Laboratory of Molecular Neurobiology, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland.
Laboratory of Bioinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland.
Glia. 2019 Dec;67(12):2312-2328. doi: 10.1002/glia.23686. Epub 2019 Jul 24.
Microglia are brain-resident, myeloid cells that play important roles in health and brain pathologies. Herein, we report a comprehensive, replicated, false discovery rate-controlled dataset of DNase-hypersensitive (DHS) open chromatin regions for rat microglia. We compared the open chromatin landscapes in untreated primary microglial cultures and cultures stimulated for 6 hr with either glioma-conditioned medium (GCM) or lipopolysaccharide (LPS). Glioma-secreted factors induce proinvasive and immunosuppressive activation of microglia, and these cells then promote tumor growth. The open chromatin landscape of the rat microglia consisted of 126,640 reproducible DHS regions, among which 2,303 and 12,357 showed a significant change in openness following stimulation with GCM or LPS, respectively. Active genes exhibited constitutively open promoters, but there was no direct dependence between the aggregated openness of DHS regions near a gene and its expression. Individual regions mapped to the same gene often presented different patterns of openness changes. GCM-regulated DHS regions were more frequent in areas away from gene bodies, while LPS-regulated regions were more frequent in introns. GCM and LPS differentially affected the openness of regions mapped to immune checkpoint genes. The two treatments differentially affected the aggregated openness of regions mapped to genes in the Toll-like receptor signaling and axon guidance pathways, suggesting that the molecular machinery used by migrating microglia is similar to that of growing axons and that modulation of these pathways is instrumental in the induction of proinvasive polarization of microglia by glioma. Our dataset of open chromatin regions paves the way for studies of gene regulation in rat microglia.
小胶质细胞是驻留于脑内的髓系细胞，在健康和脑病理中发挥重要作用。在此，我们报告了大鼠小胶质细胞的一套全面、可复制、经错误发现率校正的 DNA 酶超敏（DHS）开放染色质区域数据集。我们比较了未经处理的原代小胶质细胞培养物和用胶质瘤条件培养基（GCM）或脂多糖（LPS）刺激 6 小时的培养物中的开放染色质景观。胶质瘤分泌的因子诱导小胶质细胞的促侵袭和免疫抑制激活，这些细胞随后促进肿瘤生长。大鼠小胶质细胞的开放染色质景观由 126640 个可重复的 DHS 区域组成，其中 2303 个和 12357 个在分别用 GCM 或 LPS 刺激后，开放性发生显著变化。活性基因表现出组成性开放的启动子，但基因附近 DHS 区域的聚集开放性与其表达之间没有直接的依赖关系。映射到同一基因的单个区域通常呈现出不同的开放性变化模式。GCM 调节的 DHS 区域更频繁地出现在远离基因体的区域，而 LPS 调节的区域更频繁地出现在内含子中。GCM 和 LPS 对映射到免疫检查点基因的 DHS 区域的开放性有不同的影响。两种处理方式对映射到 Toll 样受体信号和轴突导向途径的基因的 DHS 区域的聚集开放性有不同的影响，这表明迁移的小胶质细胞使用的分子机制与生长轴突相似，并且这些途径的调节对于诱导小胶质细胞的促侵袭极化是至关重要的。我们的开放染色质区域数据集为大鼠小胶质细胞的基因调控研究铺平了道路。
