Multiple mechanisms regulate H3 acetylation of enhancers in response to thyroid hormone.

Hormone-dependent activation of enhancers includes histone hyperacetylation and mediator recruitment. Histone hyperacetylation is mostly explained by a bimodal switch model, where histone deacetylases (HDACs) disassociate from chromatin, and histone acetyl transferases (HATs) are recruited. This model builds on decades of research on steroid receptor regulation of transcription. Yet, the general concept of the bimodal switch model has not been rigorously tested genome wide. We have used a genomics approach to study enhancer hyperacetylation by the thyroid hormone receptor (TR), described to operate as a bimodal switch. H3 acetylation, HAT and HDAC ChIP-seq analyses of livers from hypo- and hyperthyroid wildtype, TR deficient and NCOR1 disrupted mice reveal three types of thyroid hormone (T3)-regulated enhancers. One subset of enhancers is bound by HDAC3-NCOR in the absence of hormone and constitutively occupy TR and HATs irrespective of T3 levels, suggesting a poised enhancer state in absence of hormone. In presence of T3, HDAC3-NCOR1 dissociates from these enhancers leading to histone hyperacetylation, suggesting a histone acetylation rheostat function of HDACs at poised enhancers. Another subset of enhancers, not occupied by HDACs, is hyperacetylated in a T3-dependent manner, where TR is recruited to chromatin together with HATs. Lastly, a subset of enhancers, is not occupied directly by TR yet require TR for histone hyperacetylation. This indirect enhancer activation involves co-association with TR bound enhancers within super-enhancers or topological associated domains. Collectively, this demonstrates various mechanisms controlling hormone-dependent transcription and adds significant details to the otherwise simple bimodal switch model. Author summary Thyroid hormone (T3) is a central regulator of growth, thermogenesis, heart rate and metabolism. In the liver T3 binds thyroid hormone receptor beta (TR beta) controlling expression of genes involved in processes such as lipid and cholesterol metabolism. The molecular mechanisms controlling TR-dependent gene regulation are centred on a bimodal switch model. In the absence of T3 co-repressors bind TR reducing gene expression. When hormone binds TR, co-repressors dissociate, and co-activators are recruited inducing gene expression. This model predominates the current understanding of T3-regulated gene expression. However, only a few studies have tested this model by genome-wide approaches. We have quantified Histone3 acetylation genome-wide in the liver of hypo- and hyperthyroid mice and identified gene regulatory regions regulated by T3. Probing TR and co-regulators at these regulatory regions, and analysing Histone3 acetylation in mouse models for disrupted co-repressor and TR activity, reveal additional insights to the mechanisms regulating T3-dependent gene expression. We suggest a revision of the prevailing bimodal switch model which helps understanding T3-regulated gene expression in tissues such as liver. We hope that this study, together with future studies, will add new perspectives on nuclear receptor-mediated transcriptional regulation to reveal general principles.