Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome

Abstract
Data availability
Article and author information
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Abstract

The DNA methyltransferase activity of DNMT1 is vital for genomic maintenance of DNA methylation. We report here that DNMT1 function is regulated by O-GlcNAcylation, a protein modification that is sensitive to glucose levels, and that elevated O-GlcNAcylation of DNMT1 from high glucose environment leads to alterations to the epigenome. Using mass spectrometry and complementary alanine mutation experiments, we identified S878 as the major residue that is O-GlcNAcylated on human DNMT1. Functional studies in human and mouse cells further revealed that O-GlcNAcylation of DNMT1-S878 results in an inhibition of methyltransferase activity, resulting in a general loss of DNA methylation that preferentially occurs at partially methylated domains (PMDs). This loss of methylation corresponds with an increase in DNA damage and apoptosis. These results establish O-GlcNAcylation of DNMT1 as a mechanism through which the epigenome is regulated by glucose metabolism and implicates a role for glycosylation of DNMT1 in metabolic diseases characterized by hyperglycemia.

Data availability

PromethION sequencing data have been deposited in the NCBI Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) under accession no. GSE201470. Mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD043031.

The following data sets were generated

1. Schones DE
2. et al
(2023) Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome
NCBI Gene Expression Omnibus, GSE201470.

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201470
1. Schones DE
2. et al
(2023) Inhibition of DNMT1 methyltransferase activity via glucose-regulated O-GlcNAcylation alters the epigenome
PRIDE, PXD043031.

http://www.ebi.ac.uk/pride/archive/projects/PXD043031

The following previously published data sets were used

1. Li X
2. Liu Y
3. Salz T
4. Hansen KD et al
(2016) Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver
NCBI Gene Expression Omnibus, GSE70091.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE70091
1. Chang C
2. Li L
3. Zhang C
4. Wu S et al
(2014) Systematic analyses of the transcriptome, translatome, and proteome provide a global view and potential strategy for the C-HPP
NCBI Gene Expression Omnibus, GSE49994.

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49994

Article and author information

Author details

Heon Shin

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5480-8492
Amy Leung

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Kevin R Costello

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Parijat Senapati

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7324-1230
Hiroyuki Kato

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Roger E Moore

Integrated Mass Spectrometry Shared Resource, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Michael Lee

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Dimitri Lin

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Xiaofang Tang

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.
Patrick Pirrotte

Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, United States

Competing interests
The authors declare that no competing interests exist.
Zhen Bouman Chen

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-3291-1090
Dustin E Schones

Department of Diabetes Complications and Metabolism, City of Hope, Duarte, United States

For correspondence
dschones@coh.org

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-7692-8583

Funding

National Institutes of Health (R01DK112041)

Dustin E Schones

National Institutes of Health (R01CA220693)

Dustin E Schones

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Ethics

Animal experimentation: All animal experiments conducted have been approved by the Institutional Animal Care and Use Committees at City of Hope. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocols (#17010).

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.