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

ABSTRACT: TTh2 cells play an important role in regulating type 2 immune responses by producing type 2 effector cytokines including IL-4 and IL-13. While GATA3, the master transcription factor for Th2 cell differentiation, is essential for type 2 cytokine production, GATA3 expression itself even at high levels is not sufficient to induce transcription of either Il4 or Il13 under certain circumstances. To better understand the transcription factors that regulate IL-4 and IL-13 expression during Th2 cell differentiation, we performed CRISPR-Cas9 screens in vitro with a retroviral library targeting 2,394 TFs and cofactors. We discovered a previously unappreciated role for Cbfβ (core binding factor beta) in promoting IL-13 expression. In the same screen, NFAT1 was found to preferentially induce IL-4 expression. The effect of Cbfβ on type 2 cytokine production which were confirmed both in vitro and in vivo was independent of GATA3 induction. We also found that early but not late deletion of Cbfβ in Th2 cells affected IL-13 production. To further explore the mechanism by which Cbfβ regulates the expression of IL-13, we used DNase I-Seq to assess chromatin accessibility. The results showed that knocking out Cbfβ reduced the accessibility at the HS-2 site in the Il13 promoter. Cbfβ ChIP-Seq in Th2 cells showed a binding peak in the HS-2 site. DNA looping between HS-2 and other enhancers were reduced when knocking out Cbfβ in Th2 cells from our Hi-TrAC analysis. These results indicating that Cbfβ regulate IL-13 expression directly by binding to Il13 promoter and bringing together enhancers to the Il13 promoter to facilitate Il13 transcription..

ORGANISM(S): Mus musculus

PROVIDER: GSE318773 | GEO | 2026/09/30

REPOSITORIES: GEO