Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain.
PLoS Comput Biol. 2010 Oct 7;6(10):e1000953. doi: 10.1371/journal.pcbi.1000953.
An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization.
越来越多的证据表明，基因并非随机分布在真核生物染色体上，而是存在于功能区域中。然而，导致这种区域形成并维持的驱动力仍然存在争议。我们首次详细绘制了富含具有相关功能的基因的基因组区域的多物种图谱，并研究了这种聚类的进化意义。我们的研究结果表明，高等真核生物基因组的染色体包含高达 12%的基因，这些基因排列在功能区域中，具有高度的基因共表达，并且在系统发育中一致分布。出乎意料的是，具有同源功能的区域是由不同物种中的不同（非同源）基因形成的。实际上，功能区域并没有被保守，它们比基因组平均水平具有更高程度的同线性断裂。这种情况与存在选择压力以优化功能相关基因的协调转录是一致的。如果这些区域被染色体重排打破，选择将有利于进一步的重排，以重建具有类似功能的其他区域。这项研究得出的结论是，基因组具有高度的功能组织，呈现出动态的景观。
