PAX8 controls proximal tubule epithelial identity and stress response through epigenetic modification of distal regulatory elements.

The kidney proximal tubule undergoes dramatic cell-state transformations during recovery from injury, serving as a unique model to study the dynamic transcriptional regulation of cell identity. The DNA-binding transcription factor paired box-8 (PAX8) contributes to proximal tubule development and recovery from injury. Here we report a mouse proximal-tubule-derived Pax2-null, Pax8-conditional cell line that enables assessment of the genome-wide effect of PAX8 on transcription and cellular function. PAX8-depleted cells lose the differentiated proximal tubule phenotype. Re-expression of Pax8 rescues the epithelial phenotype and restores expression of genes lost following PAX8 depletion. This model recapitulates the expression patterns and stress-resistance of PAX8-deficient proximal tubule cells in vivo, justifying its use to study the molecular mechanisms of PAX8 function. Across the genome, the changes in transcription caused by PAX8 loss are linked with PAX8-bound distal regulatory elements, where PAX8 can either activate or repress transcription. Among PAX8-activated genes, expression is tightly linked to PAX8-dependent H3K4me1 and H3K27ac at distal regulatory elements. In contrast, PAX8-repressed genes showed little change in these marks. These results indicate that PAX8 regulates enhancer histone marks dynamically and reversibly across the genome to control proximal-tubule-specific gene expression patterns.