Retinoic acid receptor-mediated gene repression, from molecular basis to physiological significance – ARREPRESS

We recently discovered an unforeseen mode of interaction between retinoic acid receptors and transcriptional corepressors, which fully accounts for their constitutive interaction and retinoic acid-induced dissociation. This information allowed us to design retinoic acid receptor mutants that specifically lack their interaction with corepressors without affecting their activation function. In ARREPRESS, these mutations will be transposed in vivo, through the generation of cell lines and mouse models which will constitute invaluable tools to perform genome-wide analyses of genes repressed by retinoic acid receptors through ChIP-Seq and RNA-Seq methods and to test the physiological and pathological importance of retinoic acid receptor-mediated gene repression.

Results show that the repression function exerted by the a subtype of RAR is not necessary for prenatal development, but essential for the proper functioning of Sertoli cells. They also show that the repression function of transcription relayed by the ? subtype of RAR in the absence of ligand is not essential for development and postnatal life. The interaction sites of the corepressor SMRT in the absence of ligand and of the cofactor Nrip1 in the presence of retinoic acid in promoters of RAR target genes were identified, as well as the associated epigenetic modifications of chromatin.

The strength and originality of the ARREPRESS project reside in the synergism that will emerge from the association we propose between molecular and cellular biology, and functional genomics. This profitable partnership will allow us to correlate a specific molecular mechanism in vitro with its physiological or development outcome in vivo.
This work would represent a major leap in retinoic acid receptor pharmacogenomics by providing significant advances in the understanding of molecular mechanisms underlying retinoic acid receptor signaling, and would open up new concepts and windows of possibilities for novel therapeutic opportunities.

1. Chatagnon A, et al. (2015). RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements. Nucleic Acids Res. 43(10):4833-54
2. Gely-Pernot A, et al. (2015). Retinoic acid receptors control spermatogonia cell-fate and induce expression of the SALL4A transcription factor. PLoS Genet. 11(10):e1005501
3. Mark M, et al. (2015). Role of retinoic acid receptor (RAR) signalling in post-natal male germ cell differentiation. Biochim. Biophys. Acta 1849(2):84-93
4. Nadendla E, et al. (2015). An unexpected mode of binding defines BMS948 as a full retinoic acid receptor ß (RARß, NR1B2) selective agonist. PLoS One. 10(5):e0123195
5. Teletin M, et al. (2017). Roles of Retinoic Acid in Germ Cell Differentiation. Curr Top Dev Biol. 125:191-225

The retinoic acid receptors (RARs), which include three paralogs (RARA, RARB, and RARG) mediate both organismal and cellular effects of retinoids and regulate a wide variety of essential biological processes, as well as their disorders. RARs are ligand-modulated transcription factors belonging to the nuclear hormone receptor (NHR) superfamily that act by targeting chromatin-modifying complexes and transcription machineries to cognate genetic loci. Even though multiple mechanisms are gradually being elucidated that modulate the complex retinoid signaling pathways and their cross-reactions, several crucial points remain elusive. Notably, the contribution, composition, dynamics and ligand/drug modularity of the multiple signalosomes that are involved remain largely unknown.
The gene regulatory capacity of a few NHRs comprises both activation and repression of target gene transcription. These abilities allow RARs to control gene networks critical for metazoan homeostasis, development and reproduction. Gene silencing occurs via recruitment to unliganded DNA-bound receptors of NCOR1 or NCOR2 corepressor-containing complexes, whereas gene activation involves hormone-induced corepressor release and recruitment of coactivators. Structural studies and investigation of genetic models of NHR coactivators have revealed determinants of the RAR/coactivator interaction and critical roles for RAR-dependent transcriptional activation. In contrast, the molecular basis of RAR/corepressor interaction and the physiological/pathological impact of RAR-mediated gene repression are much less defined. Moreover, although agonist binding to RARs is mostly associated with recruitment of coactivators, recent studies have shown that agonist binding can also result in corepressor binding. Then, although our view of the role of transcriptional corepressors in asserting proper gene expression outcomes has considerably evolved over the past decade, knowledge, and perhaps appreciation, of the crucial role of gene repression still lags behind that of gene activation. In this context, the aims of ARREPRESS are to uncover the mechanistic aspects of the transcriptional repression mediated by RARs, and to provide molecular tools to probe the importance of RAR-mediated repression in physiological, developmental and pathological processes. In this context, the ARREPRESS project is aimed at elucidating the molecular mechanisms underlying the repressor function of unliganded-RARs (Aim #1); understanding the role of ligand-bound RAR induced repression (Aim #2) and evaluating the physiological significance of unliganded-RAR/corepressor-mediated gene repression through the generation of genetically modified cell or animal models (Aim #3).
We recently discovered an unforeseen mode of interaction between RARs and corepressors, which fully accounts for their constitutive interaction and agonist-induced dissociation (le Maire et al., 2010). This information allowed us to design RAR mutants that specifically lack their interaction with corepressors without affecting their activation function. In ARREPRESS, these mutations will be transposed in vivo, through the generation of cell lines and mouse models which will constitute invaluable tools to perform genome-wide analyses (ChIP-seq, RNA-seq, and GRO-seq) of genes repressed by RARs and to test the physiological and pathological importance of RAR-mediated gene repression. The strength and originality of the ARREPRESS project reside in the synergism that will emerge from the association we propose between molecular and cellular biology, and functional genomics. This profitable partnership will allow us to correlate a specific molecular mechanism in vitro with its physiological or development outcome in vivo.