Long-range cis-regulatory architecture of the human IL2 gene

Abstract

Abstract Interleukin-2 is a potent T cell growth factor with crucial roles in both immunity and tolerance. The IL2 gene is regulated by multiple signaling pathways, transcription factors, and epigenetic processes operating at the 500 bp upstream regulatory region (URR). Genome-wide association studies (GWAS) in humans have shown that genetic variation in the IL2 region is associated with susceptibility to autoimmune diseases. This region harbors several conserved noncoding sequences. We are performing a comprehensive epigenomic and functional interrogation of the human IL2-IL21 multi-locus region, using a combination of open chromatin mapping (ATAC-seq), recombinant promoter-reporter assays, 3-dimensional chromosome conformation capture (Capture-C), and CRISPR/CAS9 genome editing. ATAC-seq analysis identified TCR/CD28 activation-dependent chromatin remodeling at −46, −51, −80, −83, −-85, −121, and −128 kb upstream of IL2 in human T cells. Chromatin conformation capture indicates that several of these distal regions physically interact with IL2, and are capable of enhancing transcription from the IL2-URR in recombinant reporter assays. The −128 kb element showed autoimmune disease-associated allelic variation in enhancer activity, and CRISPR/CAS9-mediated deletion of this element in human T cells resulted in a 2–3 fold reduction in activation-induced IL-2 production. These results suggest that the IL2 locus has evolved an extensive regulatory architecture that allows for variable production of IL-2, and provide insight into why most autoimmune IL2 polymorphisms are located far away from the gene.