Regulation of inflammation is of crucial importance, both for the advancement of therapeutic intervention and for the limiting of deleterious autoimmune complications. The precise tuning of the inflammatory response involves transcription and, from our recent unpublished studies, meticulous regulation of hundreds of mRNAs at many levels. Since we discovered NF-?B in 1986, we have been examining a variety of properties of this transcription factor system, focusing most of our attention on the role of NF-?B in the immune system, particularly in orchestrating the inflammatory response to pathogen challenge. In recent years, we have studied the regulatory events underpinning the precise timing of gene expression during the inflammatory response. We used RNA-seq to target only inflammatory transcripts and have quantified splicing kinetics of introns of inflammatory genes, finding that some are orders of magnitude slower to splice than expected. We find that they confer a significant reduction in gene expression as delays in splicing are often concomitant with RNA exosome engagement. We predict this may be a regulatory mechanism, and call them ?bottleneck introns.? In this proposal, we propose to test the biological relevance of bottleneck introns in tissue culture and by making mice (Aim 1) to see if limits to inflammation are altered in the context of a repaired intron. In addition, we propose to investigate whether there are biological contexts (stimulus, cell-type, developmental state) that confers improved splicing of a bottleneck (Aim 2), therefore providing a regulatory framework for this finding.
Realization of these three aims will significantly increase our understanding of the regulation of the inflammatory response that underlies the body's ability to fight infections. Chronic, unregulated inflammation is thought be involved in cancer, heart disease, autoimmunity and other conditions; this work will also help to understand and hopefully treat these ailments.
