Effects of PAX8 loss on chromatin modifications [ChIP-Seq]

PAX2 and PAX8 are homologous DNA-binding proteins that orchestrate kidney development, regulate urine concentration in the kidney medulla, and contribute to sensitivity to and recovery from acute kidney injury. In some contexts, Pax proteins can recruit KMT2C/D histone methyl-transferase complexes that deposit histone H3K4 methylation marks to promote transcription or recruit the Polycomb Repressor Complex to silence gene expression. However, the spectrum of targets and functions of Pax proteins in kidney physiology remains poorly defined. This project aimed to identify genes regulated by PAX proteins in the proximal tubule. Proximal tubule epithelial cells were derived from mice with floxed Pax2 and Pax8 alleles and expressing a constitutive tamoxifen-response CreERT2 (mice described in PMID: 32381599). During propagation, Pax2 was spontaneously recombined, yielding a Pax2-null, Pax8-conditional cell line which was named PT-22. In the experiments in this submission, PAX8 was depleted from PT-22 cells with tamoxifen and Pax8 chromatin occupancy and histone marks (H3K4me3 and H3K27me3) were measured after 6 d using chromatin immunoprecipitation followed by sequencing (ChIP-seq).