The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 [RNA-Seq]. Homo sapiens

The inflammatory gene response requires activation of the protein kinase TAK1, but it is currently unknown how TAK1-derived signals coordinate transcriptional programs in the genome. We determined the genome-wide binding of the TAK1-controlled NF-κB subunit p65 in relation to active enhancers and promoters of transcribed genes by ChIP-seq experiments. Out of 35,000 active enhancer regions, 410 H3K4me1-positive enhancers show interleukin (IL)-1-induced H3K27ac and p65 binding. Inhibition of TAK1, IKK2 or depletion of p65 blocked inducible enhancer activation and gene expression. As exemplified by the CXC chemokine cluster located on chromosome 4, the TAK1-p65 pathway also regulates the recruitment kinetics of the histone acetyltransferase CBP, of NF-κB p50 and of AP-1 transcription factors to both, promoters and enhancers. This study provides a high resolution view of epigenetic changes occurring during the IL-1 response and allows the first genome-wide identification of a novel class of inducible p65 NF-κB-dependent enhancers in epithelial cells. Overall design: RNA-seq of KB cells either untreated or treated with IL-1 alpha

炎症基因应答需要蛋白激酶TAK1的激活，但目前尚不清楚TAK1介导的信号如何协调基因组中的转录程序。我们通过染色质免疫沉淀测序（ChIP-seq）实验，解析了TAK1调控的核因子κB（NF-κB）亚基p65在活跃转录基因的活性增强子与启动子区域的全基因组结合特征。在35000个活性增强子区域中，共有410个H3K4me1阳性增强子呈现出白细胞介素（IL）-1诱导的H3K27乙酰化修饰与p65结合事件。抑制TAK1、IκB激酶2（IKK2）或敲低p65均可阻断诱导型增强子的激活及基因表达。以位于4号染色体的CXC趋化因子簇为例，TAK1-p65通路还可调控组蛋白乙酰转移酶CBP、核因子κB p50以及激活蛋白1（AP-1）转录因子在启动子与增强子区域的招募动力学。本研究清晰呈现了IL-1应答过程中发生的表观遗传变化的高分辨率图景，并首次实现了上皮细胞中一类新型的、依赖核因子κB p65的诱导型增强子的全基因组鉴定。实验整体设计：对未处理或经IL-1α处理的KB细胞进行RNA测序（RNA-seq）。