@article {5369, title = {Anatomic analysis of Gal4 expression patterns of the Rubin line collection: the central complex.}, journal = {Journal of Neurogenetics}, volume = {24}, year = {2010}, month = {2010}, pages = {71-2}, chapter = {71}, author = {Jenett, A and Wolff, T and Nern, A. and Pfeiffer, B D and Ngo, T. and Murphy, C. and Long, F. and Peng, H. and Rubin, G M} } @article {958, title = {Comparative genomics of the eukaryotes.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2204-15}, abstract = {

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

}, keywords = {Animals, Apoptosis, Biological Evolution, Caenorhabditis elegans, Cell Adhesion, Cell Cycle, Drosophila melanogaster, Duplicate, Fungal Proteins, Genes, Genetic Diseases, Genetics, Genome, Helminth Proteins, Humans, Immunity, Inborn, Insect Proteins, Medical, Multigene Family, Neoplasms, Protein Structure, Proteome, Saccharomyces cerevisiae, Signal Transduction, Tertiary}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Yandell, M D and Wortman, J R and Gabor Miklos, G L and Nelson, C R and Hariharan, I K and Fortini, M E and Li, P W and Apweiler, R and Fleischmann, W and Cherry, J M and Henikoff, S and Skupski, M P and Misra, S and Ashburner, M and Birney, E and Boguski, M S and Brody, T and Brokstein, P and Celniker, S E and Chervitz, S A and Coates, D and Cravchik, A and Gabrielian, A and Galle, R F and Gelbart, W M and George, R A and Goldstein, L S and Gong, F and Guan, P and Harris, N L and Hay, B A and Hoskins, R A and Li, J and Li, Z and Hynes, R O and Jones, S J and Kuehl, P M and Lemaitre, B and Littleton, J T and Morrison, D K and Mungall, C and O{\textquoteright}Farrell, P H and Pickeral, O K and Shue, C and Vosshall, L B and Zhang, J and Zhao, Q and Zheng, X H and Lewis, S} } @article {957, title = {The genome sequence of Drosophila melanogaster.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2185-95}, abstract = {

The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.

}, keywords = {Animals, Biological Transport, Chromatin, Cloning, Computational Biology, Contig Mapping, Cytochrome P-450 Enzyme System, DNA, DNA Repair, DNA Replication, Drosophila melanogaster, Euchromatin, Gene Library, Genes, Genetic, Genome, Heterochromatin, Insect, Insect Proteins, Molecular, Nuclear Proteins, Protein Biosynthesis, Sequence Analysis, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Adams, M D and Celniker, S E and Holt, R A and Evans, C A and Gocayne, J D and Amanatides, P G and Scherer, S E and Li, P W and Hoskins, R A and Galle, R F and George, R A and Lewis, S E and Richards, S and Ashburner, M and Henderson, S N and Sutton, G G and Wortman, J R and Yandell, M D and Zhang, Q and Chen, L X and Brandon, R C and Rogers, Y H and Blazej, R G and Champe, M and Pfeiffer, B D and Wan, K H and Doyle, C and Baxter, E G and Helt, G and Nelson, C R and Gabor, G L and Abril, J F and Agbayani, A and An, H J and Andrews-Pfannkoch, C and Baldwin, D and Ballew, R M and Basu, A and Baxendale, J and Bayraktaroglu, L and Beasley, E M and Beeson, K Y and Benos, P V and Berman, B P and Bhandari, D and Bolshakov, S and Borkova, D and Botchan, M R and Bouck, J and Brokstein, P and Brottier, P and Burtis, K C and Busam, D A and Butler, H and Cadieu, E and Center, A and Chandra, I and Cherry, J M and Cawley, S and Dahlke, C and Davenport, L B and Davies, P and de Pablos, B and Delcher, A and Deng, Z and Mays, A D and Dew, I and Dietz, S M and Dodson, K and Doup, L E and Downes, M and Dugan-Rocha, S and Dunkov, B C and Dunn, P and Durbin, K J and Evangelista, C C and Ferraz, C and Ferriera, S and Fleischmann, W and Fosler, C and Gabrielian, A E and Garg, N S and Gelbart, W M and Glasser, K and Glodek, A and Gong, F and Gorrell, J H and Gu, Z and Guan, P and Harris, M and Harris, N L and Harvey, D and Heiman, T J and Hernandez, J R and Houck, J and Hostin, D and Houston, K A and Howland, T J and Wei, M H and Ibegwam, C and Jalali, M and Kalush, F and Karpen, G H and Ke, Z and Kennison, J A and Ketchum, K A and Kimmel, B E and Kodira, C D and Kraft, C and Kravitz, S and Kulp, D and Lai, Z and Lasko, P and Lei, Y and Levitsky, A A and Li, J and Li, Z and Liang, Y and Lin, X and Liu, X and Mattei, B and McIntosh, T C and McLeod, M P and McPherson, D and Merkulov, G and Milshina, N V and Mobarry, C and Morris, J and Moshrefi, A and Mount, S M and Moy, M and Murphy, B and Murphy, L and Muzny, D M and Nelson, D L and Nelson, D R and Nelson, K A and Nixon, K and Nusskern, D R and Pacleb, J M and Palazzolo, M and Pittman, G S and Pan, S and Pollard, J and Puri, V and Reese, M G and Reinert, K and Remington, K and Saunders, R D and Scheeler, F and Shen, H and Shue, B C and Sid{\'e}n-Kiamos, I and Simpson, M and Skupski, M P and Smith, T and Spier, E and Spradling, A C and Stapleton, M and Strong, R and Sun, E and Svirskas, R and Tector, C and Turner, R and Venter, E and Wang, A H and Wang, X and Wang, Z Y and Wassarman, D A and Weinstock, G M and Weissenbach, J and Williams, S M and Williams, S M and Worley, K C and Wu, D and Yang, S and Yao, Q A and Ye, J and Yeh, R F and Zaveri, J S and Zhan, M and Zhang, G and Zhao, Q and Zheng, L and Zheng, X H and Zhong, F N and Zhong, W and Zhou, X and Zhu, S and Zhu, X and Smith, H O and Gibbs, R A and Myers, E W and Rubin, G M and Venter, J C} } @article {2705, title = {A whole-genome assembly of Drosophila.}, journal = {Science}, volume = {287}, year = {2000}, month = {2000 Mar 24}, pages = {2196-204}, abstract = {

