Department of Physics, Indian Institute of Technology Bombay, Mumbai 400076, India.
Soft Matter. 2022 Dec 21;19(1):153-163. doi: 10.1039/d2sm00612j.
Collapsed conformations of chromatin have been long suspected of being mediated by interactions with multivalent binding proteins, which can bring together distant sections of the chromatin fiber. In this study, we use Langevin dynamics simulation of a coarse grained chromatin polymer to show that the role of binding proteins can be more nuanced than previously suspected. In particular, for chromatin polymer in confinement, entropic forces can drive reswelling of collapsed chromatin with increasing binder concentrations, and this reswelling transition happens at physiologically relevant binder concentrations. Both the extent of collapse, and also of reswelling depends on the strength of confinement. We also study the kinetics of collapse and reswelling and show that both processes occur in similar timescales. We characterise this reswelling of chromatin in biologically relevant regimes and discuss the non-trivial role of multivalent binding proteins in mediating the spatial organisation of the genome.
染色质的折叠构象长期以来一直被怀疑是通过与多价结合蛋白的相互作用来介导的，这些结合蛋白可以将染色质纤维的远距离部分聚集在一起。在这项研究中，我们使用粗粒化染色质聚合物的朗之万动力学模拟表明，结合蛋白的作用可能比以前怀疑的更加微妙。特别是，对于受限的染色质聚合物，熵力可以在结合蛋白浓度增加时驱动折叠染色质的再膨胀，并且这种再膨胀转变发生在生理相关的结合蛋白浓度下。折叠和再膨胀的程度都取决于限制的强度。我们还研究了折叠和再膨胀的动力学，表明这两个过程都发生在相似的时间尺度内。我们在生物学相关的范围内对染色质的再膨胀进行了特征描述，并讨论了多价结合蛋白在介导基因组空间组织中的重要作用。
