Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome

Marianne B. Palczewski; Hannah Petraitis Kuschman; Brian M. Hoffman; Venkatesan Kathiresan; Hao Yang; Sharon A. Glynn; David L. Wilson; Eric T. Kool; William R. Montfort; Jenny Chang; Aydolun Petenkaya; Constantinos Chronis; Thomas R. Cundari; Sushma Sappa; Kabirul Islam; Daniel W. McVicar; Yu Fan; Qingrong Chen; Daoud Meerzaman; Michael Sierk; Douglas D. Thomas

doi:10.1038/s41467-025-56928-1

Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome

Marianne B. Palczewski, Hannah Petraitis Kuschman, Brian M. Hoffman, Venkatesan Kathiresan, Hao Yang, Sharon A. Glynn, David L. Wilson, Eric T. Kool, William R. Montfort, Jenny Chang, Aydolun Petenkaya, Constantinos Chronis, Thomas R. Cundari, Sushma Sappa, Kabirul Islam, Daniel W. McVicar, Yu Fan, Qingrong Chen, Daoud Meerzaman, Michael SierkDouglas D. Thomas

Research output: Contribution to journal › Article › peer-review

Abstract

DNA methylation at cytosine bases (5-methylcytosine, 5mC) is a heritable epigenetic mark regulating gene expression. While enzymes that metabolize 5mC are well-characterized, endogenous signaling molecules that regulate DNA methylation machinery have not been described. We report that physiological nitric oxide (NO) concentrations reversibly inhibit the DNA demethylases TET and ALKBH2 by binding to the mononuclear non-heme iron atom forming a dinitrosyliron complex (DNIC) and preventing cosubstrates from binding. In cancer cells treated with exogenous NO, or endogenously synthesizing NO, 5mC and 5-hydroxymethylcytosine (5hmC) increase, with no changes in DNA methyltransferase activity. 5mC is also significantly increased in NO-producing patient-derived xenograft tumors from mice. Genome-wide methylome analysis of cells chronically treated with NO (10 days) shows enrichment of 5mC and 5hmC at gene-regulatory loci, correlating with altered expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a unique epigenetic role for NO.

Original language	English (US)
Article number	1732
Journal	Nature communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-56928-1
State	Published - Dec 2025

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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Palczewski, M. B., Kuschman, H. P., Hoffman, B. M., Kathiresan, V., Yang, H., Glynn, S. A., Wilson, D. L., Kool, E. T., Montfort, W. R., Chang, J., Petenkaya, A., Chronis, C., Cundari, T. R., Sappa, S., Islam, K., McVicar, D. W., Fan, Y., Chen, Q., Meerzaman, D., ... Thomas, D. D. (2025). Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome. Nature communications, 16(1), Article 1732. https://doi.org/10.1038/s41467-025-56928-1

Palczewski, MB, Kuschman, HP, Hoffman, BM, Kathiresan, V, Yang, H, Glynn, SA, Wilson, DL, Kool, ET, Montfort, WR, Chang, J, Petenkaya, A, Chronis, C, Cundari, TR, Sappa, S, Islam, K, McVicar, DW, Fan, Y, Chen, Q, Meerzaman, D, Sierk, M & Thomas, DD 2025, 'Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome', Nature communications, vol. 16, no. 1, 1732. https://doi.org/10.1038/s41467-025-56928-1

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title = "Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome",

abstract = "DNA methylation at cytosine bases (5-methylcytosine, 5mC) is a heritable epigenetic mark regulating gene expression. While enzymes that metabolize 5mC are well-characterized, endogenous signaling molecules that regulate DNA methylation machinery have not been described. We report that physiological nitric oxide (NO) concentrations reversibly inhibit the DNA demethylases TET and ALKBH2 by binding to the mononuclear non-heme iron atom forming a dinitrosyliron complex (DNIC) and preventing cosubstrates from binding. In cancer cells treated with exogenous NO, or endogenously synthesizing NO, 5mC and 5-hydroxymethylcytosine (5hmC) increase, with no changes in DNA methyltransferase activity. 5mC is also significantly increased in NO-producing patient-derived xenograft tumors from mice. Genome-wide methylome analysis of cells chronically treated with NO (10 days) shows enrichment of 5mC and 5hmC at gene-regulatory loci, correlating with altered expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a unique epigenetic role for NO.",