We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly{\textquoteright}s sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase region indicates that sequencing accuracy within nonrepetitive segments is greater than 99. 99\% without manual curation. As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

}, keywords = {Algorithms, Animals, Chromatin, Computational Biology, Contig Mapping, DNA, Drosophila melanogaster, Euchromatin, Genes, Genome, Heterochromatin, Insect, Molecular Sequence Data, Nucleic Acid, Physical Chromosome Mapping, Repetitive Sequences, Sequence Analysis, Sequence Tagged Sites}, issn = {0036-8075}, author = {Myers, E W and Sutton, G G and Delcher, A L and Dew, I M and Fasulo, D P and Flanigan, M J and Kravitz, S A and Mobarry, C M and Reinert, K H and Remington, K A and Anson, E L and Bolanos, R A and Chou, H H and Jordan, C M and Halpern, A L and Lonardi, S and Beasley, E M and Brandon, R C and Chen, L and Dunn, P J and Lai, Z and Liang, Y and Nusskern, D R and Zhan, M and Zhang, Q and Zheng, X and Rubin, G M and Adams, M D and Venter, J C} } @article {959, title = {The Berkeley Drosophila genome project gene disruption project: single P-element insertions mutating 25\% of vital Drosophila genes.}, journal = {Genetics}, volume = {153}, year = {1999}, month = {1999 Sep}, pages = {135-77}, abstract = {

A fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25\% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67\% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking \>920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing \>250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring \>85\% of all Drosophila open reading frames under experimental control.

}, keywords = {Alleles, Animals, California, Crosses, DNA, DNA Transposable Elements, Drosophila melanogaster, Essential, Expressed Sequence Tags, Female, Genes, Genetic, Genetic Linkage, Genome, Insect, Insertional, Male, Models, Mutagenesis, Mutation, Phenotype, Recessive, Reproducibility of Results, Sequence Analysis}, issn = {0016-6731}, doi = {10.1186/gb-2007-8-7-r145}, author = {Spradling, A C and Stern, D and Beaton, A and Rhem, E J and Laverty, T and Mozden, N and Misra, S and Rubin, G M} } @article {8265, title = {The Drosophila genome project: a progress report.}, journal = {Trends in Genetics}, volume = {14}, year = {1998}, month = {1998 Sep}, pages = {340-3}, keywords = {Animals, Chromosome Mapping, Databases, Factual, Drosophila, Expressed Sequence Tags, Genome, Heterochromatin, Mutagenesis, Insertional}, issn = {0168-9525}, author = {Rubin, G M} } @article {46649, title = {eyelid antagonizes wingless signaling during Drosophila development and has homology to the Bright family of DNA-binding proteins.}, journal = {Genes \& Development}, volume = {11}, year = {1997}, month = {1997 Aug 1}, pages = {1949-62}, abstract = {

In Drosophila, pattern formation at multiple stages of embryonic and imaginal development depends on the same intercellular signaling pathways. We have identified a novel gene, eyelid (eld), which is required for embryonic segmentation, development of the notum and wing margin, and photoreceptor differentiation. In these tissues, eld mutations have effects opposite to those caused by wingless (wg) mutations. eld encodes a widely expressed nuclear protein with a region homologous to a novel family of DNA-binding domains. Based on this homology and on the phenotypic analysis, we suggest that Eld could act as a transcription factor antagonistic to the Wg pathway.

