Proliferating microglia integrate regulation of a core set of cell cycle genes with broader, context-dependent transcriptional programs

We report on the epigenomic and transcriptional programs associated with microglial proliferation in the brain. Gene expression profiles and genomic regulatory elements activity were determined on a genome-wide level. Data indicated that while the overall transcriptional out of proliferating microglia is context-dependent, a core signature of cell cycle genes accompanies proliferation across conditions. Furthermore, expression of these may be coordinated by one of two modes of regulation. A first mode augments expression of genes already expressed in quiescent microglia and is subject to regulation by Klf/Sp, Nfy, and Ets transcription factors. Alternatively, a second mode enables de novo gene transcription and requires additional regulatory input from Lin54 and E2f factors. Proliferating microglia were isolated from various contexts, and their H3K27ac (ChIP-seq) and gene expression (RNA-seq) profiles were compared. Additional analyses with H3K4me3 (ChIP-seq), RNA polymerase II subunit B (ChIP-seq) and ATAC-seq were also performed to characterize the underlying regulatory mechanisms at the chromatin level.本研究报道了与大脑中小胶质细胞增殖相关的表观基因组学与转录组学调控程序。研究在全基因组层面完成了基因表达谱与基因组调控元件活性的测定。数据表明，尽管增殖中小胶质细胞的整体转录输出具有情境依赖性，但在所有实验条件下，细胞周期基因的核心特征均伴随增殖过程出现。此外，这些基因的表达可通过两种调控模式之一实现协同调控：第一种模式可增强静息态小胶质细胞中已表达基因的转录水平，并受Klf/Sp、Nfy及Ets转录因子的调控；与之相对，第二种模式可介导全新的基因转录，并需要Lin54与E2f因子提供额外的调控输入。研究从多种实验情境中分离得到增殖中小胶质细胞，并对其H3K27ac（染色质免疫共沉淀测序，ChIP-seq）与基因表达（RNA测序，RNA-seq）谱进行了对比分析。此外还开展了H3K4me3（ChIP-seq）、RNA聚合酶II亚基B（ChIP-seq）以及转座酶可及性测序（ATAC-seq）的相关分析，以在染色质层面解析其潜在的调控机制。