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Dynamics of DNA replication speeds in single cells

Nature Reviews Molecular Cell Biology volume 25, page 841 (2024)Cite this article

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The DNA replication machinery is tasked with accurately copying the entire genome. Considering the size of the human genome, a single replicative machine (a replisome) would require over a thousand days to complete this task. Therefore, thousands of replisomes are active in a single cell to considerably reduce this timeframe to less than ten hours. However, the high number of active replisomes makes it challenging to quantify characteristics such as speed of individual replisomes using conventional ‘bulk’ sequencing technologies.

To address these limitations, we developed single-cell 5-ethynyl-2′-deoxyuridine sequencing (scEdU-seq) to detect DNA replication dynamics in single cells. scEdU-seq combines single-cell DNA sequencing methods with pulse-labelling and enrichment of the nucleotide analogue EdU to specifically measure nascent DNA dynamics in single cells. We generated new computational methods to analyse this unique dataset to enable us to quantify DNA replication speeds, the number of replication forks and replication timing. These computational methods leverage the linear and progressive aspect of the replisome. For instance, we used the pair correlation function, which detects distances between labelled stretches of DNA and extracts replication speeds from these distances. In addition, we used hidden Markov models to classify consecutive EdU reads into DNA replication forks.

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  1. Hubrecht Institute, Utrecht, the Netherlands

    Jeroen van den Berg

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  1. Jeroen van den Berg
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Correspondence to Jeroen van den Berg.

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van den Berg, J. Dynamics of DNA replication speeds in single cells. Nat Rev Mol Cell Biol 25, 841 (2024). https://doi.org/10.1038/s41580-024-00776-2

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