Genome-wide analysis of interferon regulatory factor I binding in primary human monocytes

IRF1 is a transcription factor that participates in interferon signaling. Previous studies of IRF1 binding have utilized in vitro assays. We used ChIP-seq in human monocytes to better define the recognition motif for IRF1. The newly identified 18 bp motif (RAAASNGAAAGTGAAASY) is a refinement of the 13 bp IRF1 motif commonly used. We utilized the 18 bp consensus motif and identified 345 potential target genes. To compare the 18 bp motif with the 13 bp motif, we compared putative gene targets. Only 56 potential gene targets were defined by both consensus motifs. To compare biological effects of interferon on the 13 bp and the 18 bp consensus targets, we mined expression data from cells exposed to interferons or transfected with IRF1. In all cases, the 18 bp consensus motif was more strongly associated with transcriptional responses than the 13 bp motif. Therefore, the new 18 bp consensus motif appears to have a greater association with biological activities of IRF1.