Toll-Like Receptor-induced Nucleosome Remodeling Achieved by Broadly Acting NF-kB in Collaboration with Transcription Factors Conferring Selectivity [BMDM_ATAC]

Macrophages play a critical role in bridging the innate and adaptive immune systems, which requires timely and precise transcription control when responding to danger signals. Gene expression networks in macrophages have been profiled extensively in recent decades with the advancement of high-throughput sequencing technologies. However, unveiling critical mechanistic insights into control of diverse transcriptional networks has proven to be challenging. Recent evidence has suggested that the accessibility of chromatin structure can provide an integral means of transcription regulation. We have used the relatively recent Assay for Transposase-Accessible Chromatin using Sequencing (ATAC-seq) method to assess chromatin accessibility with optimal resolution in mouse bone marrow derived macrophages during the course of lipid- A stimulation. This advanced method enabled us to characterize the chromatin state of genome-wide regulatory regions. By applying a quantitative systematic approach, we obtained mechanistic insights into the highly selective role of the major transcription factors, NF-?B and IRF3, in nucleosome remodeling and transcription regulation. Overall design: Bone-marrow derived macrophages were derived from C57/B16 and Irf3-/- mice. C57/B16 macrophages were stimulated with lipid-A for 0, 30, 60 or 120 minutes and in the presence of cycloheximide for 120 minutes. Irf3-/- macrophages were treated with lipid A with or without the presence of cycloheximide for 0 and 120 minutes. Chromatin was collected and treated with Tn5 transposase to profile DNA accessibility.