TET repression and increased DNMT activity synergistically induce aberrant DNA methylation
Hideyuki Takeshima, Tohru Niwa, Satoshi Yamashita, Takeji Takamura-Enya, Naoko Iida, Mika Wakabayashi, Sohachi Nanjo, Masanobu Abe, Toshiro Sugiyama, Young-Joon Kim, Toshikazu Ushijima
Hideyuki Takeshima, Tohru Niwa, Satoshi Yamashita, Takeji Takamura-Enya, Naoko Iida, Mika Wakabayashi, Sohachi Nanjo, Masanobu Abe, Toshiro Sugiyama, Young-Joon Kim, Toshikazu Ushijima
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Research Article Oncology

TET repression and increased DNMT activity synergistically induce aberrant DNA methylation

Abstract

Chronic inflammation is deeply involved in various human disorders, such as cancer, neurodegenerative disorders, and metabolic disorders. Induction of epigenetic alterations, especially aberrant DNA methylation, is one of the major mechanisms, but how it is induced is still unclear. Here, we found that expression of TET genes, methylation erasers, was downregulated in inflamed mouse and human tissues, and that this was caused by upregulation of TET-targeting miRNAs such as MIR20A, MIR26B, and MIR29C, likely due to activation of NF-κB signaling downstream of IL-1β and TNF-α. However, TET knockdown induced only mild aberrant methylation. Nitric oxide (NO), produced by NOS2, enhanced enzymatic activity of DNA methyltransferases (DNMTs), methylation writers, and NO exposure induced minimal aberrant methylation. In contrast, a combination of TET knockdown and NO exposure synergistically induced aberrant methylation, involving genomic regions not methylated by either alone. The results showed that a vicious combination of TET repression, due to NF-κB activation, and DNMT activation, due to NO production, is responsible for aberrant methylation induction in human tissues.

Authors

Hideyuki Takeshima, Tohru Niwa, Satoshi Yamashita, Takeji Takamura-Enya, Naoko Iida, Mika Wakabayashi, Sohachi Nanjo, Masanobu Abe, Toshiro Sugiyama, Young-Joon Kim, Toshikazu Ushijima

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Figure 2

Upregulation of Tet-targeting miRNAs by exposure to chronic inflammation.

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Upregulation of Tet-targeting miRNAs by exposure to chronic inflammation...
(A) miRNA upregulated by exposure to chronic inflammation in a mouse (G5-4). Thirty-six miRNAs were upregulated 5-fold or more by exposure to chronic inflammation. (B) In silico prediction of Tet-targeting miRNAs. Sixteen, 67, and 51 miRNAs were predicted to target Tet1, Tet2, and Tet3, respectively. (C) Identification of Tet-targeting miRNAs upregulated by the exposure to chronic inflammation. Twelve miRNAs that can potentially target one or more Tet genes (shown by red squares) were upregulated by exposure to chronic inflammation in 4 mice. Data represent mean ± SD (n = 4). (D) Potential target sites for the miRNAs in the 3′-UTR regions of the TET genes. Some miRNAs had multiple target sites in a single TET gene. (E) Repression of TET genes by MIR29C, MIR26B, and MIR20A. Introduction of these miRNAs into 293FT cells repressed the expression of the TET genes. Data represent mean ± SE (Welch’s t test, *P < 0.05; **P < 0.01). (F) MIR26B target sites within the 3′-UTR region of human TET3. The 3′-UTR regions with WT sequences (WT) and sequences with 1 mutation or 2 mutations (Mut) were cloned into a reporter vector. (G) Luciferase assay using the 3′-UTR region of human TET3. Reduction of the luciferase activity by the introduction of MIR26B mimic was canceled by introduction of the 2 mutations into the target sites. Data represent mean ± SE (Welch’s t test, **P < 0.01).