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Regulation of DNA methylation dictates Cd4 expression during the development of helper and cytotoxic T cell lineages

Nature Immunology volume 16, pages 746754 (2015) | Download Citation

Abstract

During development, progenitor cells with binary potential give rise to daughter cells that have distinct functions. Heritable epigenetic mechanisms then lock in gene-expression programs that define lineage identity. Regulation of the gene encoding the T cell–specific coreceptor CD4 in helper and cytotoxic T cells exemplifies this process, with enhancer- and silencer-regulated establishment of epigenetic memory for stable gene expression and repression, respectively. Using a genetic screen, we identified the DNA-methylation machinery as essential for maintaining silencing of Cd4 in the cytotoxic lineage. Furthermore, we found a requirement for the proximal enhancer in mediating the removal of DNA-methylation marks from Cd4, which allowed stable expression of Cd4 in helper T cells. Our findings suggest that stage-specific methylation and demethylation events in Cd4 regulate its heritable expression in response to the distinct signals that dictate lineage 'choice' during T cell development.

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Acknowledgements

We thank R. Jaenisch (Whitehead Institute for Biomedical Research) for Dnmt1L2 and Dnmt1chip mouse strains; the University of Massachusetts Medical School RNAi Core Facility for shRNAs; A. Cuesta and A. Chen for technical help; and members of the Littman laboratory for discussion. Supported by the US National Institutes of Health (R00DK091508 to J.R.H., 5 T32 CA009161-36 to M.S., and GM033977 to M.R.G.), the Jane Coffin Childs Fund (J.R.H.), the Cancer Research Institute (M.S. and P.D.I.) and the Howard Hughes Medical Institute (M.R.G. and D.R.L.).

Author information

Author notes

    • Stephane Gobeil

    Present Address: Centre Hospitalier de l'Université Laval, Québec, Canada.

    • MacLean Sellars
    •  & Jun R Huh

    These authors contributed equally to this work.

Affiliations

  1. The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York, USA.

    • MacLean Sellars
    • , Jun R Huh
    • , Priya D Issuree
    • , Carolina Galan
    •  & Dan R Littman
  2. Howard Hughes Medical Institute, New York University School of Medicine, New York, New York, USA.

    • MacLean Sellars
    • , Jun R Huh
    • , Priya D Issuree
    • , Carolina Galan
    •  & Dan R Littman
  3. Division of Infectious Disease and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • Jun R Huh
  4. HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA.

    • Kenneth Day
    •  & Devin Absher
  5. Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • Stephane Gobeil
    •  & Michael R Green
  6. Howard Hughes Medical Institute, University of Massachusetts Medical School, Worcester, Massachusetts, USA.

    • Stephane Gobeil
    •  & Michael R Green

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Contributions

M.S. performed E4P rescue experiments, proliferation assays in thymus and T4-βGT analysis; J.R.H. did the genetic screen and follow-up analyses; M.S. and K.D. did the analyses of Cd4 locus-wide methylation and nucleosome sequencing, with bioinformatics support from D.A.; P.D.I. performed oxidative bisulfite analysis; M.S. and C.G. performed amplicon bisulfite sequencing; S.G. and M.R.G. provided the mouse shRNA retroviral pools; and M.S., J.R.H. and D.R.L. designed the experiments and wrote the manuscript with input from the other authors.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Dan R Littman.

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DOI

https://doi.org/10.1038/ni.3198

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