In all vertebrates, thyroid hormones (TH) affect postembryonic development. The role of the TH receptor (TR) in mediating the TH signal is complex as evidenced by divergent phenotypes in mice lacking TH compared with TR knock-out mice. We have proposed a dual function model for TR during development based on studies of frog metamorphosis. Here we examined an important assumption of this dual function model by using the chromatin immunoprecipitation assay, namely constitutive TR binding to promoters in vivo. We examined two target genes with TH-response elements (TRE) in their promoters, TR itself and TH/bZIP (TH-responsive basic leucine zipper transcription factor). By using an antibody that recognizes both TR␣ and TR, we found that TR binding to the TR promoter is indeed constitutive. Most surprisingly, TR binding to the TH/bZIP promoter increases dramatically after TH treatment of premetamorphic tadpoles and during metamorphosis. By using an antibody specific to TR, TR binding increases at both promoters in response to TH. In vitro biochemical studies showed that TRs bind TH/bZIP TRE with 4-fold lower affinity than to TR TRE. Our data show that only high affinity TR TRE is occupied by limiting levels of TR during premetamorphosis and that lower affinity TH/bZIP TRE becomes occupied only when overall the TR expression is higher during metamorphosis. These data provide the first in vivo evidence to suggest that one mechanism for tissue-and genespecific regulation of TR target gene expression is through tissue and developmental stage-dependent regulation of TR levels, likely a critical mechanism for coordinating development in different organs during postembryonic development.All vertebrates have two types of thyroid hormone receptors (TRs), 2 TR␣ and TR, that regulate gene expression by binding thyroid hormone (TH)-response elements (TREs) of TH-inducible genes and recruiting cofactors (1). In the absence of TH, TRs recruit corepressors, including N-CoR, SMRT, TBL1/TBLR1, HDAC3, and GPS2 (2-7). Corepressor binding is associated with deacetylated histones in the TRE region and gene repression. In the presence of TH, coactivators, such as SRC, p300, TRAP, and Mediator complexes, replace corepressors (8 -11). Coactivator binding promotes transcription by acetylating histones and interacting with the basal transcriptional machinery.The above knowledge based on in vitro studies complements extensive studies on the developmental role of TRs in frogs and TR knock-out mice. TR is important for postembryonic development of many organs (12). The destruction of larval organs and the formation of adult organs during frog metamorphosis is totally dependent upon TH (13,14). Transgenic overexpression of mutant TRs and cofactors showed gene activation by TR is necessary and sufficient to initiate TH-dependent developmental transitions in frogs (15, 16). In knock-out mice lacking TRs, developmental defects are evident in brain, heart, and intestine, among other organs (17). Similar observations on the importance of TR in...