Differential nucleosome organization in human interphase and metaphase chromosomes [Mnase-seq]

Mitosis induces profound changes in chromosome structure, impacting nucleosome organization. Here, we employed chemical mapping to achieve single-base-pair resolution of nucleosome positioning in human interphase and metaphase chromosomes, unveiling distinct organizing principles between the two states. During interphase, we observe greater variability in internucleosome spacing, with a higher abundance of shorter linkers compared to metaphase, reflecting the genome's adaptability in accommodating nucleosome arrays for gene expression. Local analyses further uncover differential nucleosome landscapes at key euchromatin landmarks, including promoters, enhancers, and insulators, in each state. Moreover, we analyzed the relationship between DNA cyclizability and dyad positioning during mitosis. Our results indicate that in metaphase, nucleosomes exhibit significantly higher cyclizability around the dyad, whereas during interphase, nucleosomes more frequently position DNA with higher cyclizability in the nucleosome shoulder near regulatory genomic regions. Together, this study offers novel insights into the intricate interplay between DNA mechanics and nucleosome dynamics during mitosis. Overall design: MNase digestion of nucleosomal DNA in interphase and metaphase HeLa S3 cells was performed as described previously.

有丝分裂（Mitosis）会引发染色体结构的剧烈重塑，对核小体组织模式产生显著影响。本研究采用化学图谱法（chemical mapping），实现了人类间期与中期染色体中核小体定位的单碱基分辨率解析，揭示了两种细胞周期状态下截然不同的核小体组织原则。相较于中期细胞，间期细胞的核小体间间隔变异度更高，且短连接区DNA的丰度也显著更高，这反映出基因组在适配核小体阵列以调控基因表达过程中的适应性。局部区域分析进一步揭示了两种细胞周期状态下，启动子（promoters）、增强子（enhancers）及绝缘子（insulators）等关键常染色质（euchromatin）标志性区域的核小体景观差异。此外，本研究还分析了有丝分裂过程中DNA环化能力（DNA cyclizability）与核小体二分体（dyad）定位之间的关联。研究结果显示，在中期细胞中，核小体二分体周边区域的DNA环化能力显著更高；而在间期细胞中，调控基因组区域附近的核小体侧翼区（nucleosome shoulder）往往更倾向于定位环化能力更强的DNA片段。综上，本研究为解析有丝分裂过程中DNA力学特性（DNA mechanics）与核小体动态变化（nucleosome dynamics）之间的复杂互作关系提供了全新视角。实验整体设计：参照已发表方法，对间期与中期海拉S3（HeLa S3）细胞中的核小体DNA进行微球菌核酸酶（MNase）消化。