}, keywords = {Amino Acid Sequence, Animals, Body Patterning, Cell Differentiation, Cloning, Molecular, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Gene Expression Regulation, Developmental, Genes, Insect, Molecular Sequence Data, Mutation, Phenotype, Photoreceptor Cells, Invertebrate, Proto-Oncogene Proteins, Recombinant Fusion Proteins, Restriction Mapping, Sequence Homology, Amino Acid, Signal Transduction, Trans-Activators, Transcription Factors, Wing, Wnt1 Protein}, issn = {0890-9369}, author = {Treisman, J E and Luk, A and Rubin, G M and Heberlein, U} } @article {961, title = {Drosophila homologs of baculovirus inhibitor of apoptosis proteins function to block cell death.}, journal = {Cell}, volume = {83}, year = {1995}, month = {1995 Dec 29}, pages = {1253-62}, abstract = {

Apoptotic cell death is a mechanism by which organisms eliminate superfluous or harmful cells. Expression of the cell death regulatory protein REAPER (RPR) in the developing Drosophila eye results in a small eye owing to excess cell death. We show that mutations in thread (th) are dominant enhancers of RPR-induced cell death and that th encodes a protein homologous to baculovirus inhibitors of apoptosis (IAPs), which we call Drosophila IAP1 (DIAP1). Overexpression of DIAP1 or a related protein, DIAP2, in the eye suppresses normally occurring cell death as well as death due to overexpression of rpr or head involution defective. IAP death-preventing activity localizes to the N-terminal baculovirus IAP repeats, a motif found in both viral and cellular proteins associated with death prevention.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Apoptosis, Biological Evolution, Chromosome Deletion, Drosophila, Drosophila Proteins, Electron, Enhancer Elements, Eye, Genes, Genetic, Genetic Testing, Humans, Inhibitor of Apoptosis Proteins, Insect, Insect Proteins, Mammals, Microscopy, Molecular Sequence Data, Mutation, Neurons, Nucleic Acid, Peptides, Repetitive Sequences, Scanning, Sequence Homology, Viral Proteins}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hay, B A and Wassarman, D A and Rubin, G M} } @article {960, title = {Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway.}, journal = {Cell}, volume = {81}, year = {1995}, month = {1995 Jun 16}, pages = {857-66}, abstract = {

Drosophila yan has been postulated to act as an antagonist of the proneural signal mediated by the sevenless/Ras1/MAPK pathway. We have mutagenized the eight MAPK phosphorylation consensus sites of yan and examined the effects of overexpressing the mutant protein in transgenic flies and transfected S2 cultured cells. Our results suggest that phosphorylation by MAPK affects the stability and subcellular localization of yan, resulting in rapid down-regulation of yan activity. Furthermore, MAPK-mediated down-regulation of yan function appears to be critical for the proper differentiation of both neuronal and nonneuronal tissues throughout development, suggesting that yan is an essential component of a general timing mechanism controlling the competence of a cell to respond to inductive signals.

}, keywords = {Alleles, Animals, Binding Sites, Calcium-Calmodulin-Dependent Protein Kinases, Developmental, DNA-Binding Proteins, Down-Regulation, Drosophila, Drosophila Proteins, Eye, Eye Proteins, Gene Expression Regulation, GTP-Binding Proteins, Membrane Glycoproteins, Mutagenesis, Neurons, Phosphorylation, Receptor Protein-Tyrosine Kinases, Repressor Proteins, Signal Transduction, Site-Directed}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rebay, I and Rubin, G M} } @article {963, title = {The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway.}, journal = {Cell}, volume = {78}, year = {1994}, month = {1994 Jul 15}, pages = {137-47}, abstract = {

We show that the activities of two Ets-related transcription factors required for normal eye development in Drosophila, pointed and yan, are regulated by the Ras1/MAPK pathway. The pointed gene codes for two related proteins, and we show that one form is a constitutive activator of transcription, while the activity of the other form is stimulated by the Ras1/MAPK pathway. Mutation of the single consensus MAPK phosphorylation site in the second form abrogates this responsiveness. yan is a negative regulator of photoreceptor determination, and genetic data suggest that it acts as an antagonist of Ras1. We demonstrate that yan can repress transcription and that this repression activity is negatively regulated by the Ras1/MAPK signal, most likely through direct phosphorylation of yan by MAPK.

}, keywords = {Animals, Biological, Calcium-Calmodulin-Dependent Protein Kinases, DNA-Binding Proteins, Drosophila, Drosophila Proteins, Extracellular Signal-Regulated MAP Kinases, Eye, Eye Proteins, Gene Expression Regulation, Genes, Genetic, Insect, Invertebrate, Models, Morphogenesis, Nerve Tissue Proteins, Phenotype, Photoreceptor Cells, Proto-Oncogene Proteins, Proto-Oncogene Proteins p21(ras), ras, Repressor Proteins, Signal Transduction, Transcription, Transcription Factors}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {O{\textquoteright}Neill, E M and Rebay, I and Tjian, R and Rubin, G M} } @article {962, title = {The Drosophila peanut gene is required for cytokinesis and encodes a protein similar to yeast putative bud neck filament proteins.}, journal = {Cell}, volume = {77}, year = {1994}, month = {1994 May 6}, pages = {371-9}, abstract = {

