Nucleosomes Are Stably Evicted from Enhancers but Not Promoters upon Induction of Certain Pro-Inflammatory Genes in Mouse Macrophages

Chromatin is thought to act as a barrier for binding of cis-regulatory transcription factors (TFs) to their sites on DNA and recruitment of the transcriptional machinery. Here we have analyzed changes in nucleosome occupancy at the enhancers as well as at the promoters of three pro-inflammatory genes when they are induced by bacterial lipopolysaccharides (LPS) in primary mouse macrophages. We find that nucleosomes are removed from the distal enhancers of IL12B and IL1A, as well as from the distal and proximal enhancers of IFNB1, and that clearance of enhancers correlates with binding of various cis-regulatory TFs. We further show that for IFNB1 the degree of nucleosome removal correlates well with the level of induction of the gene under different conditions. Surprisingly, we find that nucleosome occupancy at the promoters of IL12B and IL1A does not change significantly when the genes are induced, and that a considerably fraction of the cells is occupied by nucleosomes at any given time. We hypothesize that competing nucleosomes at the promoters of IL12B and IL1A may play a role in limiting the size of transcriptional bursts in individual cells, which may be important for controlling cytokine production in a population of immune cells.

染色质（Chromatin）通常被认为会充当屏障，阻碍顺式调控转录因子（cis-regulatory transcription factors）结合DNA上的靶位点，同时阻断转录机器的招募。本研究针对原代小鼠巨噬细胞经细菌脂多糖（LPS）诱导的3种促炎基因，分析了其增强子与启动子区域的核小体占有率变化。研究结果显示：IL12B、IL1A的远端增强子区域，以及IFNB1的远端与近端增强子区域的核小体均被移除；且增强子的清除过程与多种顺式调控转录因子的结合存在显著相关性。进一步实验表明，对于IFNB1，其核小体移除程度与不同条件下的基因诱导水平呈良好相关性。令人意外的是，IL12B与IL1A的启动子区域在基因诱导后，核小体占有率并未发生显著变化，且任意时刻均有相当比例的细胞中该区域被核小体占据。本研究提出假说：IL12B与IL1A启动子区域的竞争性核小体，可能参与限制单个细胞的转录爆发规模，这或许对调控免疫细胞群体的细胞因子产生具有重要意义。