Background DNA replication in mammalian cells occurs in a defined temporal order during S phase, known as the replication timing (RT) programme. Replication timing is developmentally regulated and correlated with chromatin conformation and local transcriptional potential. Here, we present RT profiles of unprecedented temporal resolution in two human embryonic stem cell lines, human colon carcinoma line HCT116, and mouse embryonic stem cells and their neural progenitor derivatives. Results Fine temporal windows revealed a remarkable degree of cell-to-cell conservation in RT, particularly at the very beginning and ends of S phase, and identified 5 temporal patterns of replication in all cell types, consistent with varying degrees of initiation efficiency. Zones of replication initiation (IZs) were detected throughout S phase and interacted in 3D space preferentially with other IZs of similar firing time. Temporal transition regions were resolved into segments of uni-directional replication punctuated at specific sites by small, inefficient IZs. Sites of convergent replication were divided into sites of termination or large constant timing regions consisting of many synchronous IZs in tandem. Developmental transitions in RT occured mainly by activating or inactivating individual IZs or occasionally by altering IZ firing time, demonstrating that IZs, rather than individual origins, are the units of developmental regulation. Finally, haplotype phasing revealed numerous regions of allele-specific and allele-independent asynchronous replication. Allele-independent asynchronous replication was correlated with the presence of previously mapped common fragile sites. Conclusions Altogether, these data provide a detailed temporal choreography of DNA replication in mammalian cells.

中文翻译：

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高分辨率 Repli-Seq 定义了哺乳动物细胞中复制起始、延长和终止的时间编排


背景 哺乳动物细胞中的 DNA 复制在 S 期按定义的时间顺序进行，称为复制计时 (RT) 程序。复制时间受到发育调节，并与染色质构象和局部转录潜力相关。在这里，我们展示了两种人类胚胎干细胞系、人类结肠癌细胞系 HCT116 和小鼠胚胎干细胞及其神经祖细胞衍生物中前所未有的时间分辨率的 RT 图谱。结果精细时间窗口揭示了 RT 中显着程度的细胞间保守性，特别是在 S 期的开始和结束时，并确定了所有细胞类型中的 5 种时间复制模式，与不同程度的起始效率一致。在整个 S 期检测到复制起始区 (IZ)，并优先在 3D 空间中与具有相似激发时间的其他 IZ 相互作用。时间过渡区域被分解为单向复制的片段，在特定位点被小的、低效的 IZ 打断。聚合复制位点被分为终止位点或由许多串联的同步 IZ 组成的大型恒定计时区域。 RT 中的发育转变主要通过激活或失活单个 IZ 或偶尔通过改变 IZ 放电时间来发生，这表明 IZ，而不是个体起源，是发育调节的单位。最后，单倍型定相揭示了许多等位基因特异性和等位基因无关的异步复制区域。独立于等位基因的异步复制与先前映射的常见脆弱位点的存在相关。结论 总而言之，这些数据提供了哺乳动物细胞中 DNA 复制的详细时间编排。