Little is known about the overall patterns of thyroid hormone (Th)-mediated gene regulation by the main Th receptor (Tr) isoforms, Tr-α and Tr-β, in vivo. We used 48 complementary DNA microarrays to examine hepatic gene expression profiles of wildtype and Thra and Thrb knockout mice under different Th conditions: no treatment, treatment with 3,3',5-triiodothyronine (T 3 ), Th-deprivation using propylthiouracil (PTU), and treatment with a combination of PTU and T 3 . Hierarchical clustering analyses showed that positively regulated genes fit into three main expression patterns. In addition, only a subpopulation of target genes repressed basal transcription in the absence of ligand. Interestingly, Thra and Thrb knockout mice showed similar gene expression patterns to wild-type mice, suggesting that these isoforms co-regulate most hepatic target genes. Differences in the gene expression patterns of Thra/Thrb double-knockout mice and Th-deprived wild-type mice show that absence of receptor and of hormone can have different effects. This large-scale study of hormonal regulation reveals the functions of Th and of Tr isoforms in the regulation of gene expression patterns. EMBO reports 4, 581-587 (2003) doi:10.1038/sj.embor.embor862 In the absence of Th, Trs recruit co-repressor complexes (for example, nuclear corepressor (NCoR) and silencing mediator of Tr and retinoic acid receptor (Smrt)) that lead to the histone deacetylation of local chromatin in the promoter region, and decrease the basal transcription of positively regulated target genes (Burke & Baniahmad, 2000). In the presence of Th, Trs recruit co-activator complexes that contain the p160 steroidreceptor co-activator (SRC) family members and other cofactors that have histone acetyltransferase activity, as well as other complexes that can associate with the RNA polymerase II complex (Yen, 2001;Zhang & Lazar, 2000). The overall effect of these ligand-dependent interactions is to promote the transcriptional activation of positively regulated target genes. Trs also negatively regulate target genes, but the molecular mechanism by which they do this is poorly understood (Yen, 2001).Recent studies have shown that Thra and Thrb knockout mice have different phenotypes, and have also suggested that different Tr isoforms may have distinct roles (Flamant & Samarut, 2003;Forrest & Vennstrom, 2000). Two groups have generated Thra knockout mice that have distinct phenotypes (Flamant & Samarut, 2003;Forrest & Vennstrom, 2000). This was due to the targeting of different loci for homologous recombination, which resulted in the loss of different combinations of Tr-α isoforms. Thra knockout mice that lack all Tr-α isoforms (Thra 0/0 ), including short Tr-α isoforms that are generated by internal transcription initiation, are viable and fertile, and have a mild phenotype (Gauthier et al., 2001;Macchia et al., 2001).