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Official Full Name
autoimmune regulator
This gene encodes a transcriptional regulator that forms nuclear bodies and interacts with the transcriptional coactivator CREB binding protein. The encoded protein plays an important role in immunity by regulating the expression of autoantigens and negative selection of autoreactive T-cells in the thymus. Mutations in this gene cause the rare autosomal-recessive systemic autoimmune disease termed autoimmune polyendocrinopathy with candidiasis and ectodermal dystrophy (APECED). [provided by RefSeq, Jun 2012]
AIRE; autoimmune regulator; APS1; APSI; PGA1; AIRE1; APECED; autoimmune polyendocrinopathy candidiasis ectodermal dystrophy protein; si:dkey-261l2.5

In the human, the AIRE (autoimmune regulator) gene is located on chromosome 21q22. 3, which consists of 14 exons, spanning 11. 9 kb of genomic DNA, encoding a protein of 545 amino acids with a molecular weight of about 57.5 kD. The AIRE protein is mainly localized in the nucleus and distributed in the nucleosomes near the nuclear speckle, suggesting that AIRE is involved in gene transcriptional regulation. 

AIREp shares three domains with the Sp100 family, which are involved in the interaction of DNA-binding proteins and the regulation of transcription. The first is a homogeneously stained region (HSR domain) located between amino acids 1 and 106, which is expressed in all members of the Sp100 family and is thought to play a role in a variety of cellular processes, including growth control, apoptosis, and senescence. The second is the SAND domain located at amino acids 189-280. This domain is involved in chromatin remodeling activity. The Sp100 SAND domain contains a conserved KDWK sequence with a unique α/β folding structure that is predicted to play an important role in DNA binding. The third is two plant homology domains (PHD) located at amino acids 299-340 and amino acids 434-474, respectively. Their zinc finger domain may be a DNA-binding domain, and this structural mutation will cause a severe decline in AIRE transcriptional activation.

Figure 1. AIRE protein domains, key interacting partners, and mechanism of TRA gene expression. (Zumer, et al. 2016)

The molecular mechanism regulating the expression of the AIRE gene in vivo remains unclear. Current studies using luciferase reporter gene detection have identified a reasonable minimum promoter region for the AIRE gene. This region contains the binding sequences including the SP1, AP-1, NF-Y and ETS transcription factor families. In fact, luciferase reporter assays have shown that the AIRE gene promoter regulates the AIRE gene promoter. However, there have been no in vivo genetic studies to demonstrate whether these sequence-specific transcription factors play an important role in the regulation of AIRE expression.

Studies have shown that the promoter region of AIRE contains a high proportion of CpG sites that are methylated in cell lines with defective AIRE expression. Subsequent studies have shown that these CpG sites are hypomethylated in medullary thymic epithelial cells (mTEC) compared to thymocytes, suggesting that DNA demethylation may be a prerequisite of AIRE expression. However, hypomethylation was also observed in cEC and AIRE-deficient thymoma. Therefore, DNA hypomethylation appears to be necessary, but still not sufficient to induce AIRE expression. Overall, AIRE expression appears to be regulated by a combination of chromatin modifications and sequence-specific transcription factors. However, the exact mechanisms and regulatory molecules remain to be determined.

AIRE and Central Immune Tolerance

Negative selection of autoreactive thymocytes relies on mTEC-induced tissue-specific antigens (TSAs), and AIRE plays an important role in exposing these antigens. Its restricted expression in mTEC cells induces the expression of major histocompatibility complex (MHC)/human leukocyte antigen (HLA) molecules on the mTEC surface, thereby controlling the expression of thymus-specific tissue antigens. Mature thymocytes move and pass through the thymic medulla, and if their TCR recognizes the MHC-TSA complex with appropriate affinity, they will be overactivated and deleted. Through this process, the thymus reaches the role of clearing autoreactive T cells in the immune system.

Studies in transgenic mice have also shown that mice with insufficient AIRE develop clonal deletion disorders. Experiments to track autoantigen-specific T cells in mice have shown that autoreactive thymocytes can escape clone clearance in the usual sense in the case of AIRE knockout. It has been reported that mTECs can also mediate tolerance by directly presenting AIRE-regulated antigens to CD4 + and CD8 + T cells. Dendritic cells also have an effect on AIRE-driven antigen expression during central tolerance production. The recognition of MHC-TSA complexes can occur not only directly on MECs but also directly on DCs that have phagocytosed apoptotic MECs or MECs fragments.

