Thyroid hormone receptor-induced bending of specific DNA sequences is modified by an accessory factor

Transcriptional regulation by thyroid and steroid hormone receptors requires their recognition and binding of specific DNA sequences. However, little is known about the mechanisms whereby DNA bound receptors regulate transcription. In the present study, we examined the effects of thyroid hormone receptor (TR) binding on DNA conformation using various TR recognition sites contained within sets of circularly permuted flanking sequences. We show that under conditions where TR binds predominantly as monomer, the conformation of a number of binding sites is changed in a manner consistent with receptor induced bending. Despite similar affinities for receptor binding, not all binding sites tested showed evidence for receptor-induced bending. Notably, the conformation of a sequence from the frog vitellogenin 2 gene, which confers a positive transcriptional response when bound by estrogen receptor (ER), but a negative response when bound by TR, appeared to be unaffected by binding of either TR or ER. The observations suggest that the ability of the receptor to alter DNA architecture is strongly dependent on sequence characteristics other than those required for receptor binding. While both partly purified TR from rat liver and TR translated in vitro were able to induce DNA bending, the bend centers and bend angles produced by these different sources of receptor differed. However, addition of a receptor-depleted fraction from the rat liver TR preparation to in vitro translated receptor stimulated TR binding and appeared to form heterodimers with TR. This resulted in changes in both bend centers and bend angles to resemble more closely those produced by native receptor. Together, these results suggest that receptor-induced DNA bending may be specific to TRs and that the position and degree of bending is further modulated by the formation of heterodimers between TRs and accessory protein(s).