We have identified a Drosophila gene, peanut (pnut), that is related in sequence to the CDC3, CDC10, CDC11, and CDC12 genes of S. cerevisiae. These genes are required for cytokinesis, and their products are present at the bud neck during cell division. We find that pnut is also required for cytokinesis: in pnut mutants, imaginal tissues fail to proliferate and instead develop clusters of large, multinucleate cells. Pnut protein is localized to the cleavage furrow of dividing cells during cytokinesis and to the intercellular bridge connecting postmitotic daughter cells. In addition to its role in cytokinesis, pnut displays genetic interactions with seven in absentia, a gene required for neuronal fate determination in the compound eye, suggesting that pnut may have pleiotropic functions. Our results suggest that this class of proteins is involved in aspects of cytokinesis that have been conserved between flies and yeast.

}, keywords = {Amino Acid, Amino Acid Sequence, Animals, Base Sequence, Cell Division, Cell Line, Cloning, Complementary, DNA, Drosophila, Drosophila Proteins, Enhancer Elements, Female, Fungal, Fungal Proteins, Gene Library, Genes, Genetic, Insect, Larva, Male, Mice, Microfilament Proteins, Molecular, Molecular Sequence Data, Proteins, Saccharomyces cerevisiae, Sequence Analysis, Sequence Homology}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Neufeld, T P and Rubin, G M} } @article {965, title = {Analysis of genetic mosaics in developing and adult Drosophila tissues.}, journal = {Development}, volume = {117}, year = {1993}, month = {1993 Apr}, pages = {1223-37}, abstract = {

We have constructed a series of strains to facilitate the generation and analysis of clones of genetically distinct cells in developing and adult tissues of Drosophila. Each of these strains carries an FRT element, the target for the yeast FLP recombinase, near the base of a major chromosome arm, as well as a gratuitous cell-autonomous marker. Novel markers that carry epitope tags and that are localized to either the cell nucleus or cell membrane have been generated. As a demonstration of how these strains can be used to study a particular gene, we have analyzed the developmental role of the Drosophila EGF receptor homolog. Moreover, we have shown that these strains can be utilized to identify new mutations in mosaic animals in an efficient and unbiased way, thereby providing an unprecedented opportunity to perform systematic genetic screens for mutations affecting many biological processes.

}, keywords = {Animals, Drosophila, Embryo, Epidermal Growth Factor, Female, Genetic Markers, Genetic Testing, Immunohistochemistry, Male, Mosaicism, Mutation, Nonmammalian, Phenotype, Receptor}, issn = {0950-1991}, doi = {10.1186/gb-2007-8-7-r145}, author = {Xu, T and Rubin, G M} } @article {964, title = {The TGF beta homolog dpp and the segment polarity gene hedgehog are required for propagation of a morphogenetic wave in the Drosophila retina.}, journal = {Cell}, volume = {75}, year = {1993}, month = {1993 Dec 3}, pages = {913-26}, abstract = {

Development of the Drosophila retina occurs asynchronously; differentiation, its front marked by the morphogenetic furrow, progresses across the eye disc epithelium over a 2 day period. We have investigated the mechanism by which this front advances, and our results suggest that developing retinal cells drive the progression of morphogenesis utilizing the products of the hedgehog (hh) and decapentaplegic (dpp) genes. Analysis of hh and dpp genetic mosaics indicates that the products of these genes act as diffusible signals in this process. Expression of dpp in the morphogenetic furrow is closely correlated with the progression of the furrow under a variety of conditions. We show that hh, synthesized by differentiating cells, induces the expression of dpp, which appears to be a primary mediator of furrow movement.

}, keywords = {Animals, Cell Differentiation, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Hedgehog Proteins, Insect, Insect Hormones, Invertebrate, Messenger, Morphogenesis, Mosaicism, Photoreceptor Cells, Proteins, Retina, RNA, Transforming Growth Factor beta}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Heberlein, U and Wolff, T and Rubin, G M} } @article {966, title = {The argos gene encodes a diffusible factor that regulates cell fate decisions in the Drosophila eye.}, journal = {Cell}, volume = {69}, year = {1992}, month = {1992 Jun 12}, pages = {963-75}, abstract = {

The argos gene encodes a protein that is required for viability and that regulates the determination of cells in the Drosophila eye. A developmental analysis of argos mutant eyes indicates that the mystery cells, which are usually nonneuronal, are transformed into extra photoreceptors, and that supernumerary cone cells and pigment cells are also recruited. Clonal analysis indicates that argos acts nonautonomously and can diffuse over the range of several cell diameters. Conceptual translation of the argos gene suggests that it encodes a secreted protein.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Communication, Clone Cells, Cloning, DNA, Drosophila melanogaster, Embryonic Induction, Eye, Gene Expression, Genes, Messenger, Molecular, Molecular Sequence Data, Phenotype, Restriction Mapping, RNA, Signal Transduction}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Freeman, M and Kl{\"a}mbt, C and Goodman, C S and Rubin, G M} } @article {968, title = {The optic lobe projection pattern of polarization-sensitive photoreceptor cells in Drosophila melanogaster.}, journal = {Cell and Tissue Research}, volume = {265}, year = {1991}, month = {1991 Jul}, pages = {185-91}, abstract = {

