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Abstract：
The phase separation model for transcription suggests that transcription factors (TFs), coactivators, and RNA polymerases form biomolecular condensates around active gene loci and regulate transcription. However, the structural details of condensates remain elusive. In this study, for Nanog, a master TF in mammalian embryonic stem cells known to form protein condensates in vitro, we examined protein structures in the condensates using residue-level coarse-grained molecular simulations. Human Nanog formed micelle-like clusters in the condensate. In the micelle-like cluster, the C-terminal disordered domains, including the tryptophan repeat (WR) regions, interacted with each other near the cluster center primarily via hydrophobic interaction. In contrast, hydrophilic disordered N-terminal and DNA-binding domains were exposed on the surface of the clusters. Electrostatic attractions of these surface residues were responsible for bridging multiple micelle-like structures in the condensate. The micelle-like structure and condensate were dynamic and liquid-like. Mutation of tryptophan residues in the WR region which was implicated to be important for a Nanog function resulted in dissolution of the Nanog condensate. Finally, to examine the impact of Nanog cluster to DNA, we added DNA fragments to the Nanog condensate. Nanog DNA-binding domains exposed to the surface of the micelle-like cluster could recruit more than one DNA fragments, making DNA-DNA distance shorter.
摘要：
转录的相分离模型表明转录因子(TFs)，助活化剂,和RNA聚合酶在活性基因位点周围形成生物分子缩合物并调节转录。然而,冷凝物的结构细节仍然难以捉摸。在这项研究中,对于Nanog,哺乳动物胚胎干细胞中已知的在体外形成蛋白质缩合物的主TF，我们使用残基级粗粒分子模拟检查了冷凝物中的蛋白质结构。人Nanog在冷凝物中形成胶束状簇。在胶束状簇中，C端无序域，包括色氨酸重复(WR)区域，在簇中心附近主要通过疏水相互作用相互作用。相比之下,亲水性无序N端和DNA结合域暴露在簇的表面。这些表面残留物的静电吸引力负责桥接冷凝物中的多个胶束状结构。胶束状结构和冷凝物是动态的和液体状的。WR区域中的色氨酸残基的突变(其被认为对于Nanog功能是重要的)导致Nanog缩合物的溶解。最后,为了检查Nanog团簇对DNA的影响，我们将DNA片段添加到Nanog冷凝物中。暴露于胶束样簇表面的NanogDNA结合域可以招募多个DNA片段，使DNA-DNA距离更短。
