Xu Pengwei, Jiang Minjun, Chen Jianchun, Zhou Yongqiang, Wang Zhenfan
Department of Urology, Suzhou Ninth Hospital affiliated to Soochow University, Suzhou 215000, China.
ACS Omega. 2024 Dec 19;9(52):51264-51270. doi: 10.1021/acsomega.4c07967. eCollection 2024 Dec 31.
Cis-regulatory elements bridge enhancers and gene promoters to control gene expression via distal DNA interaction and three-dimensional chromosomal conformation organization. The aberrant changes of cis-acting regulatory systems as one type of the epigenetic regulative ways may be connected with human genetic diseases. Klotho, as an antiaging protein, is selectively expressed in kidney tissues and plays a crucial role in preventing chronic kidney disease (CKD) and renal fibrosis. However, the underlying transcription regulatory mechanism of Klotho in CKD is not fully understood. Herein, we analyzed the spatial organization of the chromatin region spanning 2 Mb upstream Klotho in human renal punctured CKD tissues using chromosome conformation capture (3C)-qPCR and identified the distal interaction of the Klotho promoter with certain specific chromatin regions characterized as the regulatory elements. Moreover, we determined that four DNase I hypersensitive sites (DHSs) involved in the regulation of Klotho gene expression lost their activities in CKD tissues compared to control accompanied by the reduction of H3K27ac. Finally, the CCCTC-binding factor (CTCF) sites were validated on the DHSs beyond the Klotho promoter by chromatin looping formation through the recruitment of CTCF.
顺式调控元件通过远距离DNA相互作用和三维染色体构象组织连接增强子和基因启动子，从而控制基因表达。作为一种表观遗传调控方式，顺式作用调控系统的异常变化可能与人类遗传疾病有关。Klotho作为一种抗衰老蛋白，在肾脏组织中选择性表达，在预防慢性肾脏病（CKD）和肾纤维化中起关键作用。然而，Klotho在CKD中的潜在转录调控机制尚未完全阐明。在此，我们使用染色体构象捕获（3C）-qPCR分析了人类肾穿刺CKD组织中跨越Klotho上游2 Mb的染色质区域的空间组织，并确定了Klotho启动子与某些特定染色质区域的远距离相互作用，这些区域被表征为调控元件。此外，我们确定与对照相比，参与Klotho基因表达调控的四个DNase I超敏位点（DHSs）在CKD组织中丧失了活性，同时伴随着H3K27ac的减少。最后，通过招募CTCF形成染色质环，在Klotho启动子以外的DHSs上验证了CCCTC结合因子（CTCF）位点。
