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Batf-mediated Epigenetic Control of Effector CD8+ T Cell Differentiation

The response of cytotoxic T cells to their cognate antigen involves rapid and broad changes in gene expression that are coupled with extensive chromatin remodeling. Here, we study the mechanisms by which the basic leucine zipper ATF-like transcription factor Batf helps regulate this process. Through genome-scale profiling, we observe critical roles for Batf in inducing transcriptional changes in stimulated naive cells, while affecting the chromatin at several levels, namely binding of key transcription factors, accessibility, and long range contacts. We identify a critical network of transcription factors that cooperate with Batf, including its binding partner Irf4, as well as Runx3 and T-bet, and demonstrate its synergistic activity in initiating aspects of the effector T cells’ transcriptional and epigenetic program in ectopically-induced fibroblasts. Our results provide a comprehensive resource for studying the epigenomic and transcriptomic landscape of effector differentiation of cytotoxic T cells.