Nuclear receptors (NRs) are major targets for drug discovery and have key roles in development and homeostasis as well as in many diseases such as obesity, diabetes, and cancer. NRs are ligand-dependent transcription factors that need to work in concert with so-called transcriptional coregulators, including corepressors and coactivators, to regulate transcription. Upon ligand binding, NRs undergo a conformational change, which alters their binding preference for coregulators. Short ␣-helical sequences in the coregulator proteins, LXXLL (in coactivators) or LXXXIXXXL (in corepressors), are essential for the NR-coregulator interactions. However, little is known on how specificity is dictated. To obtain a comprehensive overview of NR-coregulator interactions, we used a microarray approach based on interactions between NRs and peptides derived from known coregulators. Using the peroxisome proliferator-activated receptor ␥ (PPAR␥) as a model NR, we were able to generate ligand-specific interaction profiles (agonist rosiglitazone versus antagonist GW9662 versus selective PPAR␥ modulator telmisartan) and characterize NR mutants and isotypes (PPAR␣, -/␦, and -␥). Importantly, based on the NR-coregulator interaction profile, we were able to identify TRIP3 as a novel regulator of PPAR␥-mediated adipocyte differentiation. These findings indicate that NR-coregulator interaction profiling may be a useful tool for drug development and biological discovery. Molecular & Cellular Proteomics 8:2212-2226, 2009.
Nuclear receptors (NRs)1 are ligand-inducible transcription factors involved in development and homeostasis that play key roles in many diseases, including diabetes, cancer, and obesity (1). NRs consist of several functional domains, which exhibit varying degrees of conservation among members of the receptor family. The poorly conserved N terminus contains the activation function 1 (AF-1) domain, the activity of which is often regulated by post-translational modifications. Centrally located is the DNA binding domain, which is highly conserved among species and between nuclear receptors. The ligand binding domain (LBD), which is also relatively well conserved in terms of primary amino acid sequence, mediates ligand binding, and contains the powerful ligand-dependent activation function (AF-2). LBD crystal structures have revealed a canonical fold consisting of 13 ␣-helices and a small four-stranded -sheet (2). Upon ligand binding, the AF-2 helix (also referred to as helix 12) is stabilized in an active state (3). Depending on the conformation of the LBD and its modulation by ligand, NRs can recruit or release transcriptional coregulator proteins that perform all of the subsequent reactions needed to induce or repress transcription of target genes (4). Coregulators are often components of large multiprotein complexes that act in a sequential and/or combinatorial fashion to modify chromatin and to recruit basal transcription factors and RNA polymerase II (5). In general, the transcriptional coregulator family consists of coa...