Chain Frédéric J J, Meyer Britta S, Heckwolf Melanie J, Franzenburg Sören, Eizaguirre Christophe, Reusch Thorsten B H
Department of Biological Sciences University of Massachusetts Lowell Lowell Massachusetts USA.
Marine Evolutionary Ecology GEOMAR Helmholtz Centre for Ocean Research Kiel Kiel Germany.
Evol Appl. 2024 Jul 14;17(7):e13753. doi: 10.1111/eva.13753. eCollection 2024 Jul.
Duplicated genes provide the opportunity for evolutionary novelty and adaptive divergence. In many cases, having more gene copies increases gene expression, which might facilitate adaptation to stressful or novel environments. Conversely, overexpression or misexpression of duplicated genes can be detrimental and subject to negative selection. In this scenario, newly duplicate genes may evade purifying selection if they are epigenetically silenced, at least temporarily, leading them to persist in populations as copy number variations (CNVs). In animals and plants, younger gene duplicates tend to have higher levels of DNA methylation and lower levels of gene expression, suggesting epigenetic regulation could promote the retention of gene duplications via expression repression or silencing. Here, we test the hypothesis that DNA methylation variation coincides with young duplicate genes that are segregating as CNVs in six populations of the three-spined stickleback that span a salinity gradient from 4 to 30 PSU. Using reduced-representation bisulfite sequencing, we found DNA methylation and CNV differentiation outliers rarely overlapped. Whereas lineage-specific genes and young duplicates were found to be highly methylated, just two gene CNVs showed a significant association between promoter methylation level and copy number, suggesting that DNA methylation might not interact with CNVs in our dataset. If most new duplications are regulated for dosage by epigenetic mechanisms, our results do not support a strong contribution from DNA methylation soon after duplication. Instead, our results are consistent with a preference to duplicate genes that are already highly methylated.
基因复制为进化创新和适应性分化提供了机会。在许多情况下，拥有更多的基因拷贝会增加基因表达，这可能有助于适应压力环境或新环境。相反，复制基因的过表达或错误表达可能是有害的，并会受到负选择。在这种情况下，如果新复制的基因通过表观遗传沉默（至少是暂时的），它们可能会逃避纯化选择，从而使它们作为拷贝数变异（CNV）在种群中持续存在。在动物和植物中，较年轻的基因复制体往往具有较高水平的DNA甲基化和较低水平的基因表达，这表明表观遗传调控可能通过表达抑制或沉默来促进基因复制的保留。在这里，我们检验了一个假设，即在跨越4至30 PSU盐度梯度的三刺鱼的六个种群中，DNA甲基化变异与作为CNV分离的年轻复制基因一致。使用简化代表性亚硫酸氢盐测序，我们发现DNA甲基化和CNV分化异常值很少重叠。虽然谱系特异性基因和年轻复制体被发现高度甲基化，但只有两个基因CNV显示启动子甲基化水平与拷贝数之间存在显著关联，这表明在我们的数据集中DNA甲基化可能不与CNV相互作用。如果大多数新的复制通过表观遗传机制进行剂量调控，我们的结果不支持复制后不久DNA甲基化的强大作用。相反，我们的结果与优先复制已经高度甲基化的基因一致。
