Half-site spacing and orientation determines whether thyroid hormone and retinoic acid receptors and related factors bind to DNA response elements as monomers, homodimers, or heterodimers.

Abstract

The receptors for thyroid hormone (T3R) and retinoic acid (RAR) are members of a nuclear receptor subfamily that are capable of recognizing similar DNA sequences. Native response elements for T3R and RAR consist of two or more putative half-site binding motifs organized as imperfect direct or inverted repeats separated by different sized nucleotide gaps. To clarify how T3R, RAR, and related factors recognize DNA response elements, we analyzed the interaction of purified receptors with a series of inverted and direct repeats of an idealized AGGTCA half-site separated by different sized nucleotide gaps. Our results indicate that RAR and T3R can bind to half-sites as monomers and, depending on the orientation and distance between half-sites, also bind as homodimers or T3R-RAR heterodimers. T3R also binds to certain DNA elements as a heterodimer with one or more nuclear factors from eucaryotic cells. Thus, the orientation and spacing of half-sites play a central role in determining which configuration of receptors and nuclear factors will interact with a specific DNA element. This along with the ability of these factors to participate in reversible protein-protein interactions serve to broaden and diversify the responses mediated by T3R, RAR, and related members of this nuclear receptor subfamily.

Thyroid hormone action in metabolic regulation

“…The half sites can be arranged as an everted repeat (as in the chicken lysozyme gene), as a direct repeat (as in the malic enzyme gene) or as an inverted repeat (palindrome, as in the growth hormone gene) with 4 bps between the two half sites (DR4) (Forman et al, 1992;Cheng, 2000). To be noted, direct repeats are the most popular arrangement of TRE half sites.…”

DNA Recognition by Normal and Oncogenic Thyroid Hormone Receptors

“…Most receptors bind to DNA as protein dimers, with each receptor molecule binding to a "half-site," a conserved 6 -8-nucleotide DNA sequence (7)(8)(9)(10)(11). Recognition of the sequence of each half-site has generally been believed to be mediated exclusively by a zinc-finger motif within the center of each receptor ( Fig.…”

Multiple mutations contribute to repression by the v-Erb A oncoprotein

“…The DNA binding domain (DBD), hormone binding domain (HBD), I-box, helices 1-3 (H1-3), and helix 12 regions are indicated for c-Erb A. Retroviral gag sequences, N-and C-terminal deletions, and amino-acid substitutions (asterisks) within the v-Erb A sequence are also shown and are numbered based on the c-Erb A sequence. The locations of the sites used for constructing the various chimeras are indicated by vertical dotted lines; chimera proteins are named based on the origin of swapped fragments (right and bottom of the panel) other members of the nuclear receptor family, such as the retinoid X receptors (RXRs) (Lazar et al, 1991;Forman et al, 1992;Glass, 1994). It has been reported that gag-v-Erb A is impaired in its ability to form heterodimers with RXR compared to c-Erb A (Forman et al, 1989;Selmi and Samuels, 1991;Yen et al, 1994;Wahlstrom et al, 1996;Bauer et al, 1997;Shen and Subauste, 2000;Yoh and Privalsky, 2001;Zubkova and Subauste, 2003).…”

“…A third mode of DNA recognition by c-Erb A is the ability to bind to suitable response elements as a protein monomer (Lazar et al, 1991;Forman et al, 1992;Darling et al, 1993;Glass, 1994;Katz and Koenig, 1994;Koenig, 1995, 1998;Wahlstrom et al, 1996;Subauste, 2002, 2003). These c-Erb A monomers can be observed on DNA elements containing a single half-site, or as part of a mixed population of monomers, homodimers, and heterodimers on response elements containing two or more halfsites.…”

“…The v-Erb A I-box sequence also contributes to stabilizing receptor homodimer complexes against disruption by T3 Although c-Erb A homodimers assemble with high affinity on many DNA elements in the absence of hormone, these c-Erb A homodimers typically dissociate in the presence of T3, whereas RXR/c-Erb A heterodimers are stable to T3 (Lazar et al, 1991;Forman et al, 1992;Ribeiro et al, 1992;Yen et al, 1992Yen et al, , 1994Miyamoto et al, 1993;Piedrafita et al, 1995;Yoh and Privalsky, 2001). This T3-driven dissociation of homodimers may, in fact, function to drive an exchange of the c-Erb A/c-Erb A homodimers implicated in transcriptional repression for the RXR/c-Erb A heterodimers involved in transcriptional activation.…”