Identification and characterization of retinoic acid-responsive genes in mouse kidney development

Retinoic acid (RA) signaling regulates a variety of developmental processes through controlling the expression of numerous genes. Here, we have identified and characterized RA-responsive genes in mouse kidney development. Analysis of isolated embryonic kidneys cultured in the presence and absence of RA identified 33 candidates of RA-responsive genes. Most of these candidate genes were down-regulated by treatment with the RA receptor antagonist. Many of them have potential binding sites for Elf5, one of the RA-responsive genes, in their promoter region. Whole-mount in situ hybridization demonstrated that specific expression of Elf5 in the ureteric trunk depends on RA. RA-dependent expression in the ureteric trunk was also demonstrated for the sodium channel subunit Scnn1b, which has been shown to be the marker gene of the collecting duct. In contrast, the expression of Ecm1, Tnfsf13b and IL-33 was detected in the stromal mesenchymal cells. Both Tnfsf13b and IL-33 were previously shown to cause NF-κB activation. We have demonstrated that the inhibition of NF-κB signaling with specific inhibitors suppresses branching morphogenesis of the ureteric bud. Our study thus identifies and characterizes RA-dependent upregulated genes in kidney development, and suggests an involvement of NF-κB signaling in the branching morphogenesis. To obtain genome-wide gene expression profiles of kidneys cultured in 10% FBS DMEM, serum-free DMEM, and serum-free DMEM with RA, we performed microarray analysis on RNA prepared from these three samples. Total RNA was prepared using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instruction. Synthesis of cDNA, in vitro transcription and biotin labeling cRNA, and hybridization to GeneChip Mouse Gene 1.0 ST array (Affymetrix) were performed according to Affymetrix protocols.