Quantitative profiling of BATF family proteins/JUNB/IRF hetero-trimers using Spec-seq

Background BATFfamily transcription factors ( BATF, BATF2 and BATF3) form hetero- trimerswith JUNBand either IRF4or IRF8to regulate cell fate in T cells and dendritic cells in vivo. While each combination of the hetero- trimerhas a distinct role, some degree of cross-compensation was observed. The basis for the differential actions of IRF4and IRF8with BATFfactors and JUNBis still unknown. We propose that the differences in function between these hetero- trimersmay be caused by differences in their DNA binding preferences. While all three BATFfamily transcription factors have similar binding preferences when binding as a hetero-dimer with JUNB, the cooperative bindingof IRF4or IRF8to the hetero-dimer/DNA complex could change the preferences. We used Spec-seq, which allows for the efficient and accurate determination of relative affinity to a large collection of sequences in parallel, to find differences between cooperative DNA binding of IRF4, IRF8and BATFfamily members.