The enhancer and promoter landscape of human regulatory and conventional T-cell subpopulations

Abstract

CD4+CD25+FOXP3+ human regulatory T cells (Tregs) are essential for self-tolerance and immune homeostasis.Here, we describe the promoterome of CD4+ CD25high CD45RA + naïve and CD4+CD25highCD45RA -memory Tregs and their CD25- conventional T-cell (Tconv) counterparts both before and after in vitro expansion by cap analysis of gene expression (CAGE) adapted to single-molecule sequencing (HeliScopeCAGE). We performed comprehensive comparative digital gene expression analyses and revealed novel transcription start sites, of which severalwere validated as alternative promoters of known genes. For all in vitro expanded subsets, we additionally generated global maps of poised and active enhancer elementsmarked by histoneH3 lysine 4monomethylation and histone H3 lysine 27acetylation, describe their cell type-specificmotif signatures, and evaluate the roleof candidate transcription factors STAT5, FOXP3, RUNX1, and ETS1 in both Treg- and Tconv-specific enhancer architectures. Network analyses of gene expression data revealed additional candidate transcription factors contributing to cell type specificity and a transcription factor network in Tregs that is dominated by FOXP3 interaction partners and targets. In summary, we provide a comprehensive and easily accessible resource of gene expression and gene regulation in human Treg and Tconv subpopulations. © 2014 by The American Society of Hematology.