The specificity of interactions between nuclear hormone receptors and corepressors is mediated by distinct amino acid sequences within the interacting domains

The thyroid hormone receptor (TR) and retinoic acid receptor (RAR) isoforms interact with the nuclear corepressors [NCoR (nuclear corepressor protein) and SMRT (silencing mediator for retinoid and thyroid hormone receptors)] in the absence of ligand to silence transcription. NCoR and SMRT contain C- terminal nuclear hormone receptor (NHR) interacting domains that each conta in variations of the consensus sequence I/L-x-x-I/V-I (CoRNR box). We have previously demonstrated that TR beta1 preferentially interacts with NCoR, w hereas RAR alpha prefers SMRT. Here, we demonstrate that this is due, in pa rt, to the presence of a novel NCoR interacting domain, termed N3, upstream of the previously described domains. An analogous domain is not present in SMRT. This domain is specific for TR and interacts poorly with RAR. Our da ta suggest that the presence of two corepressor interacting domains are nec essary for full interactions with nuclear receptors in cells, Interestingly , mutation of N3 alone specifically decreases binding of NCoR to TR in cell s but does not decrease NCoR-RAR interactions. In addition, while the exact CoRNR box sequence of a SMRT interacting domain is critical for recruitmen t of SMRT by RAR, the CoRNR box sequences themselves do not explain the str ong interaction of the N2 domain with TR beta1. Additional regions distal t o the CoRNR box sequence are needed for optimal binding. Thus, through sequ ence differences in known interacting domains and the presence of a newly i dentified interacting domain, NCoR is able to preferentially bind TR beta1. These preferences are likely to be important in corepressor action in vivo .