| The eukaryotic transcription factors, IRF3 and NFkB, regulate immunity and inflammatory responsive genes. These two proteins are critical regulators of immunity and inflammatory responses, control diverse normal cellular functions, and aberrations in their activity contribute to pathologies including inflammatory diseases and cancer. The relative contributions of IRF3 and NFkB to overall virus-activated transcription, their degree of overlap within the antiviral gene regulation network, and their breadth of target sites throughout the genome are under-investigated. The mechanisms used in regulating antiviral RNA Polymerase II (Pol II) recruitment, initiation, and elongation at specific targets, as well as their abilities to regulate non-coding and protein-coding genes remain poorly understood. To investigate the mechanisms used to mediate Pol II recruitment, initiation, and elongation that contribute to the human antiviral gene regulatory network, a comprehensive genome-wide ChIP-seq analysis was conducted during the initial phase of virus infection. Results reveal extensive integration of IRF3 and NFkB with Pol II and its associated machinery, and implicate new transcriptional partners for antiviral gene regulation. In addition to mRNA-encoding loci, a majority of IRF3 and NFkB target sites stimulate RNA production at novel genomic regions not previously associated with antiviral transcription through a combination of de novo polymerase recruitment and release of paused Pol II. These factors work together to tightly regulate gene activation essential to cellular innate immunity.;In addition to these findings, a high-density nucleosome mapping strategy was used to generate locus-wide maps of human chromosome 9p21-22, which contains the type I interferon gene cluster. The nucleosome organization of this locus was determined at steady state and during a time course of Sendai virus infection, a potent inducer of interferon gene expression. Detailed computational analysis illustrates that nucleosomes in this locus exhibit preferences for particular dinucleotide and oligomer DNA sequence motifs in vivo, which are similar to those reported for lower eukaryotes. These data were used to visualize the region's chromatin architecture and reveal features of antiviral gene regulation that are generally consistent with known nucleosome-mediated gene regulatory paradigms. |
