Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency

Background

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. Despite various genetic and epigenetic signatures are found to be related with the replication efficiency of origins, a consensus in that how the selection of origins is determined has been lacking.

Results

Here, we applied dual-color stochastic optical reconstruction microscopy (STORM) super-resolution imaging to map the spatial distribution of origins within individual topologically associating domains (TADs). We found that multiple replication origins initiate separately at the spatial boundary of a TAD at the beginning of the S phase. Intriguingly, while both highly-efficient and lowly-efficient origins are distributed homogeneously in the TAD during the G1 phase, highly-efficient origins relocate to the TAD periphery before entering the S phase. We proved that such origin relocalization is dependent on both transcription and CTCF-mediated chromatin structure. Further, we observed that the replication machinery protein PCNA forms immobile clusters around the TADs at the G1/S transition, which explains why origins at the TAD periphery are preferentially fired.

背景
后生动物细胞仅会利用潜在DNA复制起点（DNA replication origin）中的一小部分，在每个细胞周期内完成全基因组的复制。复制起点的选择与细胞生长、分化及复制应激密切相关。尽管已有研究表明多种遗传与表观遗传特征与复制起点的复制效率相关，但学界迄今尚未就复制起点的选择机制达成统一共识。

结果
本研究采用双色随机光学重建显微镜（STORM）超分辨成像技术，绘制了单个拓扑关联结构域（TADs）内复制起点的空间分布图谱。我们发现，在S期起始阶段，多个复制起点会分别在TAD的空间边界处启动复制。值得注意的是，尽管在G1期，高效与低效复制起点在TAD内均呈均匀分布，但高效复制起点会在进入S期前迁移至TAD的外周区域。我们证实，此类复制起点的重定位过程同时依赖于转录活动与CCCTC结合因子（CTCF）介导的染色质结构调控。进一步研究发现，在G1/S期转换节点，复制机器蛋白增殖细胞核抗原（PCNA）会在TAD周围形成不可移动的簇集结构，这一现象解释了为何位于TAD外周的复制起点会被优先激活。