Quantifying DNA replication speeds in single cells by scEdU-seq

Jeroen van den Berg; Vincent van Batenburg; Christoph Geisenberger; Rinskje B Tjeerdsma; Anchel de Jaime-Soguero; Sergio P Acebrón; Marcel A T M van Vugt; Alexander van Oudenaarden

doi:10.1038/s41592-024-02308-4

Quantifying DNA replication speeds in single cells by scEdU-seq

Jeroen van den Berg, Vincent van Batenburg, Christoph Geisenberger, Rinskje B Tjeerdsma, Anchel de Jaime-Soguero, Sergio P Acebrón, Marcel A T M van Vugt, Alexander van Oudenaarden

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

11 Citations (Scopus)

Abstract

In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

Original language	English
Pages (from-to)	1175-1184
Number of pages	10
Journal	Nature Methods
Volume	21
Issue number	7
DOIs	https://doi.org/10.1038/s41592-024-02308-4
Publication status	Published - Jul 2024

Keywords

DNA Replication
Humans
Single-Cell Analysis/methods
Deoxyuridine/analogs & derivatives
S Phase/genetics
Sequence Analysis, DNA/methods
DNA Damage
DNA/genetics

Access to Document

10.1038/s41592-024-02308-4

Cite this

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title = "Quantifying DNA replication speeds in single cells by scEdU-seq",

abstract = "In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.",

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AU - van den Berg, Jeroen

AU - van Batenburg, Vincent

AU - Geisenberger, Christoph

AU - Tjeerdsma, Rinskje B

AU - de Jaime-Soguero, Anchel

AU - Acebrón, Sergio P

AU - van Vugt, Marcel A T M

AU - van Oudenaarden, Alexander

PY - 2024/7

Y1 - 2024/7

N2 - In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

AB - In a human cell, thousands of replication forks simultaneously coordinate duplication of the entire genome. The rate at which this process occurs might depend on the epigenetic state of the genome and vary between, or even within, cell types. To accurately measure DNA replication speeds, we developed single-cell 5-ethynyl-2'-deoxyuridine sequencing to detect nascent replicated DNA. We observed that the DNA replication speed is not constant but increases during S phase of the cell cycle. Using genetic and pharmacological perturbations we were able to alter this acceleration of replication and conclude that DNA damage inflicted by the process of transcription limits the speed of replication during early S phase. In late S phase, during which less-transcribed regions replicate, replication accelerates and approaches its maximum speed.

KW - DNA Replication

KW - Humans

KW - Single-Cell Analysis/methods

KW - Deoxyuridine/analogs & derivatives

KW - S Phase/genetics

KW - Sequence Analysis, DNA/methods

KW - DNA Damage

KW - DNA/genetics

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DO - 10.1038/s41592-024-02308-4

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