Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

  1. Christian Schmidl,
  2. Maja Klug,
  3. Tina J. Boeld,
  4. Reinhard Andreesen,
  5. Petra Hoffmann,
  6. Matthias Edinger and
  7. Michael Rehli,1
  1. Department of Hematology, University Hospital Regensburg, 93042 Regensburg, Germany

    Abstract

    DNA methylation participates in establishing and maintaining chromatin structures and regulates gene transcription during mammalian development and cellular differentiation. With few exceptions, research thus far has focused on gene promoters, and little is known about the extent, functional relevance, and regulation of cell type-specific DNA methylation at promoter-distal sites. Here, we present a comprehensive analysis of differential DNA methylation in human conventional CD4+ T cells (Tconv) and CD4+CD25+ regulatory T cells (Treg), cell types whose differentiation and function are known to be controlled by epigenetic mechanisms. Using a novel approach that is based on the separation of a genome into methylated and unmethylated fractions, we examined the extent of lineage-specific DNA methylation across whole gene loci. More than 100 differentially methylated regions (DMRs) were identified that are present mainly in cell type-specific genes (e.g., FOXP3, IL2RA, CTLA4, CD40LG, and IFNG) and show differential patterns of histone H3 lysine 4 methylation. Interestingly, the majority of DMRs were located at promoter-distal sites, and many of these areas harbor DNA methylation-dependent enhancer activity in reporter gene assays. Thus, our study provides a comprehensive, locus-wide analysis of lineage-specific methylation patterns in Treg and Tconv cells, links cell type-specific DNA methylation with histone methylation and regulatory function, and identifies a number of cell type-specific, CpG methylation-sensitive enhancers in immunologically relevant genes.

    Footnotes

    • 1 Corresponding author.

      E-mail Michael.Rehli{at}klinik.uni-regensburg.de; fax 49-941-944-5593.

    • [Supplemental material is available online at www.genome.org. The microarray data from this study have been submitted to Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) under accession no. GSE14281.]

    • Article published online before print. Article and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.091470.109.

      • Received January 21, 2009.
      • Accepted April 20, 2009.
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