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

Onderzoeksoutput: Bijdrage aan wetenschappelijk tijdschrift/periodieke uitgave › Artikel › Wetenschappelijk › peer review

11 Citaten (Scopus)

Samenvatting

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.

Originele taal-2	Engels
Pagina's (van-tot)	1175-1184
Aantal pagina's	10
Tijdschrift	Nature Methods
Volume	21
Nummer van het tijdschrift	7
DOI's	https://doi.org/10.1038/s41592-024-02308-4
Status	Gepubliceerd - jul. 2024

Toegang tot document

10.1038/s41592-024-02308-4

Citeer dit

@article{f62fb184f05c47f297a2e88f617bcd10,

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.",

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

author = "{van den Berg}, Jeroen and {van Batenburg}, Vincent and Christoph Geisenberger and Tjeerdsma, {Rinskje B} and {de Jaime-Soguero}, Anchel and Acebr{\'o}n, {Sergio P} and {van Vugt}, {Marcel A T M} and {van Oudenaarden}, Alexander",

note = "{\textcopyright} 2024. The Author(s).",

year = "2024",

month = jul,

doi = "10.1038/s41592-024-02308-4",

language = "English",

volume = "21",

pages = "1175--1184",

journal = "Nature Methods",

issn = "1548-7091",

publisher = "Nature Publishing Group",

number = "7",

}

TY - JOUR

T1 - Quantifying DNA replication speeds in single cells by scEdU-seq

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

U2 - 10.1038/s41592-024-02308-4

DO - 10.1038/s41592-024-02308-4

M3 - Article

C2 - 38886577

SN - 1548-7091

VL - 21

SP - 1175

EP - 1184

JO - Nature Methods

JF - Nature Methods

IS - 7

ER -