Comparative 3D Genome Architecture in Vertebrates (RNA-Seq)

Three-dimensional genome architecture influences the regulation of essential nuclear processes, such as gene transcription. However, how 3D genome architecture is affected by evolutionary forces within major lineages remains unclear. Here, we report a comprehensive comparison of 3D genomes, using high resolution Hi-C data in fibroblast cells of fish, chickens, and 10 mammalian species. This analysis shows a correlation between genome size and chromosome length that affects chromosomal territory (CT) organization in the upper hierarchy of genome architecture, whereas lower hierarchical features, including local transcriptional availability of DNA, are selected through vertebrate’s evolution. Further, conservation of topologically associating domains (TADs) appears strongly associated with the modularity of expression profiles across species. Additionally, LINE and SINE transposable elements likely contribute to heterochromatin and euchromatin organization, respectively, during the evolution of genome architecture. These findings can guide ongoing investigations of genome evolution by extending our understanding of the mechanisms shaping genome architecture.三维基因组架构可调控诸多关键核内生命过程，例如基因转录。然而，在各大演化支系中，三维基因组架构如何受演化动力影响，目前仍未明确。本研究利用鱼类、鸡类以及10种哺乳动物成纤维细胞的高分辨率高通量染色体构象捕获（Hi-C）数据，对三维基因组进行了全面比较分析。本分析发现，基因组大小与染色体长度之间存在相关性，该相关性会影响基因组架构上层层级的染色体区域（chromosomal territory, CT）组织；而基因组架构的下层层级特征，例如DNA的局部转录可及性，则通过脊椎动物的演化过程受到选择。此外，拓扑关联结构域（topologically associating domains, TADs）的保守性，似乎与不同物种间基因表达谱的模块化特征高度相关。另外，长散在核元件（LINE）与短散在核元件（SINE）这两类转座因子，可能分别在基因组架构的演化过程中，参与异染色质与常染色质的组织构建。本研究结果拓展了我们对塑造三维基因组架构的分子机制的认知，可为后续基因组演化相关研究提供指导。