Histological staining of wild-type and sevenless transgenic Drosophila melanogaster bearing Rh3-lacZ fusion genes permits the selective visualization of polarization-sensitive R7 and R8 photoreceptor cells located along the dorsal anterior eye margin. Diffusion of beta-galactosidase throughout these cells reveals that they project long axons to the two most peripheral synaptic target rows of the dorsal posterior medulla, defining a specialized marginal zone of this optic lobe. Comparison of the staining patterns of marginal and nonmarginal Rh3-lacZ-expressing photoreceptor cells in the same histological preparations suggest that the marginal cells possess morphologically specialized axons and synaptic terminals. These findings are discussed with reference to the neuroanatomy of the corresponding dorsal marginal eye and optic lobe regions of the larger dipterans Musca and Calliphora, and in relation to the ability of Drosophila to orient to polarized light.

}, keywords = {Animals, beta-Galactosidase, Cloning, Drosophila melanogaster, Eye, Gene Expression, Histocytochemistry, Light, Molecular, Nonmammalian, Ocular, Ocular Physiological Phenomena, Optic Lobe, Photoreceptor Cells, Vision}, issn = {0302-766X}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {967, title = {Ras1 and a putative guanine nucleotide exchange factor perform crucial steps in signaling by the sevenless protein tyrosine kinase.}, journal = {Cell}, volume = {67}, year = {1991}, month = {1991 Nov 15}, pages = {701-16}, abstract = {

We have conducted a genetic screen for mutations that decrease the effectiveness of signaling by a protein tyrosine kinase, the product of the Drosophila melanogaster sevenless gene. These mutations define seven genes whose wild-type products may be required for signaling by sevenless. Four of the seven genes also appear to be essential for signaling by a second protein tyrosine kinase, the product of the Ellipse gene. The putative products of two of these seven genes have been identified. One encodes a ras protein. The other locus encodes a protein that is homologous to the S. cerevisiae CDC25 protein, an activator of guanine nucleotide exchange by ras proteins. These results suggest that the stimulation of ras protein activity is a key element in the signaling by sevenless and Ellipse and that this stimulation may be achieved by activating the exchange of GTP for bound GDP by the ras protein.

}, keywords = {Amino Acid Sequence, DNA Mutational Analysis, Drosophila Proteins, Eye Proteins, Genes, GTP-Binding Proteins, Guanine Nucleotide Exchange Factors, Membrane Glycoproteins, Molecular Sequence Data, Photoreceptor Cells, Protein-Tyrosine Kinases, Proteins, Proto-Oncogene Proteins p21(ras), ras Guanine Nucleotide Exchange Factors, Receptor Protein-Tyrosine Kinases, Restriction Mapping, Saccharomyces cerevisiae, Schizosaccharomyces, Sequence Alignment, Signal Transduction, Structure-Activity Relationship}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Simon, M A and Bowtell, D D and Dodson, G S and Laverty, T R and Rubin, G M} } @article {970, title = {Analysis of cis-acting requirements of the Rh3 and Rh4 genes reveals a bipartite organization to rhodopsin promoters in Drosophila melanogaster.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 Mar}, pages = {444-63}, abstract = {

The rhodopsin genes of Drosophila melanogaster are expressed in nonoverlapping subsets of photoreceptor cells within the insect visual system. Two of these genes, Rh3 and Rh4, are known to display complementary expression patterns in the UV-sensitive R7 photoreceptor cell population of the compound eye. In addition, we find that Rh3 is expressed in a small group of paired R7 and R8 photoreceptor cells at the dorsal eye margin that are apparently specialized for the detection of polarized light. In this paper we present a detailed characterization of the cis-acting requirements of both Rh3 and Rh4. Promoter deletion series demonstrate that small regulatory regions (less than 300 bp) of both R7 opsin genes contain DNA sequences sufficient to generate their respective expression patterns. Individual cis-acting elements were further identified by oligonucleotide-directed mutagenesis guided by interspecific sequence comparisons. Our results suggest that the Drosophila rhodopsin genes share a simple bipartite promoter structure, whereby the proximal region constitutes a functionally equivalent promoter "core" and the distal region determines cell-type specificity. The expression patterns of several hybrid rhodopsin promoters, in which all or part of the putative core regions have been replaced with the analogous regions of different rhodopsin promoters, provide additional evidence in support of this model.

