Genomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome.

TitleGenomic analysis of the nuclear receptor family: new insights into structure, regulation, and evolution from the rat genome.
Publication TypeJournal Article
Year of Publication2004
AuthorsZhang, Z, Burch, PE, Cooney, AJ, Lanz, RB, Pereira, FA, Wu, J, Gibbs, RA, Weinstock, G, Wheeler, DA
JournalGenome Res
Volume14
Issue4
Pagination580-90
Date Published2004 Apr
ISSN1088-9051
KeywordsAmino Acid Sequence, Animals, Chromosome Mapping, DNA, Evolution, Molecular, Exons, Genome, Genome, Human, Humans, Ligands, Mice, Molecular Sequence Data, Phylogeny, Protein Structure, Quaternary, Protein Structure, Tertiary, Rats, Receptors, Androgen, Receptors, Cytoplasmic and Nuclear, Receptors, Estrogen, Receptors, Glucocorticoid, Receptors, Progesterone
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.

DOI10.1101/gr.2160004
Alternate JournalGenome Res.
PubMed ID15059999
PubMed Central IDPMC383302
Grant ListU19DK62434-01 / DK / NIDDK NIH HHS / United States
R01 DC004585 / DC / NIDCD NIH HHS / United States
5-U54 HG02345 / HG / NHGRI NIH HHS / United States
U19 DK062434 / DK / NIDDK NIH HHS / United States
5-U54 HG02051 / HG / NHGRI NIH HHS / United States
U54 HG002051 / HG / NHGRI NIH HHS / United States