Genomes and Genes
- Euteleost fish genomes are characterized by expansion of gene familiesM Robinson-Rechavi
Centre National pour la Recherche Scientifique UMR 5665, Laboratoire de Biologie Moleculaire et Cellulaire, Ecole Normale Superieure de Lyon, 46 Alleé d Italie 69364 LYON Cedex 07, France
Genome Res 11:781-8. 2001..Redundancy appears to be the rule in fish developmental genetics. Finally, our results imply that the outcome of genome projects cannot be extrapolated easily between fish species...
- How many nuclear hormone receptors are there in the human genome?M Robinson-Rechavi
CNRS UMR 5665, Laboratoire de Biologie Moleculaire et Cellulaire, Ecole Normale Superieure de Lyon, 46 allee d Italie, 69364 Cedex 07, Lyon, France
Trends Genet 17:554-6. 2001..Here, we report the identification and classification of all nuclear receptor genes in the human genome, and we discuss corresponding transcriptome and proteome diversity...
- The nuclear receptor superfamilyMarc Robinson-Rechavi
, UMR CNRS 5665, , , 69364 Lyon Cedex 07, France
J Cell Sci 116:585-6. 2003
- Characterization of oestrogen receptors in zebrafish (Danio rerio)P L Bardet
Laboratoire de Biologie Moleculaire et Cellulaire, CNRS UMR 5665, Ecole Normale Superieure de Lyon, 46 allee d Italie, 69364 Lyon, France
J Mol Endocrinol 28:153-63. 2002..After 48 h after fertilization, all ERs, but predominantly ER alpha, began to be expressed. We conclude that oestrogen signal transduction can operate during zebrafish development only within discrete time windows...
- RRTree: relative-rate tests between groups of sequences on a phylogenetic treeM Robinson-Rechavi
Department of Zoology, Tel Aviv University, Ramat Aviv 69978, Israel Institut des Sciences de l Evolution, UniversitéMontpellier 2, 34095 Montpellier, France
Bioinformatics 16:296-7. 2000..AVAILABILITY: The ANSI C source code of RRTree, and compiled versions for Macintosh, MS-DOS/Windows, SUN Solaris, and CGI, are freely available at http://pbil.univ-lyon1.fr/software/rrtree.html CONTACT: email@example.com..
- Bioinformatics of nuclear receptorsMarc Robinson-Rechavi
, UMR CNRS 5665, , , 69364 Lyon, France
Methods Enzymol 364:95-118. 2003
- NUREBASE: database of nuclear hormone receptorsJorge Duarte
, CNRS UMR 5665, , , 69364 Lyon Cedex 07, France
Nucleic Acids Res 30:364-8. 2002..NUREBASE sequence data is also accessible through a World Wide Web server, allowing complex queries. All information on accessing and installing NUREBASE may be found at http://www.ens-lyon.fr/LBMC/laudet/nurebase.html...
- Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systemsStephanie Bertrand
Laboratoire de Biologie Moleculaire de la Cellule, Ecole Normale Superieure de Lyon, Lyon, France
Mol Biol Evol 21:1923-37. 2004..Our results imply that the genes for major receptors such as steroid receptors or thyroid hormone receptors were present in Urbilateria...
- Update of NUREBASE: nuclear hormone receptor functional genomicsDavid Ruau
, CNRS UMR 5161, , , 69364 Lyon Cedex 07, France
Nucleic Acids Res 32:D165-7. 2004..The core of NUREBASE is reviewed, and it is completed by NUREBASE_DAILY, automatically updated every 24 h. All information on accessing and installing NUREBASE may be found at http://www. ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html...
- Nuclear receptors are markers of animal genome evolutionHector Escriva Garcia
Laboratoire de Biologie Moleculaire et Cellulaire, Ecole Normale Superieure de Lyon, 46 allee d Italie, F 69364 Lyon Cedex 07, France
J Struct Funct Genomics 3:177-84. 2003..We illustrate this with examples from differents nuclear receptors and different groups of species...
- Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodesMarc Robinson-Rechavi
Laboratoire de Biologie Moleculaire de la Cellule, UMR CNRS 5161, Ecole Normale Superieure de Lyon, France
J Mol Evol 60:577-86. 2005..Our results provide a framework to study nuclear receptors in nematodes, as well as to consider the functional and evolutionary consequences of lineage-specific duplications...
