Li Zhiming, Zhang Zhiguo
Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; West China School of Public Health and West China Fourth Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.
Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA.
Mol Cell. 2025 Jan 16;85(2):238-261. doi: 10.1016/j.molcel.2024.10.035.
DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.
DNA复制是所有生物体中的一个基本过程，通过DNA聚合酶ε（Pol ε）连续合成前导链，以及通过聚合酶δ（Pol δ）不连续合成滞后链来进行。每个复制叉处的这种固有不对称性使得有必要开发在体内区分这两条新生链的方法。在过去十年中，链特异性测序策略，如蛋白质相关新生DNA的富集和测序（eSPAN）以及冈崎片段测序（OK-seq），已成为研究真核细胞中染色质复制的重要工具。在这篇综述中，我们概述了这些方法的基本原理，并总结了通过其应用获得的关于DNA复制、亲本组蛋白转移、表观遗传遗传等方面的关键机制见解。最后，我们讨论了当前技术的局限性和挑战，强调了进一步技术创新的必要性，以更好地理解真核细胞中染色质复制的动态和调控。
