Noah M. Simon, Yujin Kim, Joost Gribnau, Diana M. Bautista, James R. Dutton, Rachel B. Brem
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引用次数: 0
摘要
进化基因组学的一个关键目标是利用分子数据来推断基因组的选择性作用力。这一领域的进步在很大程度上得益于先进的分子进化分析方法的发展。在这里,我们以麝亚种的干细胞为模型,探索了基于序列的经典选择测试与基于经验表达的方法之间的交叉点。通过测试通路中跨基因的定向顺式调控进化,我们发现东南亚小鼠M. m. castaneus的干细胞中翻译基因的诱导程序比其姊妹类群独特。我们随后挖掘了种群基因组序列,以探寻这种表达差异的潜在调控机制,并在翻译基因的上游区域发现了蓖麻小鼠特有等位基因的有力证据。我们根据具有高翻译能力的干细胞中整个麝香种系特异性压力变化的模型来解释我们的数据。我们的发现强调了整合基于表达和序列的方法的严谨性,从而对很久以前的进化事件提出假设。
Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes
A key goal of evolutionary genomics is to harness molecular data to draw inferences about selective forces that have acted on genomes. The field progresses in large part through the development of advanced molecular-evolution analysis methods. Here we explored the intersection between classical sequence-based tests for selection and an empirical expression-based approach, using stem cells from Mus musculus subspecies as a model. Using a test of directional, cis-regulatory evolution across genes in pathways, we discovered a unique program of induction of translation genes in stem cells of the Southeast Asian mouse M. m. castaneus relative to its sister taxa. We then mined population-genomic sequences to pursue underlying regulatory mechanisms for this expression divergence, finding robust evidence for alleles unique to M. m. castaneus at the upstream regions of the translation genes. We interpret our data under a model of changes in lineage-specific pressures across Mus musculus in stem cells with high translational capacity. Our findings underscore the rigor of integrating expression and sequence-based methods to generate hypotheses about evolutionary events from long ago.