Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy.
Dipartimento di Fisica, Università degli Studi di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant'Angelo, 80126 Naples, Italy.
Cell Rep. 2020 Feb 18;30(7):2125-2135.e5. doi: 10.1016/j.celrep.2020.01.044.
We investigate the three-dimensional (3D) conformations of the α-globin locus at the single-allele level in murine embryonic stem cells (ESCs) and erythroid cells, combining polymer physics models and high-resolution Capture-C data. Model predictions are validated against independent fluorescence in situ hybridization (FISH) data measuring pairwise distances, and Tri-C data identifying three-way contacts. The architecture is rearranged during the transition from ESCs to erythroid cells, associated with the activation of the globin genes. We find that in ESCs, the spatial organization conforms to a highly intermingled 3D structure involving non-specific contacts, whereas in erythroid cells the α-globin genes and their enhancers form a self-contained domain, arranged in a folded hairpin conformation, separated from intermingling flanking regions by a thermodynamic mechanism of micro-phase separation. The flanking regions are rich in convergent CTCF sites, which only marginally participate in the erythroid-specific gene-enhancer contacts, suggesting that beyond the interaction of CTCF sites, multiple molecular mechanisms cooperate to form an interacting domain.
我们在单个等位基因水平上，结合高分子物理模型和高分辨率捕获-C（Capture-C）数据，研究了鼠胚胎干细胞（ESCs）和红细胞中α-球蛋白基因座的三维（3D）构象。模型预测通过独立的荧光原位杂交（FISH）数据测量的成对距离和识别三链接触的 Tri-C 数据进行验证。该结构在从 ESCs 到红细胞的转变过程中发生重排，与珠蛋白基因的激活有关。我们发现，在 ESCs 中，空间组织符合高度混杂的 3D 结构，涉及非特异性接触，而在红细胞中，α-球蛋白基因及其增强子形成一个自包含的域，以折叠发夹构象排列，通过热力学微相分离机制与混杂的侧翼区域分离。侧翼区域富含会聚的 CTCF 位点，这些位点仅轻微参与红细胞特异性基因增强子接触，这表明除了 CTCF 位点的相互作用外，多种分子机制合作形成相互作用的域。
