NF-kB Broadly Orchestrates Nucleosome Remodeling during the Primary Response to Toll-Like Receptor 4 Signaling [scATAC-seq]

Inducible nucleosome remodeling at hundreds of latent enhancers and several promoters helps shape the transcriptional response to Toll-like receptor 4 (TLR4) signaling in macrophages. However, the identities of the transcription factors that promote TLR-induced remodeling have remained elusive. An analysis strategy that enriched ATAC-seq profiles for genomic regions most likely to undergo remodeling uncovered a unique relationship between NF-kB and TLR4-induced remodeling events. A critical functional role for NF-kB in remodeling was then revealed by CRISPR-Cas9 mutagenesis of NF-kB genes and binding motifs. This critical role is broad and possibly universal during the TLR4 primary response. Remodeling selectivity at defined regions is often conferred by collaboration between NF-kB and other inducible factors, including IRF3 and MAP kinase-induced factors. Thus, NF-kB is unique among TLR4-induced transcription factors in its broad contribution to inducible nucleosome remodeling, alongside its well-established ability to activate poised enhancers and promoters assembled into open chromatin. Overall design: Unstimulated or 2 hour Lipid A (100ng/ml, Sigma Aldrich, Cat# L6895-1MG) stimulated bone marrow derived macrophages (BMDM) from Wildtype male mice were harvested from the tissue culture dish (35 mm) to generate single cell suspension. Quality of cells were monitored by microscopic examination and cells viability were more than 95% based of trypan blue exclusion staining and counting in hemocytometer. About 1 million cells were processed for nuclei isolation followed by transposition as per 10X scATAC seq instruction manual, followed by NGS library prep and sequencing in Illumina NovaSees 6000 S1 platform at 100 cycle.