Weng Shr-Han, Liao Wen-Ling, Chen Linyi
Institute of Molecular Medicine, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan.
Department of Medical Science, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu 300044, Taiwan.
Cells. 2025 Feb 20;14(5):319. doi: 10.3390/cells14050319.
Brain injuries can result from accidents, warfare, sports injuries, or brain diseases. Identifying regeneration-associated genes (RAGs) during epigenome remodeling upon brain injury could have a significant impact on reducing neuronal death and subsequent neurodegeneration for patients with brain injury. We previously identified several WNT genes as RAGs involved in the neurite regrowth of injured cortical neurons. Among them, the expression of the gene increased most significantly during neurite regrowth, indicating its potential to promote neuronal regeneration. In this study, we investigated the regulatory mechanism of transcription. An algorithm was developed to predict the novel enhancer regions of candidate genes. By combining active enhancer marks, histone H3 lysine 27 acetylation (H3K27ac), and histone H3 lysine 4 mono-methylation (H3K4me1), we identified a candidate enhancer region for located 1.7 Mb upstream and 0.1 Mb downstream of the gene. This region was organized into enhancers (Ens) 1-15. Enhancer RNA expression from the predicted En1-15 regions, DNA topological dynamics, and the activity of predicted enhancers were analyzed to validate the candidate active enhancers. Our findings showed that the En8, 9, 10, 14, and 15 regions expressed higher eRNAs during neurite regrowth. Notably, the En8-2 and En14-2 subregions showed significantly up-regulated H3K4me1 modification during neurite regrowth. Using chromatin conformation capture assays and enhancer-reporter assays, we delineated that the molecular regulation of transcription during neurite regrowth occurs through looped En8-promoter interplay.
脑损伤可由事故、战争、运动损伤或脑部疾病引起。在脑损伤后的表观基因组重塑过程中识别再生相关基因（RAGs），可能对减少脑损伤患者的神经元死亡及随后的神经退行性变产生重大影响。我们之前鉴定出几个WNT基因作为参与受损皮质神经元轴突再生的RAGs。其中，该基因的表达在轴突再生过程中增加最为显著，表明其具有促进神经元再生的潜力。在本研究中，我们调查了该基因转录的调控机制。开发了一种算法来预测候选基因的新型增强子区域。通过结合活性增强子标记、组蛋白H3赖氨酸27乙酰化（H3K27ac）和组蛋白H3赖氨酸4单甲基化（H3K4me1），我们在该基因上游1.7 Mb和下游0.1 Mb处鉴定出一个候选增强子区域。该区域被组织成增强子（Ens）1 - 15。分析了预测的En1 - 15区域的增强子RNA表达、DNA拓扑动力学以及预测增强子的活性，以验证候选活性增强子。我们的研究结果表明，在轴突再生过程中，En8、9、10、14和15区域表达更高的eRNAs。值得注意的是，En8 - 2和En14 - 2子区域在轴突再生过程中显示出显著上调的H3K4me1修饰。使用染色质构象捕获分析和增强子 - 报告基因分析，我们描绘了轴突再生过程中该基因转录的分子调控是通过环状的En8 - 启动子相互作用发生的。
