Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes

Genome Biology

Volumn 2, Issue 8, 2001, Pages

  Maglich, Jodi M ^a   Sluder, Ann ^c   Guan, Xiaojun ^b   Shi, Yunling ^b   McKee, David D ^a   Carrick, Kevin ^b   Kamdar, Kim ^d   Willson, Timothy M ^a   Moore, John T ^a  

^a Nuclear Receptor Systems Research   (United States)

^b GLAXOSMITHKLINE   (United States)

^c Cambria Pharmaceuticals Inc   (United States)

^d SYNGENTA BIOTECHNOLOGY INC   (United States)

Author keywords

HMMER Package; Nuclear Receptor; Nuclear Receptor Subfamily; Nuclear Receptor Superfamily; Predict Code Sequence

Indexed keywords

CAENORHABDITIS ELEGANS PROTEIN; CELL RECEPTOR; DROSOPHILA PROTEIN; MESSENGER RNA;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; BIOLOGY; CAENORHABDITIS ELEGANS; COMPARATIVE STUDY; DROSOPHILA MELANOGASTER; GENE; GENETIC DATABASE; GENETICS; GENOME; GENOMICS; HUMAN; INTRON; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PSEUDOGENE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; EVOLUTION, MOLECULAR; GENES, HELMINTH; GENES, INSECT; GENOME; GENOMICS; HUMANS; INTRONS; MOLECULAR SEQUENCE DATA; PHYLOGENY; PSEUDOGENES; RECEPTORS, CYTOPLASMIC AND NUCLEAR; RNA, MESSENGER; SEQUENCE ALIGNMENT;

EID: 0035224757     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2001-2-8-research0029     Document Type: Article

References (21)

1. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, et al: Comparative genomics of the eukaryotes. Science. 2000, 287: 2204-2215. 10.1126/science.287.5461.2204. DOI: 10.1126/science.287.5461.2204
2. The Arabidopsis Genome Initiative: Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 2000, 408: 796-815. 10.1038/35048692. DOI: 10.1038/35048692
3. Giguere V: Orphan nuclear receptors: from gene to function. Endocr Rev. 1999, 20: 689-725.
4. McKenna NJ, Lanz RB, O'Malley BW: Nuclear receptor coregulators: cellular and molecular biology. Endocr Rev. 1999, 20: 321-344.
5. Sluder AE, Mathews SW, Hough D, Yin VP, Maina CV: The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Res. 1999, 9: 103-120.
6. Enmark E, Gustafsson J: Nematode genome sequence dramatically extends the nuclear receptor superfamily. Trends Pharmacol Sci. 2000, 21: 85-87. 10.1016/S0165-6147(99)01417-0. DOI: 10.1016/S0165-6147(99)01417-0
7. Adams MD, Celniker SE, Holt RA, Evans CA, Gocayne JD, Amanatides PG, Scherer SE, Li PW, Hoskins RA, Galle RF, et al: The genome sequence of Drosophila melanogaster. Science. 2000, 287: 2185-2195. 10.1126/science.287.5461.2185. DOI: 10.1126/science.287.5461.2185
8. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389. DOI: 10.1093/nar/25.17.3389
9. Eddy SR: Hidden Markov models. Curr Opin Struct Biol. 1996, 6: 361-365. 10.1016/S0959-440X(96)80056-X. DOI: 10.1016/S0959-440X(96)80056-X
10. Danielian PS, White R, Lees JA, Parker MG: Identification of a conserved region required for hormone dependent transcriptional activation by steroid hormone receptors. EMBO J. 1992, 11: 1025-1033.
11. Tchenio T, Segal-Bendirdjian E, Heidmann T: Generation of processed pseudogenes in murine cells. EMBO J. 1993, 12: 1487-1497.
12. Sladek R, Beatty B, Squire J, Copeland NG, Gilbert DJ, Jenkins NA, Giguere V: Chromosomal mapping of the human and murine orphan receptors ERRalpha (ESRRA) and ERRbeta (ESRRB) and identification of a novel human ERRalpha-related pseudogene. Genomics. 1997, 45: 320-326. 10.1006/geno.1997.4939. DOI: 10.1006/geno.1997.4939
13. Laudet V, Hanni C, Coll J, Catzeflis F, Stehelin D: Evolution of the nuclear receptor gene superfamily. EMBO J. 1992, 11: 1003-1013.
14. Laudet V: Evolution of the nuclear receptor superfamily: early diversification from an ancestral orphan receptor. J Mol Endocrinol. 1997, 19: 207-226. DOI: 10.1677/jme.0.0190207
15. Escriva H, Safi R, Hanni C, Langlois MC, Saumitou-Laprade P, Stehelin D, Capron A, Pierce R, Laudet V: Ligand binding was acquired during evolution of nuclear receptors. Proc Natl Acad Sci USA. 1997, 94: 6803-6308. 10.1073/pnas.94.13.6803. DOI: 10.1073/pnas.94.13.6803
16. Aguinaldo AM, Turbeville JM, Linford LS, Rivera MC, Garey JR, Raff RA, Lake JA: Evidence for a clade of nematodes, arthropods and other moulting animals. Nature. 1997, 387: 489-493. 10.1038/387489a0. DOI: 10.1038/387489a0
17. Fitch DHA, Thomas WK: Evolution. In C. elegans II. Edited by Riddle DL, Blumenthal T, Meyer BJ and Priess JR. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Pres. 1997, 815-850.,
18. The Nuclear Receptors Committee: A unified nomenclature system for the nuclear receptor superfamily. Cell. 1999, 97: 161-163. DOI: 10.1016/S0092-8674(00)80726-6
19. Robyr D, Wolffe AP, Wahli W: Nuclear hormone receptor coregulators in action: diversity for shared tasks. Mol Endocrinol. 2000, 14: 329-347. DOI: 10.1210/mend.14.3.0411
20. Gibson UE, Heid CA, Williams PM: A novel method for real time quantitative RT-PCR. Genome Res. 1996, 6: 995-1001. DOI: 10.1101/gr.6.10.995
21. Heid CA, Stevens J, Livak KJ, Williams PM: Real time quantitative PCR. Genome Res. 1996, 6: 986-994. DOI: 10.1101/gr.6.10.986