Evolution of closely linked gene pairs in vertebrate genomes
Evolution of closely linked gene pairs in vertebrate genomes
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DOI：
10.1093/molbev/msn136
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发表时间：
2008-09-01
影响因子：
10.7
通讯作者：
Madsen, Ole
中科院分区：
文献类型：
--
作者：
Franck, Erik;Hulsen, Tim;Madsen, Ole
哺乳动物基因组中紧密相连的基因的方向不是随机的：有比预期更多的头对头(H2H)基因对。为了了解H2H基因对这种富集性的起源，我们分析了基因间DNA(基因DUO)间隔小于600bp的基因对的系统发育分布。我们在这里表明，缺乏头尾(H2T)基因是哺乳动物基因组的一个更明显的特征，鸭嘴兽基因组是唯一的例外。在非哺乳类脊椎动物和非脊椎动物基因组中，H_2H、H_2T和尾巴对尾巴(T2T)基因的频率几乎是随机的。在四足类基因组中，H_2T和T_2T基因二元组比H_2H基因二元组更有可能是一个更大的基因簇的一部分，而在鱼类和尾索动物基因组中则相反。在人类和小鼠组织中，基因Duo的表达谱倾向于正向共表达，而不考虑方向。大约40%的人类基因二元组的两个成员的直系同源基因的组织可以在其他物种中追踪到，这使得能够预测节口动物、四足动物、羊膜动物和真原基胶质细胞的分支点的组织结构。H2 H基因Duo的积累始于四足动物，而H2 T和T2T基因Duos的积累仅始于羊膜动物。H_2T和T_2T基因双重复相对H_2H基因双重复明显缺乏进化保守性，这是因为它们在哺乳动物的谱系中起源较晚；我们表明，一旦它们形成，H_2T和T_2T基因双重复与H_2H基因双重复一样稳定。
The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA (gene duos). We show here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception. In nonmammalian vertebrate and in nonvertebrate genomes, the frequency of h2h, h2t, and tail-to-tail (t2t) gene duos is close to random. In tetrapod genomes, the h2t and t2t gene duos are more likely to be part of a larger gene cluster of closely spaced genes than h2h gene duos; in fish and urochordate genomes, the reverse is seen. In human and mouse tissues, the expression profiles of gene duos were skewed toward positive coexpression, irrespective of orientation. The organization of orthologs of both members of about 40% of the human gene duos could be traced in other species, enabling a prediction of the organization at the branch points of gnathostomes, tetrapods, amniotes, and euarchontoglires. The accumulation of h2h gene duos started in tetrapods, whereas that of h2t and t2t gene duos only started in amniotes. The apparent lack of evolutionary conservation of h2t and t2t gene duos relative to that of h2h gene duos is thus a result of their relatively late origin in the lineage leading to mammals; we show that once they are formed h2t and t2t gene duos are as stable as h2h gene duos.