Comparing the transcriptomes of a thymic cell line engineered to over-express the autoimmune regulator gene AIRE with that of its parental cell line (1) revealed that IFIT1, IFIT2 and IFIT3 were among the genes whose expression changed most significantly upon expression of AIRE, with a substantial increase in IFIT1, IFIT2, and IFIT3 expression. In the thymuses of mice engineered to lack a functional copy of the AIRE gene (2), IFIT3 expression was greatly reduced. In both Aire-sufficient and

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... -deficient states, IFIT3 was identified as one of the most differentially expressed genes with respect to the wild-type or baseline condition. IFIT3 expression was found to co-segregate with low rather than high expression of the class II antigen presentation complex MHC-II (3). We conclude that AIRE exerts control over the gene expression of IFIT3 through an as-of-yet unidentified mechanism not likely to reflect AIRE's role as a transcriptional inducer of gene expression of peripheral tissue antigens.