Specificity of enhancer selection by IRF3, IRF5 and IRF9 in dendritic cells

To discover the key determinants of IRF-specific enhancer selection, we identified and characterized IRF binding regions. Using chromatin immunoprecipitation coupled with deep sequencing (ChIP-seq), we mapped the binding regions of IRF3, IRF5, and IRF9 in murine dendritic cells (DCs) stimulated with TLR3 and TLR9 agonists, as well as IFNβ, respectively. We comprehensively analysed the IRF cistromes to identify characteristic features, including DNA motifs for IRFs and other transcription factors, and chromatin status. CD8-positive dendritic cells were left unstimulated or were treated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG) or 10U IFN-beta for 90 min.