The genes of TSAs in AIRE-controlled MECs are clustered in chromosomes. Some studies have found that AIRE acts as a transcription factor to directly promote TSA expression. In addition, AIRE can bind to DNA-PK or bind to hypomethylated histone 3 lysine 4 (H3K4) via its PHD domain, indicating AIRE plays a role in the repair in DNA double-strand breaks and altering chromatin in the TSA gene. They are critical for recruiting AIRE to the TSA gene locus and promoting TSA expression. In addition, it has been reported that AIRE can recruit P-TEFb to the TSA gene locus and promote the extension of captured TSA transcripts by releasing RNA polymerase II from the proximal promoter. Macedo et al. found that in addition to the expression of TSA, the expression of some microRNAs (miRNAs) was recently found to be AIRE-dependent, and genetic studies revealed that miRNA expression plays an important role in the function and maintenance of mTECs.

AIRE and Peripheral Tolerance

Lindex et al. detected AIRE in peripheral lymphoid organs, and RNA transcripts encoding AIRE have also been found in mouse and human monocytes as well as in dendritic cells (DCs), indicating either antigen presentation or it is said that AIRE has a possible extrathymic effect in regulating peripheral tolerance. The expression of AIRE in peripheral lymphoid organs can improve its function in the thymus. But the difference is that the role of AIRE in the periphery seems to be different from its function in the thymus. AIRE is found in the periphery to regulate the expression of a group of autoantigens that are not identical to those expressed in the thymus. It has also been found that AIRE has a regulatory effect on the maturation process of monocyte to dendritic cells (moDCs).

Gardner et al. found that AIRE transcripts, as well as nuclear AIRE proteins, are expressed in a unique tolerogenic stromal cell population called ETACs (extrathymosinal AIRE-expressing cells). These cells interact with and delete from naive autoreactive T cells, and some of the markers expressed are reminiscent of mTECs (eg, MHC class II, EpCAM), but these cells appear to lack expression of the canonical costimulatory molecules CD80 and CD86. Their recent studies have confirmed that ETACS is a group of bone marrow-derived antigen presenting cells (APCs) that are significantly different from dendritic cells (DCs) and stromal cell phenotypes. A comparison of wild-type and AIRE knockout mouse ETACs suggests that AIRE regulates a set of TSA, including several important autoantigens and genes important in antigen processing and presentation. This suggests that AIRE expression has a broad role in the expression of TSA in the periphery. By inactivating such cells, it was shown that AFE-mediated expression of PTA in ETACs may be an important mechanism for CD4 + T cell tolerance.

A comparison of wild-type and AIRE knockout mouse ETACs suggests that AIRE regulates a set of TSA, including several important autoantigens and genes important in antigen processing and presentation. This suggests that AIRE expression has a broad role in the expression of TSA in the periphery. By inactivating such cells, it was shown that AFE-mediated expression of PTA in ETACs may be an important mechanism for CD4 + T cell tolerance.


  1. Bruserud, Ã., Oftedal, B. E., Wolff, A. B., & Husebye, E. S. (2016). Aire-mutations and autoimmune disease. Current Opinion in Immunology, 43, 8-15.
  2. Macedo, C., Evangelista, A. F., Marques, M. M., Octacíliosilva, S., Donadi, E. A., & Sakamotohojo, E. T., et al. (2013). Autoimmune regulator (aire) controls the expression of micrornas in medullary thymic epithelial cells. Immunobiology, 218(4), 554-560.
  3. Lindmark, E., Chen, Y., Georgoudaki, A. M., Dudziak, D., Lindh, E., & Adams, W. C., et al. (2013). Aire expressing marginal zone dendritic cells balances adaptive immunity and t-follicular helper cell recruitment. Journal of Autoimmunity, 42(5), 62-70.
  4. Gardner, J., Metzger, T., Mcmahon, E., Au-Yeung, B., Krawisz, A., & Lu, W., et al. (2013). Extrathymic aire -expressing cells are a distinct bone marrow-derived population that induce functional inactivation of cd4 +, t cells. Immunity, 39(3), 560-572.
  5. Zumer, K., Saksela, K., & Peterlin, B. M. (2013). The mechanism of tissue-restricted antigen gene expression by aire. Journal of Immunology, 190(6), 2479.

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