}, keywords = {Animals, Base Sequence, DNA Mutational Analysis, Drosophila melanogaster, Eye Proteins, Gene Expression, Genes, Genetic, Histocytochemistry, Molecular Sequence Data, Mutation, Nucleic Acid, Promoter Regions, Retinal Pigments, Rhodopsin, Rod Opsins, Sequence Homology}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Fortini, M E and Rubin, G M} } @article {969, title = {The homeo domain protein rough is expressed in a subset of cells in the developing Drosophila eye where it can specify photoreceptor cell subtype.}, journal = {Genes \& Development}, volume = {4}, year = {1990}, month = {1990 May}, pages = {712-27}, abstract = {

The Drosophila homeo box gene rough is required in photoreceptor cells R2 and R5 for normal eye development. We show here that rough protein expression is limited to a subset of cells in the developing retina where it is transiently expressed for 30-60 hr. The rough protein is first expressed broadly in the morphogenetic furrow but is rapidly restricted to the R2, R3, R4, and R5 precursor cells. Ubiquitous expression of rough under the control of the hsp70 promoter in third-instar larvae suppresses the initial steps of ommatidial assembly. Structures derived from other imaginal discs are not affected. Ectopic expression of rough in the R7 precursor, through the use of the sevenless promoter, causes this cell to develop into an R1-6 photoreceptor subtype; however, this cell still requires sevenless function for its neural differentiation. Taken together with previous analyses of the rough mutant phenotype, these results suggest that the normal role of rough is to establish the unique cell identity of photoreceptors R2 and R5.

}, keywords = {Animals, Base Sequence, Cell Cycle Proteins, DNA-Binding Proteins, Drosophila melanogaster, Drosophila Proteins, Eye, Gene Expression, Genes, Genetic, Heat-Shock Proteins, Homeobox, Hot Temperature, Microtubule-Associated Proteins, Molecular Sequence Data, Morphogenesis, Phenotype, Photoreceptor Cells, Promoter Regions, Transcription Factors}, issn = {0890-9369}, doi = {10.1186/gb-2007-8-7-r145}, author = {Kimmel, B E and Heberlein, U and Rubin, G M} } @article {971, title = {Spacing differentiation in the developing Drosophila eye: a fibrinogen-related lateral inhibitor encoded by scabrous.}, journal = {Science}, volume = {250}, year = {1990}, month = {1990 Dec 7}, pages = {1370-7}, abstract = {

In the development of multicellular organisms a diversity of cell types differentiate at specific positions. Spacing patterns, in which an array of two or more cell types forms from a uniform field of cells, are a common feature of development. Identical precursor cells may adopt different fates because of competition and inhibition between them. Such a pattern in the developing Drosophila eye is the evenly spaced array of R8 cells, around which other cell types are subsequently recruited. Genetic studies suggest that the scabrous mutation disrupts a signal produced by R8 cells that inhibits other cells from also becoming R8 cells. The scabrous locus was cloned, and it appears to encode a secreted protein partly related to the beta and gamma chains of fibrinogen. It is proposed that the sca locus encodes a lateral inhibitor of R8 differentiation. The roles of the Drosophila EGF-receptor homologue (DER) and Notch genes in this process were also investigated.

}, keywords = {Alleles, Amino Acid Sequence, Animals, Cell Differentiation, DNA Transposable Elements, Drosophila, Drosophila Proteins, Epidermal Growth Factor, Eye, Fibrinogen, Glycoproteins, Humans, Molecular Sequence Data, Mosaicism, Mutation, Nucleic Acid, Phenotype, Proteins, Receptor, Sequence Homology}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Baker, N E and Mlodzik, M and Rubin, G M} } @article {972, title = {The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells.}, journal = {Nature}, volume = {340}, year = {1989}, month = {1989 Aug 17}, pages = {531-6}, abstract = {

Null mutations of glass specifically remove photoreceptor cells, leaving other cell types intact. We have isolated the glass gene and have shown that its transcript encodes a putative protein of 604 amino acids with five zinc-fingers. The glass product may be a transcription factor required for the development of a single neuronal cell type.

}, keywords = {Animals, Base Sequence, DNA, Drosophila, Gene Expression Regulation, Molecular Sequence Data, Mutation, Photoreceptor Cells}, issn = {0028-0836}, doi = {10.1186/gb-2007-8-7-r145}, author = {Moses, K and Ellis, M C and Rubin, G M} } @article {973, title = {Molecular characterization of the Drosophila trp locus: a putative integral membrane protein required for phototransduction.}, journal = {Neuron}, volume = {2}, year = {1989}, month = {1989 Apr}, pages = {1313-23}, abstract = {

Recent studies suggest that the fly uses the inositol lipid signaling system for visual excitation and that the Drosophila transient receptor potential (trp) mutation disrupts this process subsequent to the production of IP3. In this paper, we show that trp encodes a novel 1275 amino acid protein with eight putative transmembrane segments. Immunolocalization indicates that the trp protein is expressed predominantly in the rhabdomeric membranes of the photoreceptor cells.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Calcium Channels, DNA, Drosophila melanogaster, Drosophila Proteins, Genes, Inositol Phosphates, Insect Hormones, Insect Proteins, Membrane Proteins, Molecular Sequence Data, Photoreceptor Cells, Protein Conformation, Signal Transduction, Transient Receptor Potential Channels}, issn = {0896-6273}, doi = {10.1186/gb-2007-8-7-r145}, author = {Montell, C and Rubin, G M} } @article {974, title = {Localization of the sevenless protein, a putative receptor for positional information, in the eye imaginal disc of Drosophila.}, journal = {Cell}, volume = {51}, year = {1987}, month = {1987 Oct 9}, pages = {143-50}, abstract = {

