Hi-C analysis in TNF-alpha-stimulated human umblical vein endothelial cells (HUVECs). Hi-C analysis in TNF-alpha-stimulated human umblical vein endothelial cells (HUVECs)

Lysine 9 di-methylation and lysine 27 tri-methylation of histone H3 (H3K9me2 and H3K27me3) are mostly linked to gene repression. However, functions of repressive histone methylation dynamics during inflammatory responses remain poorly understood. Here, we show that lysine demethylase 7A (KDM7A) and 6A (UTX) are rapidly transported to nuclear factor kappa-B (NF-κB) related elements in human endothelial cells in response to tumor necrosis factor (TNF)-α. KDM7A and UTX demethylate H3K9me2 and H3K27me3, respectively, and cooperatively activate NF-κB dependent inflammatory genes. Furthermore, using both in situ Hi-C and other 3C based technology, loops between super enhancers (SEs) are newly formed following TNF-α-stimuli at NF-κB-dependent inflammatory loci where KDM7A- and UTX-recruitment coincide. Collectively, these findings suggest that erasing of repressive histone marks by KDM7A and UTX within NF-κB-related elements might functionally associate with formation of SE-SE three-dimensional interactions and could be a cue signal during inflammatory responses in human endothelial cells. Overall design: Total 4 Hi-C samples include [1] no treatment (replicate 1 and 2) [2] TNF-alpha 1 hr (replicate 1 and 2).

组蛋白H3的赖氨酸9二甲基化（lysine 9 di-methylation，H3K9me2）与赖氨酸27三甲基化（lysine 27 tri-methylation，H3K27me3）大多与基因阻遏相关。然而，炎性应答过程中阻遏性组蛋白甲基化动态变化的功能仍未被充分阐明。本研究发现，在人内皮细胞中，赖氨酸去甲基化酶7A（lysine demethylase 7A，KDM7A）与赖氨酸去甲基化酶6A（lysine demethylase 6A，UTX）可在肿瘤坏死因子α（tumor necrosis factor-α，TNF-α）刺激下，快速转运至核因子κB（nuclear factor kappa-B，NF-κB）相关调控元件处。KDM7A与UTX可分别催化H3K9me2与H3K27me3的去甲基化，并协同激活NF-κB依赖的炎性基因。进一步通过原位Hi-C（in situ Hi-C）及其他基于3C的染色质构象捕获技术，研究人员观察到，在TNF-α刺激后，KDM7A与UTX共同招募的NF-κB依赖型炎性基因座处，会新形成超级增强子（super enhancers，SEs）之间的染色质环。综上，上述结果表明，KDM7A与UTX通过清除NF-κB相关调控元件处的阻遏性组蛋白修饰，可能与超级增强子间的三维染色质相互作用形成存在功能关联，或是人内皮细胞炎性应答过程中的关键调控信号。

实验设计：共包含4组Hi-C样本，分别为[1] 未处理组（生物学重复1、2）；[2] TNF-α刺激1小时组（生物学重复1、2）。