Margetts Alexander V, Vilca Samara J, Bourgain-Guglielmetti Florence, Tuesta Luis M
Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, Miami, FL 33136.
Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL 33136.
bioRxiv. 2024 Aug 9:2024.08.08.607229. doi: 10.1101/2024.08.08.607229.
Microglia, the innate immune cells in the central nervous system, exhibit distinct transcriptional profiles across brain regions that are important for facilitating their specialized function. There has been recent interest in identifying the epigenetic modifications associated with these distinct transcriptional profiles, as these may improve our understanding of the underlying mechanisms governing the functional specialization of microglia. One obstacle to achieving this goal is the large number of microglia required to obtain a genome-wide profile for a single histone modification. Given the cellular and regional heterogeneity of the brain, this would require pooling many samples which would impede biological applications that are limited by numbers of available animals. To overcome this obstacle, we have adapted a method of chromatin profiling known as Cleavage Under Targets and Tagmentation (CUT&Tag-Direct) to profile histone modifications associated with regional differences in gene expression throughout the brain reward system. Consistent with previous studies, we find that transcriptional profiles of microglia vary by brain region. However, here we report that these regional differences also exhibit transcriptional network signatures specific to each region. Additionally, we find that these region-dependent network signatures are associated with differential deposition of H3K27ac and H3K7me3, and while the H3K27me3 landscape is remarkably stable across brain regions, the H3K27ac landscape is most consistent with the anatomical location of microglia which explain their distinct transcriptional profiles. Altogether, these findings underscore the established role of H3K27me3 in cell fate determination and support the active role of H3K27ac in the dynamic regulation of microglial gene expression. In this study, we report a molecular and computational framework that can be applied to improve our understanding of the role of epigenetic regulation in microglia in both health and disease, using as few as 2,500 cells per histone mark.
小胶质细胞是中枢神经系统中的固有免疫细胞，在不同脑区呈现出不同的转录谱，这对促进其特殊功能至关重要。最近，人们对识别与这些不同转录谱相关的表观遗传修饰产生了兴趣，因为这可能会增进我们对小胶质细胞功能特化潜在机制的理解。实现这一目标的一个障碍是，要获得单个组蛋白修饰的全基因组图谱需要大量的小胶质细胞。鉴于大脑的细胞和区域异质性，这就需要汇集许多样本，而这会阻碍受可用动物数量限制的生物学应用。为了克服这一障碍，我们采用了一种名为“靶向切割与标签化下的切割（直接CUT&Tag）”的染色质分析方法，来分析整个脑奖赏系统中与基因表达区域差异相关的组蛋白修饰。与之前的研究一致，我们发现小胶质细胞的转录谱因脑区而异。然而，我们在此报告，这些区域差异还呈现出每个区域特有的转录网络特征。此外，我们发现这些依赖区域的网络特征与H3K27ac和H3K7me3的差异沉积有关，虽然H3K27me3图谱在不同脑区非常稳定，但H3K27ac图谱与小胶质细胞的解剖位置最为一致，这解释了它们不同的转录谱。总之，这些发现强调了H3K27me3在细胞命运决定中的既定作用，并支持了H3K27ac在小胶质细胞基因表达动态调控中的积极作用。在这项研究中，我们报告了一个分子和计算框架，该框架可用于增进我们对表观遗传调控在健康和疾病状态下小胶质细胞中作用的理解，每个组蛋白标记只需使用少至2500个细胞。
