State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.
Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
Genome Biol. 2021 Jul 12;22(1):206. doi: 10.1186/s13059-021-02424-w.
Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined.
We apply dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We find that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both high-efficiency and low-efficiency origins are distributed homogeneously in the TAD during the G1 phase, high-efficiency origins relocate to the TAD periphery before the S phase. Origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observe that the replication machinery protein PCNA forms immobile clusters around TADs at the G1/S transition, explaining why origins at the TAD periphery are preferentially fired.
Our work reveals a new origin selection mechanism that the replication efficiency of origins is determined by their physical distribution in the chromatin domain, which undergoes a transcription-dependent structural re-organization process. Our model explains the complex links between replication origin efficiency and many genetic and epigenetic signatures that mark active transcription. The coordination between DNA replication, transcription, and chromatin organization inside individual TADs also provides new insights into the biological functions of sub-domain chromatin structural dynamics.
后生动物细胞仅利用一小部分潜在的 DNA 复制起点来在每个细胞周期中复制整个基因组。起点的选择与细胞生长、分化和复制压力有关。尽管各种遗传和表观遗传特征与起源的复制效率有关，但对于起源的选择是如何确定的，尚无共识。
我们应用双色随机光学重建显微镜（STORM）超分辨率成像技术来绘制单个拓扑关联域（TAD）内起源的空间分布。我们发现，多个复制起点在 S 期开始时在 TAD 的空间边界处分别起始。有趣的是，虽然在 G1 期，高效和低效起点在 TAD 中均匀分布，但在 S 期之前，高效起点会重新定位到 TAD 周边。起源的重新定位依赖于转录和 CTCF 介导的染色质结构。此外，我们观察到复制机器蛋白 PCNA 在 G1/S 转换时在 TAD 周围形成固定的簇，这解释了为什么 TAD 周边的起点优先被激活。
我们的工作揭示了一种新的起点选择机制，即起源的复制效率取决于它们在染色质域中的物理分布，而这种分布会经历一个依赖转录的结构重组织过程。我们的模型解释了复制起点效率与许多标记活跃转录的遗传和表观遗传特征之间的复杂联系。单个 TAD 内的 DNA 复制、转录和染色质组织之间的协调也为亚域染色质结构动力学的生物学功能提供了新的见解。
