Aire controls gene expression in the thymic epithelium with ordered stochasticity

Area of Science:

• Immunology
• Molecular Biology
• Epigenetics

Background:

• The transcription factor Aire is crucial for establishing immunological tolerance.
• Aire induces tissue-specific gene expression in the thymus, preventing autoimmunity.
• Aire's precise mechanism of action and specificity remain incompletely understood.

Purpose of the Study:

• To investigate the specificity and regulation of Aire-driven gene expression in medullary epithelial cells (mTECs).
• To understand how Aire contributes to the diversity of self-tolerance.

Main Methods:

• Single-cell RNA sequencing (scRNA-seq) was employed to analyze gene expression patterns.
• DNA methylation analysis was performed on Aire-sufficient and Aire-deficient mTECs.
• Comparative analysis of gene activation in individual mTECs.

Main Results:

• Aire target genes were found to be induced in only a subset of mTECs, not uniformly.
• Gene activation occurred in small, inter-chromosomal microclusters, independent of DNA methylation patterns.
• These microclusters displayed variability between individual mice, suggesting stochasticity.

Conclusions:

• Aire-mediated gene activation is a stochastic process, organized in stable, heritable microclusters within mTECs.
• This mechanism ensures diverse self-antigen presentation, crucial for effective self-tolerance.
• The findings reveal a novel mode of epigenetic regulation by Aire, promoting immune system diversity.