Autoimmune regulator (Aire), a transcriptional regulator expressed in medullary thymic epithelial cells (mTECs), controls the negative selection of T cells in thymus by inducing the expression of peripheral tissue antigens. However, how Aire achieves the goal of driving promiscuous expression of a large swath of the genome in mTECs remains an enigma. We addressed the hypothesis that Aire impacts chromatin organization through widespread promotion of superenhancer–promoter loops and thus enhancing the expression of a large battery of genes in mTECs.
We performed genome-wide, high-resolution chromosome-conformation capture (Hi-C) experiments on ex vivo mTECs from wild-type and Aire-mutant mice. Our results suggested that Aire has a widespread impact on higher-order chromatin structure, disfavoring architectural loops while favoring transcriptional loops. Aire promoted the accumulation of mediator and cohesin complexes at superenhancers and Aire’s association with the cohesin loader, NIPBL, further strengthened this fact. On contrary, the chromatin-domain enforcer CCCTC-binding factor (CTCF) was relatively depleted from structural domain boundaries in the presence of Aire.
We also created a mouse line with deletion of gene encoding cohesin complex subunit, SA-2 and Aire-induced transcripts were downregulated in mTECs from this mouse line. Our model explains many of the unusual features of Aire’s impact on mTEC transcription, providing molecular insight into tolerance induction.
Model for Aire-induced gene (AIG) transcription resulting from Aire’s promotion of transcriptional (superenhancer–promoter) loops (right) at the expense of architectural loops (left). CTCF–cohesin complexes underlie the latter (adapted from Proceedings of the National Academy of Sciences U S A, 118(38):e2110991118).
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