Effect of SWI/SNF pertubations on chromatin accessibility during macrophage inflammatory activation [ATAC-seq]
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ABSTRACT: To understand how macrophage chromatin respond to LipidA stimulation, we profiled accessibility for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. In addition, we also profiled accessibility for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- Pbrm1-/- BMDMs after 0hr, 1hr, or 4hr LipidA stimulation.
Project description:To characterize macrophage inflammtory activation and the role of the SWI/SNF complex, we first profiled gene expression for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. In addition, we also profiled gene expression for WT BMDMs treated with ACBI1, BRM014, or BRDK98 treatment and for Arid1A-/- or Pbrm1-/- BMDMs after 1hr or 4hr LipidA or LPS stimulation.
Project description:To understand how macrophage histone modifications respond to LipidA stimulation, we profiled H3K27ac binding for WT BMDMs with 0hr or 4hr LipidA stimulation. In addition, we also profiled H3k27ac levels for WT BMDMs treated with ACBI1, BRM014, BRDK98, or dBrd9 and for Arid1A-/- and Pbrm1-/- BMDMs after 4hr LipidA stimulation.
Project description:To understand how the SWI/SNF complex help establish appropriate epiegentic landscape during macrophage inflammatory response, we profiled the binding sites of BRG1 (all BAF), ARID1A (cBAF), BRD9 (ncBAF), and PHF10 (PBAF) for WT BMDMs with 0hr, 1hr, or 4hr LipidA stimulation. To assess the modes of action for cBAF inhibitor BRDK98, we also performed ARID1A ChIP for BRDK98-treated BDMDs after 0hr and 4hr of LipidA stimulation.
Project description:We performed ribosome profiling and RNA-seq on mouse bone marrow derived macrophages (BMDMs) treated with 100ng/ml LPS for 0hr, 1hr, 2hrs, 4hrs, 6hrs to obtain global mRNA translational landscapes during this inflammatory response.
Project description:In eukaryotes, nucleosomes participate in all DNA-templated events by regulating access to the underlying DNA sequence. However, the dynamics of nucleosomes during a genome response has not been well characterized . We stimulated DrosophilaM-BM- S2 cells with heat-killed Gram-negative bacteria Salmonella typhimurium, and mapped genome-wide nucleosome occupancy at high temporal resolution by MNase-seq using Illumina HiSeq 2500. We show widespread nucleosome occupancy change in S2 cells during the immune response, with the biggest nucleosomal loss occurring at 4hr post stimulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Salmonella typhimuriumstimulation
Project description:The innate immune response is among the strongest genomic responses and is conserved across all metazoa. Although transcription during the innate immune response has been well studied, the associated chromatin reorganizations are largely uncharacterized. Here we show that Drosophila S2 cells stimulated with Staphylococcus aureus display a dynamic change in genome-wide nucleosome occupancy and sensitivity. We found a widespread and transient nucleosomal loss peaking at 30 minutes post stimulation, and we demonstrated that the regulatory potentials of nucleosomes differ following stimulation. In addition, we identified differentially sensitive nucleosomes with response-specific potentials. Our results provide high-resolution nucleosome-distribution maps of the fly genome, revealing chromatin's role in: the innate immune response to Gram-positive bacteria, response-specific regulatory-factor binding, and nucleosome sensitivity. We identify functional chromatin regulatory features associated with immune response, and lay a foundation for a framework linking general and locus-specific roles for nucleosomes in immune regulation. Drsophila S2 cells at 0hr, 30minutes, 1hr and 4hr post heat-killed Staphylococcus aureus stimulation
Project description:Sal: Saline. Young male C57BL/6J mice received an injection of saline (5 microL per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment. MK: MK-801. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment. Keywords: time-course
Project description:Sal: Saline. Young male C57BL/6J mice received an injection of saline (5 microL per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment. MK: MK-801. Young male C57BL/6J mice received an injection of MK-801 (300 micro-g per g body weight). RNA from control mice were extracted 1hr, 2hr, 4hr, and 6hr after MK experimental mice received their last shock treatment. Keywords: time-course
Project description:To investigate the role of cBAF in regulation of Tbet binding, polyclonal naive CD8 T cells were stimulated for 48h with anti-CD3, CD28, and hIL-2. Cells were then treated with DMSO, ACBI1, or BRM014 for 6 hours, and treated with recombinant mouse IL-12 for the last two hours of inhibitor treatment. ChIP-seq against T-bet was then performed.