Dynamic Control of Transcription Factor Networks Governs Self-Antigen Diversity for Immune Tolerance

The immune system has evolved to defend against pathogens while maintaining tolerance to self. Yet immune cells are not tailored to recognize specific pathogens. Instead, they possess a broad and continuous spectrum of antigen reactivity. This raises a fundamental question: how does the immune system achieve effective pathogen recognition while avoiding self-reactivity, and what molecular mechanisms tune this balance? In medullary thymic epithelial cells (mTECs), we demonstrate that the diversity of self-antigens presented to developing thymocytes shapes the self-reactivity of the resulting T cell repertoire. We identify the Vitamin D receptor (VDR) as a key regulator of this process, acting to modulate the amplitude of NF-κB signaling and, in turn, the heterogeneity of tissuespecific antigen expression programs that underlie central tolerance. Mechanistically, VDR restricts access to higher-affinity NF-κB binding sites, thereby promoting transcriptional diversity. Loss of VDR disrupts this balance and compromises immunological self-tolerance. Finally, we propose a transcriptional relay between NF-κB and AP-1 that establishes tissue-specific gene expression. We propose a model in which NF-κB activity—particularly RELA—primes the chromatin landscape, enabling subsequent redistribution of AP-1 binding. At composite NF-κB:AP-1 sites, RELA guides AP-1 to specific genomic loci, after which AP-1 potentially replaces RELA and recruits additional transcriptional machinery to drive tissue-specific gene expression. Consistent with this model, deletion of RELA or the m6A reader YTHDF2—an mRNA decay factor that limits expression of the AP-1 component FOS—impairs AP-1 redistribution and leads to autoimmunity. Together, these studies reveal how dynamic regulation of transcription factor activity governs both the breadth and variability of gene expression within individual cells, establishing principles that extend across immune tolerance, development, and disease.