RNA-seq profiling of epithelial cells from fetal thymic organ cultures from Kat7 knockout and wildtype mice

ABSTRACT: Thymic epithelial cells (TECs) govern thymic T lymphocyte differentiation and selection. Medullary TECs are distinctive for their "promiscuous" gene expression, transcribing thousands of peripheral tissue genes (PTG) that are otherwise only expressed highly in one or two other organs. Much of this PTG expression by mTECs is controlled by the autoimmune regulator, AIRE. This experiment was part of a larger study in which we examined the impact of Kat7 loss on AIRE-mediated PTG expression. Despite the apparently normal differentiation of AIRE+ TECs in Kat7-knockout mice, it was possible that the defect in AIRE-mediated PTG expression was secondary to the developmental loss of this histone acetyltransferase. To address this hypothesis, we employed fetal thymic organ cultures (FTOC) depleted of thymocytes where AIRE+ mTEC and PTG expression was induced by an agonist anti-RANK antibody. We then used two different approaches to acutely block KAT7 function and subsequently sort purified TECs for RNA-seq analysis to assess the impact on AIRE-mediated PTG transcription. AIRE+ mTECs exhibit relatively low turnover in organ culture; therefore, this approach uncouples KAT7 impacts on AIRE function from potential influences on TEC differentiation. Our first approach employed a new small molecule inhibitor of KAT7 function, WM-3835. The second approach was an inducible genetic deletion system. FTOC established with thymi from control (Kat7fl/fl) or RosaCre-ERT2 Kat7fl/fl mice were treated with tamoxifen to activate CRE-mediated deletion of Kat7.

ORGANISM(S): Mus musculus

PROVIDER: GSE188869 | GEO | 2021/12/21

REPOSITORIES: GEO