Nucleotide substitutions differentially affect direct repeat and palindromic thyroid hormone response elements.

Thyroid hormone receptors are transcription factors that bind to specific DNA sequences and regulate gene expression in a ligand-dependent manner. Thyroid hormone response elements can be composed of direct repeat or palindromic arrangements of half-sites. The traditional half-site has been considered to be the sequence 5'-AGGTCA, although we recently demonstrated that the optimal monomer-binding site is 2 base pairs larger, 5'-TAAGGTCA. It has generally been presumed that alterations in half-site sequence have commensurate effects on gene expression from direct repeat and palindromic response elements. However, in the present studies we demonstrate that palindromic elements are highly dependent on the presence of the two 5'-nucleotides (TA) for function, whereas this portion of the response element has minimal influence on hormone induction from direct repeat elements. Hormone induction correlates poorly with binding affinity for thyroid hormone receptor monomers, homodimers, or heterodimers with retinoid X receptors, either in the absence or presence of ligands. We speculate that the magnitude of hormone induction may reflect protein conformation differences induced by a combination of the presence of the appropriate 5'-nucleotides plus half-site orientation.