Transcriptional regulation by AIRE: molecular mechanisms of central tolerance

Abstract

The negative selection of T cells in the thymus is necessary for the maintenance of self tolerance. Medullary thymic epithelial cells have a key function in this process as they express a large number of tissue-specific self antigens that are presented to developing T cells. Mutations in the autoimmune regulator (AIRE) protein cause a breakdown of central tolerance that is associated with decreased expression of self antigens in the thymus. In this Review, we discuss the role of AIRE in the thymus and recent advances in our understanding of how AIRE might function at the molecular level to regulate gene expression.

Figure 1. Schematic representation of human AIRE protein

The domains and functional elements of the AIRE protein are shown in different colors; CARD (caspase-recruitment domain), SAND (Sp100, AIRE-1, NucP41/P75 and Drosophila DEAF-1), PHD (plant homeodomain), PRR (proline-rich region), L (LXXLL motive), NLS (nuclear-localization signal). Functions of AIRE are shown in boxes and indicated by arrows pointing to the corresponding domain, if known. The CARD (caspase-recruitment domain) has been implicated in homo-oligomerization and is required for nuclear-dot formation and for the heterodimerization of CARD proteins that function in inflammation or apoptosis. Interaction of the CARD with PIAS1 (Protein Inhibitors of Activated STAT) proteins influences the transactivation ability of AIRE. SAND is a putative DNA-binding domain. The first PHD finger has been shown to interact with histone H3 unmethylated at lysine 4 and DNA-PK (DNA protein kinase). Both of these interactions are required for proper transactivation. In addition, PHD1 has been shown to have E3 ubiquitin ligase activity, a mechanism by which a ubiquitin molecule is covalently attached to the target protein. AIRE has also been shown to interact with the transcriptional coactivator CBP (CREB binding protein) and positive transcription elongation factor b (P-TEFb). The latter interaction indicates that AIRE might function in elongation rather than the initiation of transcription. In addition, AIRE has shown to bind the nuclear matrix.

Figure 2. Proposed mechanism of AIRE-mediated gene activation

AIRE is preferentially recruited to promoters with low levels of histone H3K4me3 (histone H3 trimethylated at lysine 4). In addition to histone binding, a direct interaction with DNA might be necessary to guide AIRE to specific regions. On target gene regulatory regions, AIRE recruits a P-TEFb complex that phosporylates serine residues of RNA polymerase II. This phosphorylation converts the polymerase from a paused to elongating form and results in the activation of gene expression. AIRE also interacts with CBP, which acetylates histones allowing further access to chromatin and DNA. Interaction of AIRE with DNA-PK and PIAS proteins further modulates transcriptional activation. DNA-PK can phosphorylate AIRE and, through the interaction with nuclear matrix, collaborate with AIRE in the formation of chromatin loops. Because of the adjacent localization of PIAS1- and AIRE-containing nuclear bodies, PIAS1 might also function in the nuclear organization of chromatin.

Figure 3. Stochastic and coordinated regulation of target genes

In the nucleus AIRE (green circles) is seen in nuclear bodies or recruited to target gene regions. A genomic cluster with four genes is depicted. Genes 1, 3, and 4 are regulated by AIRE; gene 2 is an AIRE-independent gene, which can be active or inactive. In the case of coordinated regulation (upper part), tight transcriptional control is used and the same genes are expressed in nucleus 1 and nucleus 2. Stochastic expression (lower part) leads to fluctuations in the genes that are activated in different nuclei, so that various combinations of clustered genes are expressed in each single cell. In both cases, all three AIRE-regulated cluster genes are expressed when analyzed on a population level. The expression of gene 2 might or might not be influenced by indirect changes in chromatin structure. For example, chromatin reorganization by AIRE might lead to mild repression of gene 2.