Thyroid hormone (T 3 ) activates nuclear receptor transcription factors, encoded by the TR␣ (NR1A1) and TR (NR1A2) genes, to regulate target gene expression. Several TR isoforms exist, and studies of null mice have identified some unique functions for individual TR variants, although considerable redundancy occurs, raising questions about the specificity of T 3 action. Thus, it is not known how diverse T 3 actions are regulated in target tissues that express multiple receptor variants. I have identified two novel TR isoforms that are expressed widely and result from alternative mRNA splicing. TR3 is a 44.6-kDa protein that contains an unique 23-amino-acid N terminus and acts as a functional receptor. TR⌬3 is a 32.8-kDa protein that lacks a DNA binding domain but retains ligand binding activity and is a potent dominant-negative antagonist. The relative concentrations of 3 and ⌬3 mRNAs vary between tissues and with changes in thyroid status, indicating that alternative splicing is tissue specific and T 3 regulated. These data provide novel insights into the mechanisms of T 3 action and define a new level of specificity that may regulate thyroid status in tissue.The actions of thyroid hormone, 3,5,3Ј-L-triiodothyronine (T 3 ), are mediated by ligand-inducible transcription factors that are members of the steroid/thyroid hormone receptor superfamily. Two T 3 receptor (TR) genes, TR␣ (NR1A1) and TR(NR1A2), are conserved in vertebrates (32, 43), while two TR␣ and two TR genes have arisen by gene duplication in Xenopus laevis (65). TR␣ encodes three C-terminal variants in mammals: ␣1 (NR1A1a) binds T 3 and DNA and is a functional receptor, whereas ␣2 (NR1A1b) and ␣3 (NR1A1c) do not bind T 3 and are weak dominant negative antagonists in vitro, although their roles in vivo are unclear (33,40,50,57). Recent studies have described a promoter in intron 7 of TR␣, which generates two truncated variants, ⌬␣1 and ⌬␣2, that are repressors in vitro but are of unknown physiological significance (9). In contrast, TR encodes two N-terminal variants, 1 (NR1A2a) and 2 (NR1A2b), which are transcribed from separate promoters (24,28,42,61). The 1 N terminus is encoded by two exons that are replaced by a single exon in 2. These exons are alternatively spliced to six common exons that encode the DNA binding, ligand binding, and dimerization domains of the receptor (32). This arrangement is conserved in vertebrates, and the invariant splice site between the divergent N termini and the first of the common exons is known as the changing point (65). The changing point is retained in both Xenopus TR genes, although additional splicing in the 5Ј untranslated region (5Ј-UTR) results in many transcripts that are temporo-spatially restricted during development (51, 64). TR0 is expressed in chicken; it contains only 2 amino acids proximal to the changing point and is similar to a short TR in Xenopus, although a mammalian homologue has not been identified (18,52,65). T 3 -regulated development in chicken also involves temporospatially...