The Drosophila gene sevenless encodes a putative trans-membrane receptor required for the formation of one particular cell, the R7 photoreceptor, in each ommatidium of the compound eye. Mutations in this gene result in the cell normally destined to form the R7 cell forming a non-neuronal cell type instead. These observations have led to the proposal that the sevenless protein receives at least part of the positional information required for the R7 developmental pathway. We have generated antibodies specific for sevenless and have examined expression of the protein by light and electron microscopy. sevenless protein is present transiently at high levels in at least 9 cells in each developing ommatidium and is detectable several hours before any overt differentiation of R7. The protein is mostly localized at the apices of the cells, in microvilli, but is also found deeper in the tissue where certain cells contact the R8 cell. This finding suggests that R8 expresses a ligand for the sevenless protein.

}, keywords = {Animals, Drosophila melanogaster, Electron, Epithelium, Eye, Eye Proteins, Histocytochemistry, Immunologic Techniques, Insect Hormones, Microscopy, Microvilli, Peptide Fragments, Photoreceptor Cells}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Tomlinson, A and Bowtell, D D and Hafen, E and Rubin, G M} } @article {975, title = {Sevenless, a cell-specific homeotic gene of Drosophila, encodes a putative transmembrane receptor with a tyrosine kinase domain.}, journal = {Science}, volume = {236}, year = {1987}, month = {1987 Apr 3}, pages = {55-63}, abstract = {

The determination of cell fates during the assembly of the ommatidia in the compound eye of Drosophila appears to be controlled by cell-cell interactions. In this process, the sevenless gene is essential for the development of a single type of photoreceptor cell. In the absence of proper sevenless function the cells that would normally become the R7 photoreceptors instead become nonneuronal cells. Previous morphological and genetic analysis has indicated that the product of the sevenless gene is involved in reading or interpreting the positional information that specifies this particular developmental pathway. The sevenless gene has now been isolated and characterized. The data indicate that sevenless encodes a transmembrane protein with a tyrosine kinase domain. This structural similarity between sevenless and certain hormone receptors suggests that similar mechanisms are involved in developmental decisions based on cell-cell interaction and physiological or developmental changes induced by diffusible factors.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cell Surface, Chromosome Mapping, Cloning, DNA Restriction Enzymes, Drosophila melanogaster, Eye, Gene Expression Regulation, Genes, Genetic, Growth Substances, Homeobox, Membrane Proteins, Molecular, Phenotype, Protein-Tyrosine Kinases, Receptors, Transcription}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Hafen, E and Basler, K and Edstroem, J E and Rubin, G M} } @article {976, title = {Tissue specificity of Drosophila P element transposition is regulated at the level of mRNA splicing.}, journal = {Cell}, volume = {44}, year = {1986}, month = {1986 Jan 17}, pages = {7-19}, abstract = {

We show that the germline specificity of P element transposition is controlled at the level of mRNA splicing and not at the level of transcription. In the major P element RNA transcript, isolated from somatic cells, the first three open reading frames are joined by the removal of two introns. Using in vitro mutagenesis and genetic analysis we demonstrate the existence of a third intron whose removal is required for transposase production. We propose that this intron is only removed in the germline and that its removal is the sole basis for the germline restriction of P element transposition.

}, keywords = {Animals, Base Sequence, Cricetinae, DNA Transposable Elements, Drosophila melanogaster, Gene Expression Regulation, Genetic, Heat-Shock Proteins, Messenger, Nucleotidyltransferases, Organ Specificity, Promoter Regions, RNA, RNA Splicing, Transcription, Transposases}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Laski, F A and Rio, D C and Rubin, G M} } @article {977, title = {Isolation and structure of a rhodopsin gene from D. melanogaster.}, journal = {Cell}, volume = {40}, year = {1985}, month = {1985 Apr}, pages = {851-8}, abstract = {

Using a novel method for detecting cross-homologous nucleic acid sequences we have isolated the gene coding for the major rhodopsin of Drosophila melanogaster and mapped it to chromosomal region 92B8-11. Comparison of cDNA and genomic DNA sequences indicates that the gene is divided into five exons. The amino acid sequence deduced from the nucleotide sequence is 373 residues long, and the polypeptide chain contains seven hydrophobic segments that appear to correspond to the seven transmembrane segments characteristic of other rhodopsins. Three regions of Drosophila rhodopsin are highly conserved with the corresponding domains of bovine rhodopsin, suggesting an important role for these polypeptide regions.

