Retinoic Acid Receptors Recognize the Mouse Genome through Binding Elements with Diverse Spacing and Topology

• Published in: The Journal of biological chemistry 2012-07, Vol.287 (31), p.26328-26341
• Main Authors: Moutier, Emmanuel, Ye, Tao, Choukrallah, Mohamed-Amin, Urban, Sylvia, Osz, Judit, Chatagnon, Amandine, Delacroix, Laurence, Langer, Diana, Rochel, Natacha, Moras, Dino, Benoit, Gerard, Davidson, Irwin
• Format: Article
• Language: English
• Subjects: Animals; Base Sequence; Binding Sites; Binding, Competitive; Biochemistry, biophysics & molecular biology; Biochemistry, Molecular Biology; Biochimie, biophysique & biologie moléculaire; Cells, Cultured; Chromatin Immunoprecipitation; Coculture Techniques; Consensus Sequence; DNA binding; DNA-binding Protein; Electrophoretic Mobility Shift Assay; Embryoid Bodies - metabolism; Gene Regulation; Genome; Isothermal Titration Calorimetry; Life Sciences; Mice; Molecular biology; Nuclear Receptors; Protein Binding; Receptors, Retinoic Acid - chemistry; Receptors, Retinoic Acid - metabolism; Repetitive Sequences, Nucleic Acid; Response Elements; retinoic acid receptors; Retinoid X Receptors - chemistry; Retinoid X Receptors - metabolism; Sciences du vivant; Sequence Analysis, DNA; Titrimetry; Transcription; Transcription, Genetic; transcriptional activation; Vitamin D
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1074/jbc.M112.361790

Background: Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) to regulate gene expression. Results: This heterodimer recognizes the genome via a large and diverse repertoire of direct and inverted repeat DNA elements. Conclusion: The observed diversity of binding elements changes the paradigm of how RAR-RXR recognizes the genome. Significance: Half-site spacing in the DNA binding element allosterically regulates RAR function. Retinoic acid receptors (RARs) heterodimerize with retinoid X receptors (RXRs) and bind to RA response elements (RAREs) in the regulatory regions of their target genes. Although previous studies on limited sets of RA-regulated genes have defined canonical RAREs as direct repeats of the consensus RGKTCA separated by 1, 2, or 5 nucleotides (DR1, DR2, DR5), we show that in mouse embryoid bodies or F9 embryonal carcinoma cells, RARs occupy a large repertoire of sites with DR0, DR8, and IR0 (inverted repeat 0) elements. Recombinant RAR-RXR binds these non-canonical spacings in vitro with comparable affinities to DR2 and DR5. Most DR8 elements comprise three half-sites with DR2 and DR0 spacings. This specific half-site organization constitutes a previously unrecognized but frequent signature of RAR binding elements. In functional assays, DR8 and IR0 elements act as independent RAREs, whereas DR0 does not. Our results reveal an unexpected diversity in the spacing and topology of binding elements for the RAR-RXR heterodimer. The differential ability of RAR-RXR bound to DR0 compared to DR2, DR5, and DR8 to mediate RA-dependent transcriptional activation indicates that half-site spacing allosterically regulates RAR function.