Figure 3.

Foxp3 cofactors are bound at pre-accessible enhancers prior to Foxp3 expression. (A) Motifs within Foxp3 binding sites identified by sequence analysis of ChIP-seq peaks and corresponding motif enrichment plots. Flanking regions were sampled 200bp away from centers of peaks. (B) Proportion of Foxp3 binding sites that contain the indicated motifs or their combinations. (C) Motif occurrence is enriched in Foxp3 peaks with more ChIP-seq reads. (D) Representative plots of Ets-1 and Elf-1 ChIP-seq reads aligned to the Foxp3 binding sites at the Junb promoter. (E) ChIP-seq analysis of Foxp3 cofactor occupancy at Foxp3 bound sites in Treg cells containing the corresponding motif demonstrates significant overlap between cofactor and Foxp3 binding. ChIP signal is shown in units of RPM within a 200bp window around Foxp3 peaks. Elf1 and Ets1 signal is transformed by Log₂(x+0.5) and Cbfβ signal was transformed by Log₂(x+1).