Genomic Organization and Regulation of Gene Expression in the Distal Convoluted Tubule

Background: The distal convoluted tubule regulates blood pressure, K+ balance and Mg2+ homeostasis. The complex regulation of DCT-specific ion channels, metabolic activity and hormonal signaling pathways depends on DNA accessibility, polymerase binding and transcription factor activity. Here, we aimed to determine DCT-specific transcriptional regulation by integration of RNA-seq, ATAC-seq, chromosome confirmation capture and histone-modification ChIP-seq datasets. Methods: We generated a comprehensive atlas of transcriptional regulation in a mouse DCT cell line by generating and integrating chromatin accessibility (ATAC-seq), gene expression (RNA-seq) and histone mark ChIP-seq datasets (H3K4me3, H3K27ac). Moreover, we generated a chromosome conformation capture (Hi-C) map to unravel 3D genomic interactions. Results: ATAC sequencing demonstrated 14,231 open chromatin regions in the mouse DCT cells. Fifty percent of these regions contained promoter elements and twenty percent active enhancer regions, characterized by H3K4me3 and H3K27ac respectively. GO-term analysis of these regulatory regions demonstrated enrichment of epithelial pathways, such as cilia development, cell junctions and cytoskeleton organization. Hi-C uncovered the basis of 3D genome characteristics in the DCT. As example of how our map of DCT genome organization can be used, we studied the importance of long-range chromatin interactions in transcriptional regulation mediated by transcription factor HNF1β. Our analysis revealed that promoter bound HNF1β primarily controls the expression of genes with general cell functions, such as mRNA processing and protein transport. In contrast, HNF1β binding to enhancer regions at large distance of the promoter was associated with expression of HNF1β-specific processes, such as kidney and urogenital development. Conclusion: In conclusion, we describe the first comprehensive map of genome organization in a DCT cell line and demonstrate that the 3D architecture of the genome controls specificity of HNF1β-mediated gene transcription.