Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Scotland's Rural College (SRUC), The Roslin Institute Building, Easter Bush, Midlothian, UK.
Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK; Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
Cell Rep. 2024 Apr 23;43(4):113895. doi: 10.1016/j.celrep.2024.113895. Epub 2024 Mar 21.
Topologically associated domains (TADs) are interaction subnetworks of chromosomal regions in 3D genomes. TAD boundaries frequently coincide with genome breaks while boundary deletion is under negative selection, suggesting that TADs may facilitate genome rearrangements and evolution. We show that genes co-localize by evolutionary age in humans and mice, resulting in TADs having different proportions of younger and older genes. We observe a major transition in the age co-localization patterns between the genes born during vertebrate whole-genome duplications (WGDs) or before and those born afterward. We also find that genes recently duplicated in primates and rodents are more frequently essential when they are located in old-enriched TADs and interact with genes that last duplicated during the WGD. Therefore, the evolutionary relevance of recent genes may increase when located in TADs with established regulatory networks. Our data suggest that TADs could play a role in organizing ancestral functions and evolutionary novelty.
拓扑关联域（TADs）是三维基因组中染色体区域的交互子网。TAD 边界经常与基因组断裂重合，而边界缺失受到负选择的影响，这表明 TAD 可能促进了基因组重排和进化。我们表明，人类和小鼠的基因根据进化年龄共定位，导致 TAD 具有不同比例的年轻和年老基因。我们观察到在脊椎动物全基因组复制（WGD）期间或之前产生的基因与之后产生的基因之间的年龄共定位模式发生了重大转变。我们还发现，当最近在灵长类动物和啮齿动物中复制的基因位于富含旧基因的 TAD 中并与 WGD 期间最后复制的基因相互作用时，它们更经常是必需的。因此，当位于具有既定调控网络的 TAD 中时，最近基因的进化相关性可能会增加。我们的数据表明，TAD 可能在组织祖先功能和进化新颖性方面发挥作用。
