Department of Biomedical Engineering, Tel Aviv University, Tel Aviv 6997801, Israel.
Department of Computer Science, Technion-Israel Institute of Technology, Haifa 32000, Israel.
Nat Commun. 2014 Dec 16;5:5876. doi: 10.1038/ncomms6876.
It has been shown that the distribution of genes in eukaryotic genomes is not random; however, formerly reported relations between gene function and genomic organization were relatively weak. Previous studies have demonstrated that codon usage bias is related to all stages of gene expression and to protein function. Here we apply a novel tool for assessing functional relatedness, codon usage frequency similarity (CUFS), which measures similarity between genes in terms of codon and amino acid usage. By analyzing chromosome conformation capture data, describing the three-dimensional (3D) conformation of the DNA, we show that the functional similarity between genes captured by CUFS is directly and very strongly correlated with their 3D distance in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, mouse and human. This emphasizes the importance of three-dimensional genomic localization in eukaryotes and indicates that codon usage is tightly linked to genome architecture.
已经表明，真核基因组中的基因分布并非随机；然而，以前报道的基因功能与基因组组织之间的关系相对较弱。先前的研究表明，密码子使用偏好与基因表达的各个阶段以及蛋白质功能有关。在这里，我们应用了一种评估功能相关性的新工具，即密码子使用频率相似性（CUFS），它根据密码子和氨基酸使用来衡量基因之间的相似性。通过分析描述 DNA 三维（3D）构象的染色体构象捕获数据，我们表明，通过 CUFS 捕获的基因之间的功能相似性与它们在酿酒酵母、裂殖酵母、拟南芥、小鼠和人类中的 3D 距离直接且非常强相关。这强调了三维基因组定位在真核生物中的重要性，并表明密码子使用与基因组结构紧密相关。
