Open chromatin landscape of rat microglia upon inflammatory or pro-invasive polarization

Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. While data on chromatin accessibility in activated murine microglia are available, there is no such data on rat microglia subjected to different stimuli. Herein, we report a comprehensive, replicated, FDR-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for the rat microglia. We compared open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6h with either lipopolysaccharide (LPS) or glioma-conditioned medium (GCM). Glioma-secreted factors induce the pro-invasive and immunosuppressive activation of microglia, in which these cells promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, of which 12,357 and 2,303 significantly changed openness following the stimulation with LPS and GCM, respectively. Active genes had constitutively open promoters, but there was no direct dependence between cumulative openness of DHS regions near to a gene and its expression. LPS-regulated DHS regions were more frequent in introns, while GCM-regulated regions were more frequent away from gene bodies. GCM and LPS treatment differentially affected open chromatin regions mapped to genes in the pathways of Toll-like-receptor signaling and the Axon guidance, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and, moreover, that modulation of these pathways is instrumental for glioma to induce a pro-invasive polarization of microglia. Our dataset of open chromatin regions active in rat microglia will constitute a useful resource for studies of the transcriptional regulation in this system.小胶质细胞（Microglia）是脑内驻留的髓系细胞，在机体健康与脑部病理进程中发挥关键调控作用。目前已有激活状态小鼠小胶质细胞的染色质可及性相关数据，但针对不同刺激条件下大鼠小胶质细胞的同类数据集仍属空白。本研究公开了一套经过重复验证、错误发现率（False Discovery Rate, FDR）校正的大鼠小胶质细胞DNase超敏位点（DNase-hypersensitive, DHS）开放染色质区域综合数据集。我们对比了未处理的原代小胶质细胞培养物，以及分别经脂多糖（lipopolysaccharide, LPS）或胶质瘤条件培养基（glioma-conditioned medium, GCM）刺激6小时的培养物的开放染色质景观。胶质瘤分泌的因子可诱导小胶质细胞向促侵袭、免疫抑制表型活化，活化后的小胶质细胞会促进肿瘤生长。大鼠小胶质细胞的开放染色质景观共包含126,640个可重复的DHS区域，其中分别有12,357个和2,303个区域在经LPS或GCM刺激后，其开放程度发生显著改变。活跃基因的启动子呈组成型开放状态，但基因邻近区域DHS的累积开放程度与该基因的表达水平之间不存在直接关联。受LPS调控的DHS区域更多富集于内含子区域，而受GCM调控的DHS区域则更多分布于基因本体之外的序列区间。GCM与LPS处理分别对映射到Toll样受体信号通路（Toll-like-receptor signaling）及轴突导向（Axon guidance）通路相关基因的开放染色质区域产生差异化调控影响，这提示迁移中的小胶质细胞所依赖的分子机制与生长中的轴突高度相似；进一步而言，对这些通路的调控是胶质瘤诱导小胶质细胞向促侵袭表型极化的核心环节。本研究生成的大鼠小胶质细胞活性开放染色质区域数据集，将为该体系的转录调控研究提供极具价值的参考资源。