Leach Lindsey J, Zhang Ze, Lu Chenqi, Kearsey Michael J, Luo Zewei
School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom.
Mol Biol Evol. 2007 Nov;24(11):2556-65. doi: 10.1093/molbev/msm188. Epub 2007 Sep 10.
Expression divergence of duplicate genes is widely believed to be important for their retention and evolution of new function, although the mechanism that determines their expression divergence remains unclear. We use a genetical genomics approach to explore divergence in genetical control of yeast duplicate genes created by a whole-genome duplication that occurred about 100 MYA and those with a younger duplication age. The analysis reveals that duplicate genes have a significantly higher probability of sharing common genetic control than pairs of singleton genes. The expression quantitative trait loci (eQTLs) have diverged completely for a high proportion of duplicate pairs, whereas a substantially larger proportion of duplicates share common regulatory motifs after 100 Myr of divergent evolution. The similarity in both genetical control and cis motif structure for a duplicate pair is a reflection of its evolutionary age. This study reveals that up to 20% of variation in expression between ancient duplicate gene pairs in the yeast genome can be explained by both cis motif divergence (approximately 8%) and by trans eQTL divergence (approximately 10%). Initially, divergence in all 3 aspects of cis motif structure, trans-genetical control, and expression evolves coordinately with the coding sequence divergence of both young and old duplicate pairs. These findings highlight the importance of divergence in both cis motif structure and trans-genetical control in the diverse set of mechanisms underlying the expression divergence of yeast duplicate genes.
尽管决定重复基因表达差异的机制尚不清楚，但普遍认为重复基因的表达差异对于它们的保留和新功能的进化很重要。我们采用遗传基因组学方法，探究由约1亿年前发生的全基因组复制产生的酵母重复基因以及复制年龄较新的重复基因在遗传控制方面的差异。分析表明，与单拷贝基因对相比，重复基因共享共同遗传控制的概率显著更高。对于很大一部分重复基因对，表达数量性状位点（eQTL）已经完全分化，而在经历1亿年的分化进化后，相当大比例的重复基因共享共同的调控基序。重复基因对在遗传控制和顺式基序结构上的相似性反映了其进化年龄。这项研究表明，酵母基因组中古老重复基因对之间高达20%的表达差异可由顺式基序差异（约8%）和反式eQTL差异（约10%）共同解释。最初，顺式基序结构、反式遗传控制和表达这三个方面的差异与年轻和古老重复基因对的编码序列差异协同进化。这些发现突出了顺式基序结构和反式遗传控制差异在酵母重复基因表达差异的多种机制中的重要性。
