Cbfβ regulates DNA looping at the Il4-Il13 loci to control their differential expression in Th2 cells

Th2 cells play a central role in orchestrating type 2 immune responses by producing type 2 cytokines including IL-4 and IL-13. The master transcription factor GATA3 is essential but not sufficient for type 2 cytokine production. To better define other transcription factors that regulate type 2 cytokine expression, we performed a CRISPR-Cas9 screen after preparing a retroviral library expressing sgRNAs targeting 2,394 mouse transcription factors and cofactors. The screen revealed core-binding factor beta (Cbfβ) as a specific inducer of IL-13 that simultaneously inhibited IL-4 expression. The effect of Cbfβ on IL-13 production was confirmed both in vitro and in vivo and was independent of GATA3 induction. Mechanistically, Cbfβ induced chromatin accessibility at the HS-2 site within the Il13 promoter where the Cbfβ/Runx complex bound. Hi-TrAC analysis indicated that DNA looping between HS-2 and other enhancers was reduced upon Cbfβ deletion. Overall, our results indicate that Cbfβ directly regulates IL-13 expression by binding the Il13 promoter via the Cbfβ/Runx complex and promoting enhancer–promoter interactions that facilitate Il13 transcription.