Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS
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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 journal › Journal article › Research › peer-review
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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