Maintenance DNA Methyltransferase Activity in the Presence of Oxidized Forms of 5-Methylcytosine: Structural Basis for Ten Eleven Translocation-Mediated DNA Demethylation

Christopher L. Seiler, Jenna Fernandez, Zoe Koerperich, Molly P. Andersen, Delshanee Kotandeniya, Megin E. Nguyen, Yuk Y Sham, Natalia Y Tretyakova

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

A precise balance of DNA methylation and demethylation is required for epigenetic control of cell identity, development, and growth. DNA methylation marks are introduced by de novo DNA methyltransferases DNMT3a/b and are maintained throughout cell divisions by DNA methyltransferase 1 (DNMT1), which adds methyl groups to hemimethylated CpG dinucleotides generated during DNA replication. Ten eleven translocation (TET) dioxygenases oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC), a process known to induce DNA demethylation and gene reactivation. In this study, we investigated the catalytic activity of human DNMT1 in the presence of oxidized forms of mC. A mass spectrometry-based assay was employed to study the kinetics of DNMT1-mediated cytosine methylation in CG dinucleotides containing C, mC, hmC, fC, or caC across from the target cytosine. Homology modeling, coupled with molecular dynamics simulations, was used to explore the structural consequences of mC oxidation with regard to the geometry of protein-DNA complexes. The DNMT1 enzymatic activity was strongly affected by the oxidation status of mC, with the catalytic efficiency decreasing in the following order: mC > hmC > fC > caC. Molecular dynamics simulations revealed that DNMT1 forms an unproductive complex with DNA duplexes containing oxidized forms of mC as a consequence of altered interactions of the target recognition domain of the protein with the C-5 substituent on cytosine. Our results provide new structural and mechanistic insight into TET-mediated DNA demethylation.

Original languageEnglish (US)
Pages (from-to)6061-6069
Number of pages9
JournalBiochemistry
Volume57
Issue number42
DOIs
StatePublished - Oct 23 2018

Bibliographical note

Funding Information:
Natalia Y. Tretyakova: 0000-0002-0621-6860 Author Contributions C.L.S. and J.F. contributed equally to this work. Funding This work was supported by National Cancer Institute Grant 2R01 CA-095039. Notes The authors declare no competing financial interest.

Publisher Copyright:
Copyright © 2018 American Chemical Society.

Fingerprint Dive into the research topics of 'Maintenance DNA Methyltransferase Activity in the Presence of Oxidized Forms of 5-Methylcytosine: Structural Basis for Ten Eleven Translocation-Mediated DNA Demethylation'. Together they form a unique fingerprint.

Cite this