UC San Diego

The broad role of interferons in innate immune signaling complicates study of their regulatory dynamics. To determine the mechanism underlying the specificity of Type I vs Type II IFN responses, I examined the composition of regulatory elements associated with transcriptional responses specific to each pathway. Here I used csRNA-seq to capture short capped RNAs and identify sites of transcription initiation in both promoters and enhancers at base-pair resolution. I applied this method to analyze the transcriptional responses in RAW264.7 murine macrophages responding to a time course of stimulation with Type I and Type II Interferon (IFN). I classified differentially regulated promoters and enhancers based on csRNA-seq-enabled identification of these TSRs and supporting ATAC-seq and ChIP-seq data. The time course of stimulation over 4 hours allowed visualization of the temporal dynamics of IFN signaling. I identified a novel variation of the classical Interferon DNA motif, the Interferon Stimulated Response Element (ISRE), called the Type I Interferon Response Element (T1ISRE). The T1ISRE is enriched in the promoters and enhancers of genes preferentially regulated by Type I IFN compared to Type II IFN and is preferentially bound by the ISGF3 complex. This new element underscores how small variations in cis-regulatory sequences can tune transcriptional programs, a strategy observed in other signaling pathways.