Genes involved in cell adhesion and signaling: A new repertoire of Retinoic Acid Receptors target genes in mouse embryonic fibroblasts

Abstract

Nuclear retinoic acid (RA) receptors (RARα, β and γ) are ligand dependent transcription factors that regulate the expression of a battery of genes involved in cell differentiation and proliferation. They are also phosphoproteins and we evidenced the importance of their phosphorylation in their transcriptional activity. Here we conducted a genome-wide analysis of the genes that are regulated by RARs, in mouse embryonic fibroblasts (MEFs), by comparing MEFs WT to MEFs knockout for the three RARs. We found that in the absence of RA, RARs control the expression of several gene transcripts associated to cell adhesion. Consequently the knockout MEFs have lost their ability to adhere and to spread on substrates and display a disrupted network of actin filaments, compared to the WT cells. In contrast, in the presence of ligand, RARs control the expression of other genes involved in signaling and in RA metabolism. Then taking advantage of rescue cell lines expressing the RARα or RARγ subtypes (either WT or mutated at the N-terminal phosphorylation sites) in the null background, we found that the expression of RA-target genes can be controlled either by a specific single RAR or by a combination of RAR isotypes, depending on the gene. We also selected genes, which require the phosphorylation of the receptors for their regulation by RA. Our results increase the repertoire of genes that are regulated by RARs and highlight the complexity and diversity of the transcriptional programs regulated by RARs, depending on the gene.