author = "Palczewski, {Marianne B.} and Kuschman, {Hannah Petraitis} and Hoffman, {Brian M.} and Venkatesan Kathiresan and Hao Yang and Glynn, {Sharon A.} and Wilson, {David L.} and Kool, {Eric T.} and Montfort, {William R.} and Jenny Chang and Aydolun Petenkaya and Constantinos Chronis and Cundari, {Thomas R.} and Sushma Sappa and Kabirul Islam and McVicar, {Daniel W.} and Yu Fan and Qingrong Chen and Daoud Meerzaman and Michael Sierk and Thomas, {Douglas D.}",

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doi = "10.1038/s41467-025-56928-1",

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AU - Palczewski, Marianne B.

AU - Kuschman, Hannah Petraitis

AU - Hoffman, Brian M.

AU - Kathiresan, Venkatesan

AU - Yang, Hao

AU - Glynn, Sharon A.

AU - Wilson, David L.

AU - Kool, Eric T.

AU - Montfort, William R.

AU - Chang, Jenny

AU - Petenkaya, Aydolun

AU - Chronis, Constantinos

AU - Cundari, Thomas R.

AU - Sappa, Sushma

AU - Islam, Kabirul

AU - McVicar, Daniel W.

AU - Fan, Yu

AU - Chen, Qingrong

AU - Meerzaman, Daoud

AU - Sierk, Michael

AU - Thomas, Douglas D.

PY - 2025/12

Y1 - 2025/12

N2 - DNA methylation at cytosine bases (5-methylcytosine, 5mC) is a heritable epigenetic mark regulating gene expression. While enzymes that metabolize 5mC are well-characterized, endogenous signaling molecules that regulate DNA methylation machinery have not been described. We report that physiological nitric oxide (NO) concentrations reversibly inhibit the DNA demethylases TET and ALKBH2 by binding to the mononuclear non-heme iron atom forming a dinitrosyliron complex (DNIC) and preventing cosubstrates from binding. In cancer cells treated with exogenous NO, or endogenously synthesizing NO, 5mC and 5-hydroxymethylcytosine (5hmC) increase, with no changes in DNA methyltransferase activity. 5mC is also significantly increased in NO-producing patient-derived xenograft tumors from mice. Genome-wide methylome analysis of cells chronically treated with NO (10 days) shows enrichment of 5mC and 5hmC at gene-regulatory loci, correlating with altered expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a unique epigenetic role for NO.

AB - DNA methylation at cytosine bases (5-methylcytosine, 5mC) is a heritable epigenetic mark regulating gene expression. While enzymes that metabolize 5mC are well-characterized, endogenous signaling molecules that regulate DNA methylation machinery have not been described. We report that physiological nitric oxide (NO) concentrations reversibly inhibit the DNA demethylases TET and ALKBH2 by binding to the mononuclear non-heme iron atom forming a dinitrosyliron complex (DNIC) and preventing cosubstrates from binding. In cancer cells treated with exogenous NO, or endogenously synthesizing NO, 5mC and 5-hydroxymethylcytosine (5hmC) increase, with no changes in DNA methyltransferase activity. 5mC is also significantly increased in NO-producing patient-derived xenograft tumors from mice. Genome-wide methylome analysis of cells chronically treated with NO (10 days) shows enrichment of 5mC and 5hmC at gene-regulatory loci, correlating with altered expression of NO-regulated tumor-associated genes. Regulation of DNA methylation is distinctly different from canonical NO signaling and represents a unique epigenetic role for NO.

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Nitric oxide inhibits ten-eleven translocation DNA demethylases to regulate 5mC and 5hmC across the genome

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