The orientation and spacing of core DNA-binding motifs dictate selective transcriptional responses to three nuclear receptors

Characterization of several thyroid hormone (T 3), retlnolc acid, and estrogen response elements has led to the identification of conserved DNA half-sites (core binding motifs). We present evidence that differences in both the relative orientation and spacing of these motifs within hormone response elements determine the distinct transcriptional responses of three members of the nuclear receptor superfamily. When separated by 3 bp, direct repeat, palindromic, and inverted palindromic arrangements of these motifs impart selective transcriptional responses to retinoic acid, estrogen, and T 3 receptors, respectively. Varying the spacing between core motifs alters the specificity. Without spacing, a direct repeat of the core motif paradoxically configures the T 3 receptor to confer transactivation in the absence of T 3 and repression in its presence. Such an element occurs naturally in the mouse β-thyrotropin promoter, physiologically under negative regulation by T 3. The orientation and spacing of core binding motifs may thus function in concert as a code that accounts for the selective patterns of transcriptional responses of hormonally regulated promoters.