Quantifying propagation of DNA methylation and hydroxymethylation with iDEMS
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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.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Nature Cell Biology |
| Vol/bind | 25 |
| Sider (fra-til) | 183-193 |
| Antal sider | 11 |
| ISSN | 1465-7392 |
| DOI | |
| Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:
We are grateful to members of the Groth and Hajkova labs for providing fruitful discussion and input. We thank M. Michault and the CPR/ reNEW Genomics Platform for sequencing and bioinformatics assistance. We thank members of the FACS facilities at BRIC and CPR/ reNEW for flow cytometry assistance. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747332 and from the Lundbeck Foundation (R219-2016-394) as grants to K.R.S.-M. Q.D. is a NHMRC Investigator grant recipient 1177792. The contents of this paper are the responsibility of the individual authors and the University of Copenhagen and Imperial College London, and do not reflect the views of NHMRC. Research in the Groth laboratory is supported by grants from the Lundbeck Foundation (R198-2015-269; R313-2019-448), the European Research Council (ERC CoG no. 724436), the Independent Research Fund Denmark (7016-00042B), and the Novo Nordisk Foundation (NNF21OC0067425) to A.G. Research at CPR is supported by the Novo Nordisk Foundation (NNF14CC0001). Work in the Hajkova laboratory is supported by MRC funding (MC_US_A652_5PY70) and an ERC grant (ERC CoG no. 648879–dynamicmodifications) to P.H.
Funding Information:
We are grateful to members of the Groth and Hajkova labs for providing fruitful discussion and input. We thank M. Michault and the CPR/ reNEW Genomics Platform for sequencing and bioinformatics assistance. We thank members of the FACS facilities at BRIC and CPR/ reNEW for flow cytometry assistance. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement no. 747332 and from the Lundbeck Foundation (R219-2016-394) as grants to K.R.S.-M. Q.D. is a NHMRC Investigator grant recipient 1177792. The contents of this paper are the responsibility of the individual authors and the University of Copenhagen and Imperial College London, and do not reflect the views of NHMRC. Research in the Groth laboratory is supported by grants from the Lundbeck Foundation (R198-2015-269; R313-2019-448), the European Research Council (ERC CoG no. 724436), the Independent Research Fund Denmark (7016-00042B), and the Novo Nordisk Foundation (NNF21OC0067425) to A.G. Research at CPR is supported by the Novo Nordisk Foundation (NNF14CC0001). Work in the Hajkova laboratory is supported by MRC funding (MC_US_A652_5PY70) and an ERC grant (ERC CoG no. 648879–dynamicmodifications) to P.H.
Publisher Copyright:
© 2023, The Author(s).
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