Ly6 family proteins are mainly expressed by myeloid-cell lineages such as granulocytes (expressing Ly6G) and monocytes (expressing Ly6C). However, exact function of Ly6 family protein in each cell-type remains unknown. For example, although expression of Ly6C has been used to define functionally distinct subset of monocytes (Ly6C+ monocytes vs. Ly6C- monocytes), molecular basis for the expression of Ly6C and functional difference between the two populations are largely unknown. Medullary thymic epithelial cells (mTECs) are composed of heterogeneous populations in terms of the spectrum of tissue-restricted antigens (TRAs) expression for ensuring the elimination of autoreactive T-cell repertoire. We have recently identified mTEC subset(s) that express Ly6C and Ly6G both recognized by monoclonal antibody Gr-1 (i.e., Ly6C/6G+ mTECs). Approximately 10% of total mTECs expressed Ly6C/6G and Ly6C/6G+ mTECs were preferentially localized at the cortico-medullary junction. We found that Ly6C/6G+ mTECs and Ly6C/6G- mTECs do not form distinct lineage(s). Instead, Ly6C/6G- mTECs are able to convert into Ly6C/6G+ mTECs and vice versa in a reaggregated thymic organ culture (RTOC). Interestingly, this conversion required Aire and/or Aire+ mTECs that are essential for the establishment of self-tolerance. Consistent with this finding, Aire-deficient mice do not possess Ly6C/6G+ mTECs. RNA-seq analyses have revealed that Ly6C/6G+ mTECs express higher levels of chemokines, integrins and extracellular matrix proteins compared with those from Ly6C/6G- mTECs, suggesting that Ly6C/6G+ mTECs might constitute a unique tolerogenic subset among heterogenous mTECs. In order to elucidate the function of Ly6C, we have established a mouse strain that is deficient for Ly6C (both Ly6C1 and Ly6C2). Although Ly6C-deficient mice showed grossly normal development of mTECs and thymocytes, other immunological aspect of Ly6C/6G+ mTECs needs to be further investigated.