ATAC-seq profiling of medullary thymic epithelial cells from wildtype and Kat7-knockout mice

Thymic epithelial cells govern thymic T lymphocyte differentiation and selection. Medullary TECs (mTECs) facilitate the negative selection of self-reactive thymocytes and the differentiation of FOXP3+ regulatory T cells. Medullary TECs are also 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. To probe the mechanism by which KAT7 promotes AIRE function, we performed ATAC-seq to compare chromatin accessibility in MHCII-high medullary thymic epithelial cells from Kat7-knockout and wildtype mice. Overall design: Three biological replicates were prepared from wildtype and from Kat7 knockout mice to produce in six ATAC-seq libraries in all. Sequencing was conducted on an Illumina NextSeq 500 to produce 75bp paired-end reads.