# The molecular mechanism of Aire

> **NIH NIH R01** · HARVARD MEDICAL SCHOOL · 2021 · $423,750

## Abstract

Aire regulates central T cell tolerance by controlling thymic medullary epithelial cell (MEC) expression of a
battery of transcripts encoding peripheral-tissue antigens. From early on, Aire was recognized to be a
transcriptional regulator, but it soon became apparent that it does not operate like a conventional transcription
factor, i.e. binding to promoters and inducing initiation of transcription. Studies completed during the last
funding-cycle demonstrated that Aire-induced genes occur as intra- or inter-chromosomal clusters within
individual cells, that Aire participates in multiple multi-protein complexes, and that it preferentially localizes to
and activates so-called “super-enhancers.” Super-enhancers (a.k.a “stretch” or “serial” enhancers) are
extended regions of chromatin that are over-loaded with general and cell-type-specific transcription factors,
and are thought to serve as depots for coordinate and efficient delivery of these factors to targeted promoters
via chromatin looping. In addition, preliminary data documented herein indicate that Aire associates, directly or
indirectly, with cohesin, one of the major orchestrators of long-range chromatin interactions (in collaboration
with CTCF and/or mediator). Thus, the overall goal of this proposed project is to determine how Aire integrates
into the three-dimensional organization of chromatin. This goal will be addressed via three Specific Aims:
● To determine whether Aire associates with proteins known to orchestrate 3D chromatin interactions:
CTCF, cohesin, NIPBL and mediator. Experiments under this Aim will employ primarily biochemical
approaches to determine whether Aire associates with the three major 3D-chromatin-organizing elements (and
a cohesin-loader, NIPBL).
● To integrate Aire’s distribution along MEC chromatin with those of CTCF, cohesin and mediator; to
determine how Aire impacts CTCF/cohesin/mediator placement and, vice versa, how cohesin
influences Aire’s placement. This series of experiments will exploit recent improvements in ChIP-seq (and
other whole-genome) technologies to map the binding sites of the three chromatin organizers in relation to Aire
binding and other landmarks – in wild-type, Aire-knockout and inducible Smc1-knockdown mice
● To define the relationship between Aire and three-dimensional chromatin organization. This set of
experiments will use HiC technology to generate whole-genome interaction maps for MEC chromatin from
Aire+/+ and Aire-/- mice.
 Successful completion of these studies will bring our understanding of Aire control of T cell tolerance to a
new level of molecular understanding, and is likely to resolve several of the outstanding conundrums related to
Aire function. The Aire story continues to intrigue!

## Key facts

- **NIH application ID:** 10153655
- **Project number:** 5R01AI088204-10
- **Recipient organization:** HARVARD MEDICAL SCHOOL
- **Principal Investigator:** DIANE J MATHIS
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $423,750
- **Award type:** 5
- **Project period:** 2010-12-10 → 2023-11-14

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10153655

## Citation

> US National Institutes of Health, RePORTER application 10153655, The molecular mechanism of Aire (5R01AI088204-10). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10153655. Licensed CC0.

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