Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells

Shin Ichi Hashimoto, Katsumi Ogoshi, Atsushi Sasaki, Jun Abe, Wei Qu, Yoichiro Nakatani, Budrul Ahsan, Kenshiro Oshima, Francis H W Shand, Akio Ametani, Yutaka Suzuki, Shuichi Kaneko, Takashi Wada, Masahira Hattori, Sumio Sugano, Shinichi Morishita, Kouji Matsushima

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23 Citations (Scopus)

Abstract

Memory CD4+ T cells are central regulators of both humoral and cellular immune responses. T cell differentiation results in specific changes in chromatin structure and DNA methylation of cytokine genes. Although the methylation status of a limited number of gene loci in T cells has been examined, the genome-wide DNA methylation status of memory CD4+ T cells remains unexplored. To further elucidate the molecular signature of memory T cells, we conducted methylome and transcriptome analyses of memory CD4 + T cells generated using T cells from TCR-transgenic mice. The resulting genome-wide DNA methylation profile revealed 1144 differentially methylated regions (DMRs) across the murine genome during the process of T cell differentiation, 552 of which were associated with gene loci. Interestingly, the majority of these DMRs were located in introns. These DMRs included genes such as CXCR6, Tbox21, Chsy1, and Cish, which are associated with cytokine production, homing to bone marrow, and immune responses. Methylation changes in memory T cells exposed to specific Ag appeared to regulate enhancer activity rather than promoter activity of immunologically relevant genes. In addition, methylation profiles differed between memory T cell subsets, demonstrating a link between T cell methylation status and T cell differentiation. By comparing DMRs between naive and Ag-specific memory T cells, this study provides new insights into the functional status of memory T cells.

Original languageEnglish
Pages (from-to)4076-4091
Number of pages16
JournalJournal of Immunology
Volume190
Issue number8
DOIs
Publication statusPublished - 2013 Apr 15
Externally publishedYes

ASJC Scopus subject areas

  • Immunology

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    Hashimoto, S. I., Ogoshi, K., Sasaki, A., Abe, J., Qu, W., Nakatani, Y., Ahsan, B., Oshima, K., Shand, F. H. W., Ametani, A., Suzuki, Y., Kaneko, S., Wada, T., Hattori, M., Sugano, S., Morishita, S., & Matsushima, K. (2013). Coordinated changes in DNA methylation in antigen-specific memory CD4 T cells. Journal of Immunology, 190(8), 4076-4091. https://doi.org/10.4049/jimmunol.1202267