ReviewNuclear retinoid receptors and the transcription of retinoid-target genes
Introduction
Vitamin A and its active derivatives referred to as retinoids are non-steroid hormones which play a critical role in the development and homeostasis of virtually every vertebrate tissues through their regulatory effects on cell differentiation, proliferation and apoptosis Ross et al., 2000, Altucci and Gronemeyer, 2001a. It has long been established that retinoids exert their action by regulating the expression of specific subsets of genes within target tissues. However, it is only during the last 15 years that the understanding for retinoids action rapidly increased, subsequently to the cloning of nuclear retinoid receptors and the identification, within the promoters of retinoid-responsive genes, of elements exhibiting a high affinity for these receptors (for review, see Chambon, 1996, Laudet and Gronemeyer, 2001, and references therein). Then these nuclear receptors have been shown to work as ligand-activated transcription activators in a spatiotemporal specific manner during embryonic development.
During the last decade, the molecular rationale for retinoid receptors action has been facilitated by the identification of the DNA- and ligand-binding domains (DBD and LBD, respectively) (Chambon, 1996), and by the determination of their crystal structure (Renaud and Moras, 2000). Moreover, a number of studies demonstrated that they have to contend with repressive chromatin structures in order to activate gene expression. Indeed, as most target genes are initially silent and packed in a dense chromatin structure, liganded retinoid receptors recruit a battery of intermediary proteins, including coactivators, chromatin remodellers and modifyers which act in a coordinated and/or combinatorial manner to decompact chromatin and direct RNA polymerase II (RNA Pol II) and the general transcription factors (GTFs) to the promoter (Dilworth and Chambon, 2001).
Then an important question was what happens after the retinoid-activated receptors have bound their DNA reponse elements and recruited the transcription machinery. Now, there is increasing evidence that the ubiquitin–proteasome machinery degrades the retinoid receptors subsequently to their activation Zhu et al., 1999, Boudjelal et al., 2000, Kopf et al., 2000, Gianni et al., 2002a. This degradation process may either disrupt the transcription initiation complex, allowing elongation to proceed, and/or terminate the response to retinoids in order to allow rapidly other transcriptional programs.
Finally, the last years have witnessed a new way of regulation of retinoid receptors. Indeed, ongoing studies revealed that they can integrate multiple signaling pathways through their phosphorylation (Rochette-Egly, 2003). Alternatively, retinoids cross-talk with a number of signaling pathways. All these processes converge towards finely tuned transcriptional control.
This review will describe our current knowledge about the molecular mechanisms through which retinoid receptors regulate transcription, ranging from DNA binding, dynamics of ligand binding and chromatin remodeling and finally to their degradation. It will also focus on how sequential and/or coordinated phosphorylation events regulate their functionality.
Section snippets
Retinoid receptors contain a DNA-binding domain and two activation functions AF-1 and AF-2
The retinoid signal is transduced by two families of nuclear receptors, the retinoic acid receptors (RARs) and the retinoid X receptors (RXRs), which work as RXR/RAR heterodimers Kastner et al., 1997, Mark et al., 1999. Each family consists of three isotypes (α, β and γ) encoded by separate genes Leid et al., 1992, Mangelsdorf and Evans, 1995, Chambon, 1996. RARs are activated by all-trans retinoic acid (RA) and its 9-cis isomer, while RXRs are only activated by 9-cis RA. For each isotype,
First step: retinoid receptors binding to responsive elements located in the regulatory sequences of target genes
In the absence of ligand, retinoid receptors are found primarily in the nucleus. They bind as asymetric, oriented RAR/RXR heterodimers to specific DNA sequences or RA response elements (RAREs) composed typically of two direct repeats of a core hexameric motif, PuG(G/T)TCA Leid et al., 1992, Mangelsdorf and Evans, 1995 (Fig. 4A). The classical RARE is a 5-bp-spaced direct repeat (referred to as DR5). However, RAR/RXR heterodimers also bind to direct repeats separated by 1 bp (DR1) or 2 bp (DR2).
Second step: ligand binding, coactivators recruitment and chromatin decompaction
When genes are silent, DNA is packaged into a highly organized and compact nucleoprotein structure known as chromatin which impedes all the transcription steps. The basic unit of chromatin is the nucleosome which consists of DNA wrapped around a protein core containing two copies each of four histone proteins. Protruding from the nucleosomes are the N-terminal «tails» of the core histones whose interaction with DNA can be modulated upon covalent modifications (acetylation, phosphorylation,
Third step: recruitment of the transcriptional machinery
Once repressive chromatin has been decondensed, it has been proposed that a coregulators exchange occurs, in order to allow the RARE-bound heterodimers to participate in the entry of RNA-Pol II and GTFs into the preinitiation complex Chen et al., 1999b, Malik and Roeder, 2000. The current working hypothesis is that the p160 coactivators dissociate, subsequent to their acetylation which decreases their ability to interact with the receptors (Chen et al., 1999b), or to their degradation by the
Control of RAR/RXR transactivation by the ubiquitin–proteasome system
In recent years, it has become evident that the transcriptional activity of retinoid receptors, as that of most transcription factors, is also regulated by the ubiquitin–proteasome pathway. Paradoxically, both the proteolytic and non-proteolytic activities of this system appear to modulate transcription at different levels Ferdous et al., 2001, Salghetti et al., 2001, Tansey, 2001, Conaway et al., 2002, Muratani and Tansey, 2003.
One main role of the ubiquitin–proteasome system is to degrade
Regulation of RAR/RXR-mediated transcription through phosphorylation
RARs and RXRs are substrates for a multitude of kinases (see Fig. 1, Fig. 6) (Rochette-Egly, 2003). Importantly, subsequent to their interaction with TFIIH, RARs (RARα and RARγ) are phosphorylated in their N-terminal A/B region by the cdk7 subunit of TFIIH which has a cyclin-dependent kinase activity Rochette-Egly et al., 1997, Bastien et al., 2000. This phosphorylation process which has been extensively studied, especially in the case of RARα, plays a critical role in the retinoid response.
Retinoid receptors cross-talk with other signaling pathways
Due to the ability of RXRs to serve as heterodimeric partners not only to RARs, but also to several other nuclear receptors (PPARs, LXR) (Willy and Mangelsdorf, 1999), it is evident that retinoids can also control, the transcription of a wider set of hormone-responsive genes Leid et al., 1992, Mangelsdorf and Evans, 1995, Chambon, 1996. Moreover, one has to consider that, as is true for many other genes, the promoters of retinoid-target genes contain, in addition to the cognate response
Conclusion and perspectives
Retinoids are essential for the control of normal cell differentiation and proliferation. Therefore they are morphogens and essential regulators of embryogenesis. In adults, they are required for the proper functioning of a number of organs. All these functions involve the transcriptional control of a large number of genes by RXR/RAR heterodimers, as gene-ablation experiments generate embryonic development defects and abrogate the differentiative and antiproliferative effects of RA.
According to
Acknowledgements
We are particularly grateful to Gaetan Bour and Emilie Gaillard for enthusiastic discussions and for critics. Many thanks also to all the past members of the group for their contribution to the work. We are also very grateful to Prof. P. Chambon for constant support. Our studies mentioned in the text have been supported by funds from the Centre National de la Recherche Scientifique (CNRS), the Institut National de la Santé et de la Recherche Médicale (INSERM), the Hôpital Universitaire de
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