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Onodera A, González-Avalos E, Lio CJ, et al. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol. 2021;22(1):186doi: 10.1186/s13059-021-02384-1.
Onodera, A., González-Avalos, E., Lio, C. J., Georges, R. O., Bellacosa, A., Nakayama, T., & Rao, A. (2021). Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome biology, 22(1), 186. https://doi.org/10.1186/s13059-021-02384-1
Onodera, Atsushi, et al. "Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells." Genome biology vol. 22,1 (2021): 186. doi: https://doi.org/10.1186/s13059-021-02384-1
Onodera A, González-Avalos E, Lio CJ, Georges RO, Bellacosa A, Nakayama T, Rao A. Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells. Genome Biol. 2021 Jun 22;22(1):186. doi: 10.1186/s13059-021-02384-1. PMID: 34158086; PMCID: PMC8218415.
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Genome Biol. 2021 Jun 22;22(1):186. doi: 10.1186/s13059-021-02384-1.

Roles of TET and TDG in DNA demethylation in proliferating and non-proliferating immune cells.

Genome biology

Atsushi Onodera, Edahí González-Avalos, Chan-Wang Jerry Lio, Romain O Georges, Alfonso Bellacosa, Toshinori Nakayama, Anjana Rao

Affiliations

  1. Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA.
  2. Department of Immunology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
  3. Institute for Global Prominent Research, Chiba University, 1-33, Yayoicho, Inage-ku, Chiba, 263-8522, Japan.
  4. Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
  5. Present address: Department of Microbial Infection and Immunity, Ohio State University, 460 W 12th Ave, Columbus, OH, 43210, USA.
  6. Cancer Signaling and Epigenetics Program & Cancer Epigenetics Institute, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
  7. AMED-CREST, AMED, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
  8. Division of Signaling and Gene Expression, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA. [email protected].
  9. Department of Pharmacology and Moores Cancer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. [email protected].
  10. Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Drive, La Jolla, CA, 92037, USA. [email protected].

PMID: 34158086 PMCID: PMC8218415 DOI: 10.1186/s13059-021-02384-1

Abstract

BACKGROUND: TET enzymes mediate DNA demethylation by oxidizing 5-methylcytosine (5mC) in DNA to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). Since these oxidized methylcytosines (oxi-mCs) are not recognized by the maintenance methyltransferase DNMT1, DNA demethylation can occur through "passive," replication-dependent dilution when cells divide. A distinct, replication-independent ("active") mechanism of DNA demethylation involves excision of 5fC and 5caC by the DNA repair enzyme thymine DNA glycosylase (TDG), followed by base excision repair.

RESULTS: Here by analyzing inducible gene-disrupted mice, we show that DNA demethylation during primary T cell differentiation occurs mainly through passive replication-dependent dilution of all three oxi-mCs, with only a negligible contribution from TDG. In addition, by pyridine borane sequencing (PB-seq), a simple recently developed method that directly maps 5fC/5caC at single-base resolution, we detect the accumulation of 5fC/5caC in TDG-deleted T cells. We also quantify the occurrence of concordant demethylation within and near enhancer regions in the Il4 locus. In an independent system that does not involve cell division, macrophages treated with liposaccharide accumulate 5hmC at enhancers and show altered gene expression without DNA demethylation; loss of TET enzymes disrupts gene expression, but loss of TDG has no effect. We also observe that mice with long-term (1 year) deletion of Tdg are healthy and show normal survival and hematopoiesis.

CONCLUSIONS: We have quantified the relative contributions of TET and TDG to cell differentiation and DNA demethylation at representative loci in proliferating T cells. We find that TET enzymes regulate T cell differentiation and DNA demethylation primarily through passive dilution of oxi-mCs. In contrast, while we observe a low level of active, replication-independent DNA demethylation mediated by TDG, this process does not appear to be essential for immune cell activation or differentiation.

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