Genome-wide profiles of chromatin interaction in mouse nephron progenitor cells [HiC]

During embryonic kidney development, nephron progenitor cells (NPCs) self-renew and differentiate into all cells in mature nephrons. The Wnt signaling components Wnt9b and ß-catenin are required for both NPC self-renewal and differentiation. A low level of Wnt/ß-catenin are associated with NPC self-renewal while a high level with differentiation. To investigate the transcriptional mechanisms behind Wnt/ß-catenin-driven regulation of NPCs states, we modeled NPC self-renewal and differentiation in vitro with NPEM (Brown et al., 2015) supplemented with low (1.25 µM) or high (5 µM) concentration of CHIR22091 (CHIR), a small molecule GSK3ß inhibitor that stabilizes ß-catenin. To investigate change of higher-order chromatin structure of NPC under influence of CHIR treatment, here we generated HiC data from primary NPC, as well as NPC cultured in low and high CHIR concentration. Overall design: HiC was performed in primary NPCs, as well as NPCs cultured in low (1.25 µM) CHIR and high (5 µM) CHIR conditions.