title: Retinoid X receptor alpha binds with the highest affinity to an imperfect direct repeat response element.
abstract: The regulation of gene expression by retinoids is mediated by two classes of receptors, retinoic acid receptors and retinoid X receptors (RXR). RXR can bind to specific target genes as homodimers, and these homodimers can activate gene expression in the presence of the ligand 9-cis-retinoic acid. A direct repeat of AGGTCA with a 1 base pair spacer (DR1) acts as a RXR homodimer response element in the presence of 9-cis-retinoic acid. However, it is not known if this represents the highest affinity binding site for the RXR homodimer. To investigate this question, we used a nonbiased strategy to isolate from a pool of random DNA those sequences that have the highest affinity for RXR alpha homodimers. The imperfect DR1 sequence 5'-GGGGTCAAAGGTCA displayed the highest in vitro binding affinity for RXR alpha homodimers. Transient transfection studies confirmed that this sequence is a more potent response element than is a perfect DR1 of either AGGTCA or GGGGTCA. The results also indicate that for RXR alpha homodimers, the receptor bound to the 5' half-site dislays different DNA binding specificity than that bound to the 3' half-site. Thus, DNA binding specificity is determined not only by the amino acid sequence of the protein but also by its protein-protein interactions and its position on the response element (5' vs. 3').
authors.affiliation: Division of Endocrinology and Metabolism, University of Michigan Medical Center, Ann Arbor 48109-0678, USA.
authors.forename: Y Z
authors.initials: YZ
authors.lastname: Yang
authors.forename: J S
authors.initials: JS
authors.lastname: Subauste
authors.forename: R J
authors.initials: RJ
authors.lastname: Koenig
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D001667:Binding, Competitive; D002460:Cell Line; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D004926:Escherichia coli; D015870:Gene Expression; D006147:Guanine / Q000378:metabolism; D046911:Macromolecular Substances; D008745:Methylation; D051379:Mice; D008969:Molecular Sequence Data; D016296:Mutagenesis; D018168:Receptors, Retinoic Acid / Q000378:metabolism*; D011994:Recombinant Proteins / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D047488:Retinoid X Receptors; D014157:Transcription Factors / Q000378:metabolism*; D014162:Transfection
chemical_list: D046911:Macromolecular Substances; D018168:Receptors, Retinoic Acid; D011994:Recombinant Proteins; D047488:Retinoid X Receptors; D014157:Transcription Factors; D006147:Guanine; D004247:DNA