Identification of an Intronic Regulatory Element Necessary for Tissue-Specific Expression of <i>Foxn1</i> in Thymic Epithelial Cells

Abstract

The thymus is critical for the establishment of the adaptive immune system and the development of a diverse T cell repertoire. T cell development depends upon cell-cell interactions with epithelial cells in the thymus. The thymus is composed of two different types of epithelial cells: cortical and medullary epithelial cells. Both of these express and critically depend on the transcription factor <i>Foxn1</i> <i>Foxn1</i> is also expressed in the hair follicle, and disruption of <i>Foxn1</i> function in mice results in severe thymic developmental defects and the hairless (nude) phenotype. Despite its importance, little is known about the direct regulation of <i>Foxn1</i> expression. In this study, we identify a <i>cis</i>-regulatory element (RE) critical for expression of <i>Foxn1</i> in mouse thymic epithelial cells but dispensable for expression in hair follicles. Analysis of chromatin accessibility, histone modifications, and sequence conservation identified regions within the first intron of <i>Foxn1</i> that possessed the characteristics of REs. Systematic knockout of candidate regions lead us to identify a 1.6 kb region that, when deleted, results in a near total disruption of thymus development. Interestingly, <i>Foxn1</i> expression and function in the hair follicle were unaffected. RNA fluorescent in situ hybridization showed a near complete loss of <i>Foxn1</i> mRNA expression in the embryonic thymic bud. Our studies have identified a genomic RE with thymic-specific control of <i>Foxn1</i> gene expression.