Changes in nucleosome occupancy at enhancers
Studies in the lab have focused on understanding regulation of three pro-inflammatory cytokines, IL12B, IL1A and IFNB1 (Gjidoda et al. 2014). These cytokines are expressed when macrophages are stimulated by LPS, and we demonstrated that in resting macrophages distal and proximal enhancers of these genes are occupied by nucleosomes in only 40-60% of the population, while regions surrounding the enhancers and in their ORFs are often more highly occupied (80-100%). Upon LPS induction nucleosomes are rapidly remove, which correlates with binding of signal-induced TFs to the enhancers and allows recruitment of the transcriptional machinery to enhancers and promoters resulting in gene expression.
Our results indicate certain transcription factors, including the signal-induced transcription factors NFkB, AP1 and IRF3 preferentially bind to their sites in the absence of nucleosomes, and our data suggest that these sites are kept nucleosome-free by an active process involving nucleosome remodelers. In contrast, we found that the promoters of two of these genes, IL12B and IL1A, are associated with nucleosomes in a large fraction of the population under inducing conditions, suggesting that nucleosomes may rapidly reform at promoters. We hypothesize that reformation of promoter nucleosomes may contribute to the highly stochastic expression of many cytokines that was previously reported.