件的特征可用于预测个体 DNA 序列内的调控位点。
Patterns of similarity between genomes of related species reflect the distribution of selective constraint within DNA. We analyzed alignments of 142 orthologous intergenic regions of Caenorhabditis elegans and Caenorhabditis briggsae and found a mosaic pattern with regions of high similarity (phylogenetic footprints) interspersed with non-alignable sequences. Footprints cover similar to20% of intergenic regions, often occur in clumps and are rare within 5' UTRs but common within 3' UTRs. The footprints have a higher ratio of transitions to transversions than expected at random and a higher GC content than the rest of the intergenic region. The number of footprints and the GC content of footprints within an intergenic region are higher when genes are oriented so that their 5' ends form the boundaries of the intergenic region. Overall, the patterns and characteristics identified here, along with other comparative and experimental studies, suggest that many footprints have a regulatory function, although other types of function are also possible. These conclusions may be quite general across eukaryotes, and the characteristics of conserved regulatory elements determined from genomic comparisons can be useful in prediction of regulation sites within individual DNA sequences.