Department of Mathematical and Life Sciences , Hiroshima University , 1-3-1 Kagamiyama , Higashi-Hiroshima 739-8526 , Japan.
Research Center for Mathematics on Chromatin Live Dynamics , Hiroshima University , 1-3-1 Kagamiyama , Higashi-Hiroshima 739-8526 , Japan.
J Phys Chem B. 2019 Feb 7;123(5):1035-1043. doi: 10.1021/acs.jpcb.8b10518. Epub 2019 Jan 23.
Chromosomes consist of various domains with different transcriptional activities separated by chromatin boundary sequences such as insulator sequences. Recent studies suggested that CTCF or other chromatin loop-forming protein binding sequences represented typical insulators. Alternatively, some long nucleosome-excluding DNA sequences were also reported to exhibit insulator activities in yeast and sea urchin chromosomes, although specific binding of loop-forming proteins was not expected for them. However, the mechanism of the insulator activities of these sequences and the possibilities of similar insulators existing in other organisms remained unclear. In this study, we first constructed and performed simulations of a coarse-grained chromatin model containing nucleosome-rich and nucleosome-excluding DNA regions. We found that a long nucleosome-excluding region between two nucleosome-rich regions could markedly hinder the associations of two neighboring chromatin regions owing to the stronger long-term-averaged rigidity of the nucleosome-excluding region compared to that of nucleosome-rich regions. Subsequent analysis of the genome-wide nucleosome positioning, protein binding, and DNA rigidity in human cells revealed that some nucleosome-excluding rigid DNA sequences without bound chromatin looping proteins could exhibit insulator activities, functioning as chromatin boundaries in various regions of human chromosomes.
染色体由不同转录活性的各种结构域组成，这些结构域由染色质边界序列（如绝缘子序列）隔开。最近的研究表明，CTCF 或其他染色质环形成蛋白结合序列代表典型的绝缘子。或者，一些长的核小体排除 DNA 序列也被报道在酵母和海胆染色体中具有绝缘子活性，尽管它们不期望与环形成蛋白特异性结合。然而，这些序列的绝缘子活性的机制以及在其他生物体中存在类似绝缘子的可能性仍然不清楚。在这项研究中，我们首先构建并模拟了一个包含核小体丰富区和核小体排除区的粗粒化染色质模型。我们发现，两个核小体丰富区之间的一个长的核小体排除区由于核小体排除区的长期平均刚性比核小体丰富区更强，因此可以显著阻碍两个相邻染色质区的关联。随后对人类细胞中的全基因组核小体定位、蛋白质结合和 DNA 刚性进行分析表明，一些没有结合染色质环形成蛋白的核小体排除刚性 DNA 序列可以表现出绝缘子活性，作为人类染色体各个区域的染色质边界。
