Transcriptional regulator which regulates the development, differentiation, and function of thymic epithelial cells (TECs) both in the prenatal and postnatal thymus. Acts as a master regulator of the TECs lineage development and is required from the onset of differentiation in progenitor TECs in the developing fetus to the final differentiation steps through which TECs mature to acquire their full functionality. Regulates, either directly or indirectly the expression of a variety of genes that mediate diverse aspects of thymus development and function, including MHC Class II, DLL4, CCL25, CTSL, CD40 and PAX1. Regulates the differentiation of the immature TECs into functional cortical TECs (cTECs) and medullary TECs (mTECs) (PubMed:22072979). Essential for maintenance of mTECs population in the postnatal thymus (PubMed:19955175). Involved in the morphogenesis and maintenance of the three-dimensional thymic microstructure which is necessary for a fully functional thymus (PubMed:21109991). Plays an important role in the maintenance of hematopoiesis and particularly T lineage progenitors within the bone marrow niche with age (PubMed:24184560). Essential for the vascularization of the thymus anlage (PubMed:19853842). Promotes the terminal differentiation of epithelial cells in the epidermis and hair follicles, partly by negatively regulating the activity of protein kinase C (PubMed:17459087). Bone marrow (at protein level). Expressed in thymus and skin. Defects in FOXN1 are the cause of the nude/severe combined immunodeficiency (SCID) phenotype which is characterized by athymia and hairlessness. Mice develop largely normal hair follicles and produce hair shafts. However, presumably because of a lack of certain hair keratins, the hair shafts that are generated twist and coil in the hair follicle infundibulum, which becomes dilated. Since hair shafts fail to penetrate the epidermis, macroscopic nudity results and generates the grossly misleading impression that nude mice are hairless. Mice exhibit nude skin phenotype and acute thymic atrophy with a severe early block in thymic epithelial cells (TECs) differentiation. A more severe deterioration seen in medullary thymic epithelial cells (mTECs) than in cortical thymic epithelial cells (cTECs).