AIRE is an unconventional transcription factor that enhances the expression of thousands of genes in medullary thymic epithelial cells and promotes clonal deletion or phenotypic diversion of self-reactive T cells^1,2,3,4. The biological logic of AIRE’s target specificity remains largely unclear as, in contrast to many transcription factors, it does not bind to a particular DNA sequence motif. Here we implemented two orthogonal approaches to investigate AIRE’s cis-regulatory mechanisms: construction of a convolutional neural network and leveraging natural genetic variation through analysis of F1 hybrid mice⁵. Both approaches nominated Z-DNA and NFE2–MAF as putative positive influences on AIRE’s target choices. Genome-wide mapping studies revealed that Z-DNA-forming and NFE2L2-binding motifs were positively associated with the inherent ability of a gene’s promoter to generate DNA double-stranded breaks, and promoters showing strong double-stranded break generation were more likely to enter a poised state with accessible chromatin and already-assembled transcriptional machinery. Consequently, AIRE preferentially targets genes with poised promoters. We propose a model in which Z-DNA anchors the AIRE-mediated transcriptional program by enhancing double-stranded break generation and promoter poising. Beyond resolving a long-standing mechanistic conundrum, these findings suggest routes for manipulating T cell tolerance.

AIRE 是一种非常规转录因子，可增强胸腺髓质上皮细胞中数千个基因的表达，并促进自身反应性 T 细胞的克隆缺失或表型转移^1,2,3,4。AIRE 靶标特异性的生物学逻辑在很大程度上仍不清楚，因为与许多转录因子相比，它不与特定的 DNA 序列基序结合。在这里，我们实施了两种正交方法来研究 AIRE 的顺式调节机制：构建卷积神经网络并通过分析 F1 杂交小鼠⁵来利用自然遗传变异。两种方法都将 Z-DNA 和 NFE2-MAF 指定为对 AIRE 目标选择的假定积极影响。全基因组作图研究表明，Z-DNA 形成和 NFE2L2 结合基序与基因启动子产生 DNA 双链断裂的固有能力呈正相关，并且表现出强双链断裂产生的启动子更有可能进入一种具有可接近的染色质和已经组装的转录机器的平衡状态。因此，AIRE 优先靶向具有稳定启动子的基因。我们提出了一个模型，其中 Z-DNA 通过增强双链断裂的产生和启动子平衡来锚定 AIRE 介导的转录程序。除了解决长期存在的机制难题之外，这些发现还提出了操纵 T 细胞耐受性的途径。