Thyroid hormone (T3) exerts a pleiotropic action on vertebrate development and homeostasis mainly by acting on two nuclear receptors: TRa1 and TRß1. The receptors are transcription factors of the nuclear hormone superfamily that exert a broad control on gene expression. TRa1 and TRß1 structures and functions have been extensively studied both in vitro and in vivo, leading to the following results. Although T3 stimulates energy metabolism in most cell types, each cell responds to T3 in a very different manner with the regulation of a different set of target genes. Moreover TRa1 and TRß1 germline mutations in mice have very different consequences even though in vitro studies indicate little functional or structural divergences between the two isoforms. If the different phenotypes of TRa and TRß KO mice result for a large part from the specific expression pattern of each receptor, many evidences recently arose that in cells that express both isoforms TRa1 and TRß1 would also possess non-overlapping repertoires of target genes. This strongly suggests that TRa1 and TRß1 are likely to fulfill different functions in a given cell. To date the molecular bases responsible for both cell- and TR isoform- specifity of T3 response remain elusive. In this program we propose to tackle these two important aspects of T3 differential action: between two cell types and for the two TR in a given cell type. To assess the extent of cell and TR isoform specificity of T3 response we will combine transcriptome and metabolome analyses in three cell types (neurons, hepatocytes and adipocytes) expressing different combinations of endogenous TR isoforms and for which we have extensive expertise. Comparison of these systems should address the impact of the cell environment (in the presence of one given isoform) or the TR isoform expressed (in a given cell environment) on T3 response. This response will be evalatued ex vivo, to avoid potential paracrine effects, by analyzing both transcriptomic and metabolomic data. Transcriptoms will also be determined in vivo, in mice harboring mutation of TRa1 or TRß1 limited to the cell type of interest, to take into account indirect T3 action in these cell types under physiological conditions. To address the molecular mechanisms underlying these specificities we will check for specific TRa1 and TRß1 binding to chromatin at the genome wide scale occupancy for, and search for some cofactors that would interact with TR in an isoform- or cell- specific manner. Finally we will map the T3 response elements in promoters maintained in a chromatin environment, to more precisely analyze the molecular mechanisms responsible for the restriction of T3 response (cell or TR isoform) of some of the genes identified to be cell and/or TR isoform selectively regulated. By using an ambitious combination of in vitro and in vivo approaches, we aim to clarify the complex and poorly documented mechanisms underlying T3 diversity of functions at a molecular level. This study will also bring valuable information about the functional divergence of TRa1 and TRß1 in terms of physiology and development that will be very useful to evaluate the potential of future isoform selective T3 mimetics in therapy.