Dynamic control of gene expression by ISGF3 and IRF1 during IFNbeta and IFNgamma signaling

Type I interferons (IFN-I, including IFNbeta) and IFNgamma produce overlapping, yet clearly distinct immunological activities. Recent data show that distinctness of global transcriptional responses to the two IFN types is not apparent when comparing their immediate effects. By analyzing nascent transcripts induced by IFN-I or IFNgamma over a period of 48hrs we now show that the distinctiveness of the transcriptomes emerges over time and is based on a different employment of the ISGF3 complex as well as the second-tier transcription factor IRF1. The distinct transcriptional properties of ISGF3 and IRF1 correspond with a largely diverse nuclear protein interactome. Mechanistically, we describe specific input of ISGF3 and IRF1 into enhancer activation and the regulation of chromatin accessibility at interferon-induced genes (ISG). We further report differences between the IFN types in altering RNA polymerase II pausing at ISG 5' ends. Our data provide insight how transcriptional regulators create immunological identities of IFN-I and IFNgamma.