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Although the mechanisms underlying Aire-dependent expression of TRAs need to be explored, the physical identification of the target(s) of Aire has been hampered by the low and promiscuous expression of TRAs. We have tackled this issue by engineering mice with augmented Aire expression. Integration of the transcriptomic data from Aire-augmented and Aire-deficient mTECs revealed that a large proportion of so-called Aire-dependent genes, including those of TRAs, may not be direct transcriptional targets downstream of Aire. Rather, Aire induces TRA expression indirectly through controlling the heterogeneity of mTECs, as revealed by single-cell analyses. In contrast, Ccl25 emerged as a canonical target of Aire, and we verified this both in vitro and in vivo. Our approach has illuminated the Aire\u2019s primary targets while distinguishing them from the secondary targets.<\/jats:p>","DOI":"10.4049\/jimmunol.2100692","type":"journal-article","created":{"date-parts":[[2021,12,20]],"date-time":"2021-12-20T16:00:11Z","timestamp":1640016011000},"page":"303-320","source":"Crossref","is-referenced-by-count":36,"title":["Aire Controls Heterogeneity of Medullary Thymic Epithelial Cells for the Expression of Self-Antigens"],"prefix":"10.1093","volume":"208","author":[{"given":"Hitoshi","family":"Nishijima","sequence":"first","affiliation":[{"name":"Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minoru","family":"Matsumoto","sequence":"additional","affiliation":[{"name":"Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University , Tokushima,","place":["Japan"]},{"name":"Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences , Tokushima,","place":["Japan"]},{"name":"Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junko","family":"Morimoto","sequence":"additional","affiliation":[{"name":"Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2712-1825","authenticated-orcid":false,"given":"Kazuyoshi","family":"Hosomichi","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University , Ishikawa,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nobuko","family":"Akiyama","sequence":"additional","affiliation":[{"name":"Laboratory for Immunogenetics, RIKEN Center for Integrative Medical Sciences , Yokohama,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Taishin","family":"Akiyama","sequence":"additional","affiliation":[{"name":"Laboratory for Immune Homeostasis, RIKEN Center for Integrative Medical Sciences , Yokohama,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Oya","sequence":"additional","affiliation":[{"name":"Department of Molecular Pathology, Tokushima University Graduate School of Biomedical Sciences , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0670-9868","authenticated-orcid":false,"given":"Koichi","family":"Tsuneyama","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Tokushima University Graduate School of Biomedical Sciences , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideyuki","family":"Yoshida","sequence":"additional","affiliation":[{"name":"YCI Laboratory for Immunological Transcriptomics, RIKEN Center for Integrative Medical Science , Yokohama,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3844-8110","authenticated-orcid":false,"given":"Mitsuru","family":"Matsumoto","sequence":"additional","affiliation":[{"name":"Division of Molecular Immunology, Institute for Enzyme Research, Tokushima University , Tokushima,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,1,15]]},"reference":[{"key":"2025021008494153800_r1","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.coi.2017.10.003","article-title":"Insights into immune tolerance from AIRE deficiency","volume":"49","author":"Proekt","year":"2017","journal-title":"Curr. 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