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Abstract
In mammalian cells, DNA replication timing is controlled at the level of megabase (Mb)-sized chromosomal domains and correlates well with transcription, chromatin structure, and three-dimensional (3D) genome organization. Because of these properties, DNA replication timing is an excellent entry point to explore genome regulation at various levels and a variety of studies have been carried out over the years. However, DNA replication timing studies traditionally required at least tens of thousands of cells, and it was unclear whether the replication domains detected by cell population analyses were preserved at the single-cell level. Recently, single-cell DNA replication profiling methods became available, which revealed that the Mb-sized replication domains detected by cell population analyses were actually well preserved in individual cells. In this article, we provide a brief overview of our current knowledge on DNA replication timing regulation in mammals based on cell population studies, outline the findings from single-cell DNA replication profiling, and discuss future directions and challenges.
Highlights
Over half a century ago when the discovery of the double helical DNA structure immediately invoked the possibility of semi-conservative DNA replication [1], researchers at the time must have naturally been attracted to solving the mechanism of DNA replication [2]
We provide an overview of DNA replication timing studies of cell populations carried out mainly in mammalian cells over the years, explain the key findings made by the scRepli-seq method, and discuss the potential of this powerful methodology and its impact in the coming years
DNA replication timing program in mammalian cells is established at the timing decision point (TDP) in early G1 phase, 2–3 h after exit from mitosis [55], the timing of TDP during G1-phase varies slightly between cell types [67]
Summary
Over half a century ago when the discovery of the double helical DNA structure immediately invoked the possibility of semi-conservative DNA replication [1], researchers at the time must have naturally been attracted to solving the mechanism of DNA replication [2]. Under such circumstances, temporal control of DNA replication was discovered more or less by chance, by the use of tritium-labeled thymidine for studying DNA replication and chromosome structure [2]. We provide an overview of DNA replication timing studies of cell populations carried out mainly in mammalian cells over the years, explain the key findings made by the scRepli-seq method, and discuss the potential of this powerful methodology and its impact in the coming years
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