Thyroid Hormone Action in Liver: A Coregulator Shift Rather Than the Canonical Switch

Abstract Thyroid hormone receptors (TR) are transcription factors that mediate the effects of thyroid hormones (TH) in development, physiology, and metabolism. TR canonically activates gene expression via a “switch” whereby TH converts chromatin-bound TR from a transcriptional repressor to an activator. In this model, the unliganded repressed state is mediated by binding of the nuclear receptor corepressor (NCoR), while the TH-activated state is caused by dismissal of NCoR and stabilization of binding of coactivators including CREB-binding protein (CBP). TH also negatively regulates gene expression, although the mechanism is controversial. Elucidation of the TR transcriptional mechanism in vivo has been hampered by the low concentration of endogenous TRs and the unavailability of high quality antibodies. To address this, we generated a mouse line in which endogenous TRβ1 was epitope-tagged to allow precise analysis at physiological levels, and explored TR function in liver where the actions of TR regulate body weight, cholesterol, and liver fat. ChIP-seq analysis revealed TRβ binding at genomic sites with epigenomic characteristics of enhancers, at sequences enriched for the canonical DR4 motif bound by TR with its RXR partner, at both positively- as well as negatively-regulated genes. The NCoR/HDAC3 corepressor complex was reduced but not completely dismissed by TH at positive enhancers and, surprisingly, at enhancers associated with negatively. CBP binding was also not “all or none” but, rather, shifted toward increased binding at enhancers in their active state, i.e., in the presence of TH for activated genes, but in the absence of TH for repressed genes. Thus, TH action is due to a shift, not an on/off switch, in coregulator association with TRβ-regulated enhancers determines their activity and transcriptional outcomes.