The Long-Range Chromosomal Interaction Controlling Klotho Gene Expression in Human Chronic Kidney Disease

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.