Transcription factor binding sites are frequently under accelerated evolution in primates.
Transcription factor binding sites are frequently under accelerated evolution in primates.
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DOI：
10.1038/s41467-023-36421-3
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发表时间：
2023-02-11
影响因子：
16.6
通讯作者：
Huang, Yi-Fei
中科院分区：
文献类型：
--
作者：
Zhang, Xinru;Fang, Bohao;Huang, Yi-Fei
最近的比较基因组学研究已经确定了许多人类加速因子（HARs）在人类谱系中具有升高的替代率。然而，转录因子结合位点（TFBS）在人类和其他灵长类动物中的加速进化程度仍然未知。在这里，我们介绍了两个池为基础的系统发育方法，显着增强的灵敏度，以检查加速进化TFBS。使用这些新方法，我们表明，在人类基因组中注释的6000多个TFBS在人类、猿和旧世界猴中经历了加速进化。虽然这些TFBS单独显示出相对较弱的加速进化信号，但它们总体上比HARs更丰富。此外，我们表明，加速进化的Pol III结合位点可能是由谱系特异性的积极选择，而加速进化的其他TFBS可能是由非适应性进化力量。最后，加速的TFBS在发育基因周围富集，这表明TFBS的加速进化可能驱动灵长类动物之间发育过程的分化。描述加速进化下的基因组元件对于理解人类进化和疾病的基因组基础至关重要。在这里，Zhang等人介绍了GroupAcc，这是两种基于池的系统发育方法的集合，具有增强的灵敏度，可以检查转录因子结合位点的加速进化。
Recent comparative genomic studies have identified many human accelerated elements (HARs) with elevated substitution rates in the human lineage. However, it remains unknown to what extent transcription factor binding sites (TFBSs) are under accelerated evolution in humans and other primates. Here, we introduce two pooling-based phylogenetic methods with dramatically enhanced sensitivity to examine accelerated evolution in TFBSs. Using these new methods, we show that more than 6000 TFBSs annotated in the human genome have experienced accelerated evolution in Hominini, apes, and Old World monkeys. Although these TFBSs individually show relatively weak signals of accelerated evolution, they collectively are more abundant than HARs. Also, we show that accelerated evolution in Pol III binding sites may be driven by lineage-specific positive selection, whereas accelerated evolution in other TFBSs might be driven by nonadaptive evolutionary forces. Finally, the accelerated TFBSs are enriched around developmental genes, suggesting that accelerated evolution in TFBSs may drive the divergence of developmental processes between primates. Characterizing genomic elements under accelerated evolution is crucial for understanding the genomic basis of human evolution and disease. Here, Zhang et al. introduce GroupAcc, a collection of two pooling-based phylogenetic methods with enhanced sensitivity to examine accelerated evolution in transcription factor binding sites.
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