Derangement of a Factor Upstream of RARα Triggers the Repression of a Pleiotropic Epigenetic Network

Background: Chromatin adapts and responds to extrinsic and intrinsic cues. We hypothesize that inheritable aberrant chromatin states in cancer and aging are caused by genetic/environmental factors. In previous studies we demonstrated that either genetic mutations, or loss, of retinoic acid receptor alpha (RAR alpha), can impair the integration of the retinoic acid (RA) signal at the chromatin of RA-responsive genes downstream of RAR alpha, and can lead to aberrant repressive chromatin states marked by epigenetic modifications. In this study we tested whether the mere interference with the availability of RA signal at RAR alpha, in cells with an otherwise functional RAR alpha, can also induce epigenetic repression at RA-responsive genes downstream of RAR alpha. Methodology/Principal Findings: To hamper the availability of RA at RAR alpha in untransformed human mammary epithelial cells, we targeted the cellular RA-binding protein 2 (CRABP2), which transports RA from the cytoplasm onto the nuclear RARs. Stable ectopic expression of a CRABP2 mutant unable to enter the nucleus, as well as stable knock down of endogenous CRABP2, led to the coordinated transcriptional repression of a few RA-responsive genes downstream of RAR alpha. The chromatin at these genes acquired an exacerbated repressed state, or state "of no return''. This aberrant state is unresponsive to RA, and therefore differs from the physiologically repressed, yet "poised'' state, which is responsive to RA. Consistent with development of homozygosis for epigenetically repressed loci, a significant proportion of cells with a defective CRABP2-mediated RA transport developed heritable phenotypes indicative of loss of function. Conclusion/Significance: Derangement/lack of a critical factor necessary for RARa function induces epigenetic repression of a RA-regulated gene network downstream of RARa, with major pleiotropic biological outcomes.