Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS.
Kathleen R Stewart-MorganCristina E RequenaValentin FluryQian DuZoe HeckhausenPetra HajkovaAnja GrothPublished in: Nature cell biology (2023)
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.
Keyphrases
- dna methylation
- genome wide
- circulating tumor
- gene expression
- mass spectrometry
- cell free
- single molecule
- high resolution
- copy number
- nucleic acid
- liquid chromatography
- dna damage
- circulating tumor cells
- embryonic stem cells
- mesenchymal stem cells
- oxidative stress
- transcription factor
- bone marrow
- density functional theory
- gas chromatography
- molecular dynamics
- tandem mass spectrometry