- Phylogenetic dating and characterization of gene duplications in vertebrates: the cartilaginous fish referenceMarc Robinson-Rechavi
Laboratoire de Biologie Moleculaire de la Cellule, UMR CNRS5161, Ecole Normale Superieure de Lyon, Lyon, France
Mol Biol Evol 21:580-6. 2004..Our results support rounds of gene or genome duplications during a limited period of early vertebrate evolution and allow a better characterization of these events...
- Gene loss and evolutionary rates following whole-genome duplication in teleost fishesFrédéric G Brunet
Laboratoire de Biologie Moleculaire de la Cellule, INRA LA 1237, CNRS UMR5161, IFR 128 Biosciences Lyon Gerland, Ecole Normale Superieure de Lyon, Lyon, France
Mol Biol Evol 23:1808-16. 2006..These results show that similar mechanisms are at work in fishes as in yeast or plants and provide a framework for future investigation of the consequences of duplication in fishes and other animals...
- Neofunctionalization in vertebrates: the example of retinoic acid receptorsHector Escriva
Structure and Evolution of Nuclear Hormone Receptors, UMR 5161 du CNRS, INRA LA 1237, , IFR128 BioSciences Lyon-Gerland, , Lyon, France
PLoS Genet 2:e102. 2006..We thus suggest that neofunctionalization occurred at both the expression and the functional levels to shape RAR roles during development in vertebrates...
- Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotypeOlivier Jaillon
UMR 8030 Genoscope, , , 91057 Evry Cedex, France
Nature 431:946-57. 2004....
- Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMYGeorges Lutfalla
, UMR CNRS 5124, 1919, route de Mende, 34293 Montpellier Cedex 5, France
J Mol Evol 57:S148-53. 2003..Its role in sex determination was not acquired through an acceleration of evolutionary rates, but by translocation to the Y chromosome and possibly changes at key positions...
- The amphioxus genome and the evolution of the chordate karyotypeNicholas H Putnam
Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
Nature 453:1064-71. 2008..These genome-scale events shaped the vertebrate genome and provided additional genetic variation for exploitation during vertebrate evolution...
- Contribution of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritimaMarc Robinson-Rechavi
Joint Center for Structural Genomics, University of California, San Diego, La Jolla, 92093 0527, USA
J Mol Biol 356:547-57. 2006..These features account for changes in 96% of the protein pairs studied. Our results provide a clear picture of protein thermostability in one species, and a framework for future studies of thermal adaptation...
- Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXRFrançois Bonneton
UMR 5534 du CNRS, Universite Claude Bernard Lyon 1, Villeurbanne Cedex, France
Mol Biol Evol 20:541-53. 2003..These results have general implications on fundamental aspects of insect development, evolution of nuclear receptors, and the design of specific insecticides...
- A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation networkGregory D Amoutzias
Faculty of Life Sciences, University of Manchester, Manchester, M13 9PT, UK
BMC Syst Biol 1:34. 2007..They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved...
- Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitisKirsten Crossgrove
Department of Biological Sciences, University of Wisconsin Whitewater, Whitewater, WI 53190 USA
Mol Biochem Parasitol 157:92-7. 2008..We have identified Bm-nhr-11and Di-nhr-6, B. malayi and D. immitis orthologues of E75. Both genes encode canonical nuclear receptor proteins, are developmentally regulated, and are expressed in a sex-specific manner in adults...
- Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genesRomain A Studer
Department of Ecology and Evolution, Biophore, Lausanne University, CH 1015 Lausanne, Switzerland
Genome Res 18:1393-402. 2008..Thus positive selection has not been limited to a few gene classes, or to specific evolutionary events such as duplication, but has been pervasive during vertebrate evolution...
- The amphioxus genome illuminates vertebrate origins and cephalochordate biologyLinda Z Holland
Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, California 92093 0202, USA
Genome Res 18:1100-11. 2008..Our results indicate that the amphioxus genome is elemental to an understanding of the biology and evolution of nonchordate deuterostomes, invertebrate chordates, and vertebrates...