title: Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome.
abstract: Completion of the Rattus norvegicus genome sequence enabled a global inventory and analysis of the nuclear receptors (NRs) in three mammalian species. Forty-nine NR members were found in mouse, 48 in human. Forty-seven were found in the rat, with gaps at the locations expected for the other two. Pairwise comparisons of their distribution in rat, mouse, and human identified 11 syntenic NR gene blocks, including three small clusters of two or three closely related genes, each spanning 40 kb to 1700 kb. The exon structure of the ligand-binding domain suggests that exon shuffling has played a role in the evolution of this family. An invariant splice junction in all members of the NR family except LXRbeta suggests a functional role for the intron. The ligand-binding domains of PXR and CAR are among the most divergent in the family. Their higher nucleotide substitution rates may be related to the central role played by these two NRs in the metabolism of the foreign compounds and may have resulted from limited positive selection.
authors.affiliation: Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA.
authors.forename: Zhengdong
authors.initials: Z
authors.lastname: Zhang
authors.forename: Paula E
authors.initials: PE
authors.lastname: Burch
authors.forename: Austin J
authors.initials: AJ
authors.lastname: Cooney
authors.forename: Rainer B
authors.initials: RB
authors.lastname: Lanz
authors.forename: Fred A
authors.initials: FA
authors.lastname: Pereira
authors.forename: Jiaqian
authors.initials: J
authors.lastname: Wu
authors.forename: Richard A
authors.initials: RA
authors.lastname: Gibbs
authors.forename: George
authors.initials: G
authors.lastname: Weinstock
authors.forename: David A
authors.initials: DA
authors.lastname: Wheeler
mesh_terms: D000595:Amino Acid Sequence / Q000235:genetics; D000818:Animals; D002874:Chromosome Mapping; D004247:DNA / Q000378:metabolism; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D016678:Genome; D015894:Genome, Human; D006801:Humans; D008024:Ligands; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D020836:Protein Structure, Quaternary / Q000235:genetics / Q000502:physiology; D017434:Protein Structure, Tertiary / Q000235:genetics / Q000502:physiology; D051381:Rats; D011944:Receptors, Androgen / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D018160:Receptors, Cytoplasmic and Nuclear / Q000737:chemistry* / Q000235:genetics / Q000502:physiology*; D011960:Receptors, Estrogen / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D011965:Receptors, Glucocorticoid / Q000737:chemistry / Q000235:genetics / Q000502:physiology; D011980:Receptors, Progesterone / Q000737:chemistry / Q000235:genetics / Q000502:physiology
chemical_list: D008024:Ligands; D011944:Receptors, Androgen; D018160:Receptors, Cytoplasmic and Nuclear; D011960:Receptors, Estrogen; D011965:Receptors, Glucocorticoid; D011980:Receptors, Progesterone; D004247:DNA