Nuclear hormone receptors comprise a large family of zinc finger transcription factors, some with hydrophobic ligands, such as thyroid hormone, vitamin D, steroids, etc., and others for which no ligand has been found. Thyroid hormone receptors (TRs) generally are considered to be confined to the vertebrata that possess a thyroid gland. Tunicates represent the most primitive of the chordates, and there are data supporting a role for thyroid hormone in their metamorphosis, but no data are available on TRs in this genus; hence, we have studied Ciona intestinalis. Screening of a Ciona library with the DNA binding domain of Xenopus laevis TR (xTR) resulted in the isolation of a nuclear hormone receptor, C. intestinalis nuclear receptor 1 (CiNR1). CiNR1 is similar to TRs of more evolved species with a conserved DNA binding domain whereas the ligand binding domain shows poor homology to vertebrate sequences. The C-terminal part of CiNR1 spans Ϸ200 amino acids more than other TRs, lacks the AF2 transactivation domain, and is not able to bind triiodothyronine. Phylogenetically, CiNR1 appears to be close to the common ancestral gene of TRs. Expression of CiNR1 was limited to the developing embryo and the larval stage, which suggests a role during development and metamorphosis. In transfection experiments, CiNR1 down-regulated basal transcription of a reporter gene driven by the TR palindrome responsive element. When CiNR1 was cotransfected with chicken TR␣, it attenuated the normal thyroid hormone response in a dominant negative fashion. This attenuation required the C-terminal portion of the molecule.Nuclear receptors are zinc finger transcription factors that regulate gene expression by binding to specific cis-acting sequences in the promoter region (1-3) and include receptors for several hydrophobic ligands, such as steroids, retinoic acid, thyroid hormone, vitamin D, ecdysone, as well as a variety of receptors, called orphans, without a known ligand (4). To date, Ͼ150 different members of this superfamily, spanning a large diversity of species from nematode to human, have been described (5).From the evolutionary point of view, all nuclear receptors can be grouped into six subfamilies: (i) a large one containing thyroid receptors (TRs), retinoic acid receptors (RARs), vitamin D receptors, ecdysone receptors, and numerous orphan receptors; (ii) one clustering retinoid X receptors, COUP, HNF4, and other orphan receptors; (iii) one containing steroid hormone receptors; (iv) one the NGFB group of orphan receptors; (v) one containing FTZ-F1 orphan receptors; and (vi) the last one containing only the GCNF1 orphan receptor (6). Although the TR͞RAR and steroid receptor subfamilies are well characterized in vertebrates, little is known about their presence in lower species. Orphan receptors are found in most primitive animals, many of which have homologues or closely related genes in vertebrates (4). The common modular structure of nuclear receptors, their genomic organization, and their conservation in the respective d...