The initiation, amplification and quenching of an innate immune response involves tightly regulated gene expression changes that are coordinated by a variety of transcription factors (TFs). To allow for the rapid activation of inflammatory gene expression in macrophages, pioneer TFs sit poised at promoter and enhancer regions. Following an immune stimulus, such as the bacterial protein LPS, signal-regulated transcription factors are recruited to these sites to induce a potent pro-inflammatory response, that is specific to each type of inflammatory stimulus. While the initiation of a pro-inflammatory response by factors such as NfΚB has been very well studied, what determines why only a subset of primed genes are activated at any one time, or how the inflammatory state is turned off, is less well understood.
Mice with a genetic deletion in the TF Klf3 have an inflammatory phenotype, with increased macrophages. To explore the role of KLF3 in the macrophage inflammatory response we performed chromatin immunoprecipitation sequencing (ChIPseq) using the RAW264.7 macrophage cell line. We found that in many cases KLF3 and the pioneer TF PU.1 were co-localised at key inflammatory genes. Furthermore, RNAseq of cells treated with LPS revealed that when KLF3 is overexpressed, the upregulation of these inflammatory genes was perturbed.
We propose that KLF3 acts as a repressor of the inflammatory response through modulation of PU.1 binding to inflammatory gene promoters and enhancers, and alters the accessibility of these regions to pro-inflammatory TFs. This work sheds light on a novel role for KLF3 in (1) the silencing of a subset of inflammatory genes to allow for distinct, context dependent patterns of gene activation, and (2) the repression of activated genes to prevent prolonged and potentially deleterious inflammatory responses.