Diverse Functions of Distal Regulatory Elements at the IFNG Locus

Previous studies have identified multiple conserved noncoding sequences (CNS) at the mouse Ifng locus sufficient for enhancer activity in cell-based assays. These studies do not directly address biology of the human IFNG locus in a genomic setting. IFNG enhancers may be functionally redundant or each may be functionally unique. We test the hypothesis that each IFNG enhancer has a unique necessary function using a bacterial artificial chromosome transgenic model. We find that CNS 30, CNS-4, and CNS+20 are required at distinct stages of Th1 differentiation, whereas CNS 16 has a repressive role in Th1 and Th2 cells. CNS +20 is required for IFN-gamma expression by memory Th1 cells and NKT cells. CNS-4 is required for IFN-gamma expression by effector Th1 cells. In contrast, CNS-16, CNS-4, and CNS+20 are each partially required for human IFN-gamma expression by NK cells. Thus, IFNG CNS enhancers have redundant necessary functions in NK cells but unique necessary functions in Th cells. These results also demonstrate that distinct CNSs are required to transcribe IFNG at each stage of the Th1 differentiation pathway. The Journal of Immunology, 2012, 188: 1726-1733.