Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

Research output: Contribution to journalJournal articlepeer-review

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Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS. / Stewart-Morgan, Kathleen R.; Requena, Cristina E.; Flury, Valentin; Du, Qian; Heckhausen, Zoe; Hajkova, Petra; Groth, Anja.

In: Nature Cell Biology, Vol. 25, 2023, p. 183-193.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Stewart-Morgan, KR, Requena, CE, Flury, V, Du, Q, Heckhausen, Z, Hajkova, P & Groth, A 2023, 'Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS', Nature Cell Biology, vol. 25, pp. 183-193. https://doi.org/10.1038/s41556-022-01048-x

APA

Stewart-Morgan, K. R., Requena, C. E., Flury, V., Du, Q., Heckhausen, Z., Hajkova, P., & Groth, A. (2023). Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS. Nature Cell Biology, 25, 183-193. https://doi.org/10.1038/s41556-022-01048-x

Vancouver

Stewart-Morgan KR, Requena CE, Flury V, Du Q, Heckhausen Z, Hajkova P et al. Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS. Nature Cell Biology. 2023;25:183-193. https://doi.org/10.1038/s41556-022-01048-x

Author

Stewart-Morgan, Kathleen R. ; Requena, Cristina E. ; Flury, Valentin ; Du, Qian ; Heckhausen, Zoe ; Hajkova, Petra ; Groth, Anja. / Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS. In: Nature Cell Biology. 2023 ; Vol. 25. pp. 183-193.

Bibtex

@article{c9e2dd104ea54df8a41ec0cfbe1368a8,
title = "Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS",
abstract = "DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows that hydroxymethylation is perpetually asymmetric between sister strands in favour of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation–histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.",
author = "Stewart-Morgan, {Kathleen R.} and Requena, {Cristina E.} and Valentin Flury and Qian Du and Zoe Heckhausen and Petra Hajkova and Anja Groth",
note = "Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
doi = "10.1038/s41556-022-01048-x",
language = "English",
volume = "25",
pages = "183--193",
journal = "Nature Cell Biology",
issn = "1465-7392",
publisher = "nature publishing group",

}

RIS

TY - JOUR

T1 - Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS

AU - Stewart-Morgan, Kathleen R.

AU - Requena, Cristina E.

AU - Flury, Valentin

AU - Du, Qian

AU - Heckhausen, Zoe

AU - Hajkova, Petra

AU - Groth, Anja

N1 - Publisher Copyright: © 2023, The Author(s).

PY - 2023

Y1 - 2023

N2 - DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows that hydroxymethylation is perpetually asymmetric between sister strands in favour of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation–histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.

AB - DNA methylation is a critical epigenetic mark in mammalian cells. Many aspects of DNA methylation maintenance have been characterized; however, the exact kinetics of post-replicative methylation maintenance remain a subject of debate. Here we develop isolation of DNA by 5-ethynyl-deoxyuridine labelling for mass spectrometry (iDEMS), a highly sensitive, quantitative mass spectrometry-based method for measuring DNA modifications on metabolically labelled DNA. iDEMS reveals an unexpectedly hemi-methylated landscape on nascent DNA. Combining iDEMS with metabolic labelling reveals that methylation maintenance is outpaced by cell division in mouse embryonic stem cells. Our approach shows that hydroxymethylation is perpetually asymmetric between sister strands in favour of the parental, template strand. iDEMS can be coupled with immunoprecipitation of chromatin proteins, revealing features of DNA methylation–histone modification crosstalk and suggesting a model for interplay between methylation and nucleosome assembly. iDEMS therefore elucidates long-standing questions about DNA modification propagation and provides an important orthogonal technology to understanding this process in dynamic cellular contexts.

U2 - 10.1038/s41556-022-01048-x

DO - 10.1038/s41556-022-01048-x

M3 - Journal article

C2 - 36635504

AN - SCOPUS:85146168936

VL - 25

SP - 183

EP - 193

JO - Nature Cell Biology

JF - Nature Cell Biology

SN - 1465-7392

ER -

ID: 335962346