Jun Suckjoon, Herrick John, Bensimon Aaron, Bechhoefer John
Department of Physics, Simon Fraser University, Burnaby, British Columbia, Canada.
Cell Cycle. 2004 Feb;3(2):223-9.
In Xenopus early embryos, replication origins neither require specific DNA sequences nor is there an efficient S/M checkpoint, even though the whole genome (3 billion bases) is completely duplicated within 10-20 minutes. This leads to the "random-completion problem" of DNA replication in embryos, where one needs to find a mechanism that ensures complete, faithful, timely reproduction of the genome without any sequence dependence of replication origins. We analyze recent DNA replication data in Xenopus laevis egg extracts and find discrepancies with models where replication origins are distributed independently of chromatin structure. Motivated by these discrepancies, we have investigated the role that chromatin looping may play in DNA replication. We find that the loop-size distribution predicted from a wormlike-chain model of chromatin can account for the spatial distribution of replication origins in this system quantitatively. Together with earlier findings of increasing frequency of origin firings, our results can explain the random-completion problem. The agreement between experimental data (molecular combing) and theoretical predictions suggests that the intrinsic stiffness of chromatin loops plays a fundamental biological role in DNA replication in early-embryo Xenopus in regulating the origin spacing.
在非洲爪蟾早期胚胎中，复制起点既不需要特定的DNA序列，也不存在有效的S/M检查点，尽管整个基因组（30亿个碱基）在10 - 20分钟内就能完全复制。这导致了胚胎中DNA复制的“随机完成问题”，即需要找到一种机制，确保基因组在没有复制起点的序列依赖性的情况下，能够完整、准确、及时地复制。我们分析了非洲爪蟾卵提取物中最新的DNA复制数据，发现这些数据与复制起点独立于染色质结构分布的模型存在差异。受这些差异的启发，我们研究了染色质环化在DNA复制中可能发挥的作用。我们发现，从染色质的蠕虫状链模型预测的环大小分布可以定量地解释该系统中复制起点的空间分布。结合早期关于复制起点激发频率增加的发现，我们的结果可以解释随机完成问题。实验数据（分子梳技术）与理论预测之间的一致性表明，染色质环的固有刚性在非洲爪蟾早期胚胎的DNA复制中，对调节起点间距起着基本的生物学作用。
