Homodimer and heterodimer DNA binding and transcriptional responsiveness to triiodothyronine (T3) and 9-cis-retinoic acid are determined by the number and order of high affinity half-sites in a T3 response element.

T3 (triiodothyronine) response elements (TREs) consist of pairs of strong and weak (S and W), 10-nucleotide T3 receptor (TR) monomer binding sites (half-sites). We report that the number and order of S and W half-sites in a direct repeat TRE determines whether it mediates ligand-dependent or independent transcriptional activation or inhibition in the presence of TR or TR and 9-cis-retinoic acid receptor (RXR); and whether a TRE is preferentially bound by TR homodimers, TR-RXR heterodimers, or CV1 cell TR accessory protein (TRAP)-TR heterodimers. TR homodimers bound equally to TREs composed of the 5'-S and 3'-W (SW) and the opposite (WS) arrangement of half-sites. TR-RXR gamma heterodimers bound SW better than WS. TR-TRAP heterodimers bound WS better than SW. Transcription of a reporter gene cis-linked to WS responded to unliganded TR and RXR, and either ligand stimulated expression 2-fold more. Reporter expression cis-linked to SW was not altered by unliganded receptors, and T3 stimulated transcription only in the presence of both TR and RXR. SS was strongly activated by liganded, but not by unliganded TR. SS was activated by unliganded TR and RXR gamma together, and T3 further stimulated transcription 2-fold. Under these conditions, transcription was inhibited 60% by 9-cis-retinoic acid.