DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes

Abstract

The autoimmune regulator (AIRE) protein is the key factor in thymic negative selection of autoreactive T cells by promoting the ectopic expression of tissue-specific genes in the thymic medullary epithelium. Mutations in AIRE cause a monogenic autoimmune disease called autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy. AIRE has been shown to promote DNA breaks via its interaction with topoisomerase 2 (TOP2). In this study, we investigated topoisomerase-induced DNA breaks and chromatin structural alterations in conjunction with AIRE-dependent gene expression. Using RNA sequencing, we found that inhibition of TOP2 religation activity by etoposide in AIRE-expressing cells had a synergistic effect on genes with low expression levels. AIRE-mediated transcription was not only enhanced by TOP2 inhibition but also by the TOP1 inhibitor camptothecin. The transcriptional activation was associated with structural rearrangements in chromatin, notably the accumulation of γH2AX and the exchange of histone H1 with HMGB1 at AIRE target gene promoters. In addition, we found the transcriptional up-regulation to co-occur with the chromatin structural changes within the genomic cluster of carcinoembryonic antigen-like cellular adhesion molecule genes. Overall, our results suggest that the presence of AIRE can trigger molecular events leading to an altered chromatin landscape and the enhanced transcription of low-expressed genes.

Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development

“…Our gene ontology analysis (Supplementary Figure 15 ) of multiple different chromatin marks identified pathways involved in immune system function. Our finding that there was additionally enrichment of pathways involved in the response to ionizing radiation in mTEC hi was interesting because AIRE is thought to cause DNA double-strand breaks as part of its dynamic remodeling of chromatin ( 42 ). It was also noteworthy that H3K27me3 peaks in mTEC lo were enriched for genes known to be conventional targets of the Polycomb Repressive Complex 2 but this was not the case in mTEC hi .…”

Nucleotide Excision Repair and Transcription‐Associated Genome Instability

“…In agreement, neuronal activity requires the presence of DSBs on promoters to trigger the expression of Fos and Npas4 genes in the absence of any exogenously derived genotoxic insult or stimulus . Likewise, the autoimmune regulator protein (AIRE) interacts with TOP2a to promote DSBs on promoters, activating DNA–PK and other partners that attract chromatin‐remodeling complexes to energize the transcription of low‐expressed genes . Interestingly, Helicobacter pylori induces transcription‐dependent XPF/XPG‐mediated DSBs that promote gene expression and cell survival .…”

Dual functions of Aire CARD multimerization in the transcriptional regulation of T cell tolerance

“…Aire binds only weakly and nonspecifically to DNA, and no common sequence motif has been identified for Aire target genes 11,12 . Recent chromatin immunoprecipitation experiments suggest that Aire recognizes general epigenetic features and alters chromatin structure including superenhancer and Polycomb-repressed regions, which may lead to indirect regulation of multiple target genes [13][14][15][16] . This idea is further supported by the stochastic nature of target gene expression at a single cell level 15,17,18 , and the variance of Aire-dependent target genes depending on the cell type 19 .…”