Lee UnJin, Arsala Deanna, Xia Shengqian, Li Cong, Ali Mujahid, Svetec Nicolas, Langer Christopher B, Sobreira Débora R, Eres Ittai, Sosa Dylan, Chen Jianhai, Zhang Li, Reilly Patrick, Guzzetta Alexander, Emerson J J, Andolfatto Peter, Zhou Qi, Zhao Li, Long Manyuan
Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
Laboratory of Evolutionary Genetics and Genomics, Rockefeller University, New York, NY, USA.
Sci Adv. 2024 Dec 20;10(51):eadn6625. doi: 10.1126/sciadv.adn6625. Epub 2024 Dec 18.
Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment by distally duplicated genes is an efficient mechanism for modulating tissue-specific production of preexisting proteins. By leveraging genomic asymmetries, we performed a coexpression analysis on tissue data to show the generality of enhancer capture-divergence (ECD) as a significant evolutionary driver of asymmetric, distally duplicated genes. We use the recently evolved gene / as an example of the ECD process. By assaying genome-wide chromosomal conformations in multiple species, we show that was inserted near a preexisting, long-distance three-dimensional genomic interaction. We then use this data to identify a newly found enhancer (), buried within the coding region of the highly conserved, essential gene , that likely neofunctionalized . Last, we demonstrate ancestral transcriptional coregulation of 's future insertion site, illustrating how enhancer capture provides a highly evolvable, one-step solution to Ohno's dilemma.
先前关于基因重复进化的模型忽略了基因组结构的关键作用。在这里，我们表明，远端重复基因基于邻近性的调控招募是调节现有蛋白质组织特异性产生的有效机制。通过利用基因组不对称性，我们对组织数据进行了共表达分析，以表明增强子捕获-分化（ECD）作为不对称远端重复基因的重要进化驱动因素的普遍性。我们以最近进化的基因/为例说明ECD过程。通过检测多个物种全基因组的染色体构象，我们表明该基因插入到了一个先前存在的远距离三维基因组相互作用附近。然后，我们利用这些数据鉴定出一个新发现的增强子（），它埋藏在高度保守的必需基因的编码区域内，该增强子可能使该基因产生了新功能。最后，我们展示了该基因未来插入位点的祖先转录共调控，说明了增强子捕获如何为大野困境提供了一个高度可进化的一步解决方案。
