Epigenomic, cistromic, and transcriptomic profiling of primary kidney tubular cells

Spatiotemporal regulation of gene expression is essential for maintaining cellular homeostasis throughout kidney development and disease progression. Transcription factors (TFs) and epigenetic modifications play pivotal roles in controlling gene expression. Profiling chromatin modifications across the genome, along with the distribution and target regulation by TFs in specific kidney cell types, is crucial for understanding the dynamic changes in gene expression. Here, we presented a comprehensive workflow for epigenomic, cistromic, and transcriptomic analyses of primary kidney tubular cells. Specifically, our methodologies included the isolation of primary kidney tubular epithelial cells, RNA extraction, assay for transposase-accessible chromatin using sequencing, ultra-low-input micrococcal nuclease-based native chromatin immunoprecipitation, cleavage under targets and release using nuclease, and subsequent bioinformatic analysis. This protocol provides a methodological framework for investigating the roles of TFs and epigenetic modifications in kidney development and diseases.