| Summary: | The autoimmune regulator (AIRE), a key player in negative selection of developing thymocytes, acts as a transcriptional regulator, inducing the expression of tissue restricted antigens (TRA) within medullary thymic epithelial cells in a process known as promiscuous gene expression (PGE). Here we demonstrate how AIRE influences PGE through a direct impact on post-translational modifications of core histones which are associated with the regulation of transcription. Through native chromatin immunoprecipitation on thymic epithelial cells transfected with AIRE, we show how in vitro, TRA are enriched in active acetylation and methylation of core histones, yet retain silencing modifications. Furthermore, across a cluster of AIRE-regulated genes, histone modifications were deposited across the entire domain, dependent upon the expression profile of each gene, suggesting a role for domain-wide epigenetic regulation by AIRE. Extension of these studies in vivo, utilising the recently developed carrier ChIP technique, allowed examination of the epigenetic status of TRA throughout the thymic developmental pathway. We report how poised TRA are marked with combinations of active and silent modifications early in thymic development and that the chromatin signatures re-organise as the cells differentiate. The epigenetic patterning differs on a gene by-gene basis, however their significance is implied upon disruption to normal development as the predictive pattern of modifications is lost.
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