}, keywords = {Amino Acid Sequence, Animals, Base Sequence, Cattle, Chromosome Mapping, DNA, Drosophila melanogaster, Genes, Messenger, Nucleic Acid Hybridization, Poly A, Retinal Pigments, Rhodopsin, RNA, Tissue Distribution}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Zuker, C S and Cowman, A F and Rubin, G M} } @article {978, title = {Analysis of P transposable element functions in Drosophila.}, journal = {Cell}, volume = {38}, year = {1984}, month = {1984 Aug}, pages = {135-46}, abstract = {

We have made a P-element derivative called Pc[ry], which carries the selectable marker gene rosy, but which acts like a nondefective, intact P element. It transposes autonomously into the germline chromosomes of an M-strain Drosophila embryo and it mobilizes in trans the defective P elements of the singed-weak allele. Frameshift mutations introduced into any of the four major open reading frames of the P sequence were each sufficient to eliminate the transposase activity, but none affected signals required in cis for transposition of the element. Complementation tests between pairs of mutant elements suggest that a single polypeptide comprises the transposase. We have examined transcripts of P elements both from natural P strains and from lines containing only nondefective Pc[ry] elements, and have identified two RNA species that appear to be specific for autonomous elements.

}, keywords = {Alleles, Animals, Base Sequence, Crosses, DNA Restriction Enzymes, DNA Transposable Elements, Drosophila, Female, Genes, Genetic, Genetic Complementation Test, Male, Mutation, Nucleic Acid Hybridization}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Karess, R E and Rubin, G M} } @article {979, title = {The effect of chromosomal position on the expression of the Drosophila xanthine dehydrogenase gene.}, journal = {Cell}, volume = {34}, year = {1983}, month = {1983 Aug}, pages = {47-57}, abstract = {

Thirty-six isogenic D. melanogaster strains that differed only in the chromosomal location of a 7.2 or an 8.1 kb DNA segment containing the (autosomal) rosy gene were constructed by P-element-mediated gene transfer. Since the flies were homozygous for a rosy- allele, rosy gene function in these indicated the influence of flanking sequences on gene expression. The tissue distribution of XDH activity in all the strains was normal. Each line exhibited a characteristic level of adult XDH-specific activity. The majority of these values were close to wild-type levels; however, the total variation in specific activity among the lines was nearly fivefold. Thus position effects influence expression of the rosy gene quantitatively but do not detectably alter tissue specificity. X-linked rosy insertions were expressed on average 1.6 times more activity in males than in females. Hence the gene acquires at least partial dosage compensation upon insertion into the X chromosome.

}, keywords = {Animals, Chromosomes, DNA Transposable Elements, Dosage Compensation, Drosophila melanogaster, Female, Gene Expression Regulation, Genetic, Ketone Oxidoreductases, Tissue Distribution, Transformation, X Chromosome, Xanthine Dehydrogenase}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Spradling, A C and Rubin, G M} } @article {980, title = {Genetic transformation of Drosophila with transposable element vectors.}, journal = {Science}, volume = {218}, year = {1982}, month = {1982 Oct 22}, pages = {348-53}, abstract = {

Exogenous DNA sequences were introduced into the Drosophila germ line. A rosy transposon (ry1), constructed by inserting a chromosomal DNA fragment containing the wild-type rosy gene into a P transposable element, transformed germ line cells in 20 to 50 percent of the injected rosy mutant embryos. Transformants contained one or two copies of chromosomally integrated, intact ry1 that were stably inherited in subsequent generations. These transformed flies had wild-type eye color indicating that the visible genetic defect in the host strain could be fully and permanently corrected by the transferred gene. To demonstrate the generality of this approach, a DNA segment that does not confer a recognizable phenotype on recipients was also transferred into germ line chromosomes.

}, keywords = {Animals, Chromosome Mapping, DNA Transposable Elements, Drosophila, Genes, Genetic, Genetic Engineering, Mutation, Nucleic Acid Hybridization, Plasmids, Transformation, Xanthine Dehydrogenase}, issn = {0036-8075}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M and Spradling, A C} } @article {981, title = {The molecular basis of P-M hybrid dysgenesis: the role of the P element, a P-strain-specific transposon family.}, journal = {Cell}, volume = {29}, year = {1982}, month = {1982 Jul}, pages = {995-1004}, abstract = {

We have shown previously that four of five white mutant alleles arising in P-M dysgenic hybrids result from the insertion of strongly homologous DNA sequence elements. We have named these P elements. We report that P elements are present in 30-50 copies per haploid genome in all P strains examined and apparently are missing entirely from all M strains examined, with one exception. Furthermore, members of the P family apparently transpose frequently in P-M dysgenic hybrids; chromosomes descendant from P-M dysgenic hybrids frequently show newly acquired P elements. Finally, the strain-specific breakpoint hotspots for the rearrangement of the pi 2 P X chromosome occurring in P-M dysgenic hybrids are apparently sites of residence of P elements. These observations strongly support the P factor hypothesis for the mechanistic basis of P-M hybrid dysgenesis.

}, keywords = {Base Sequence, Biological Evolution, DNA Transposable Elements, Drosophila, Female, Gene Expression Regulation, Genetic, Hybridization, Infertility, Male, Nucleic Acid, Recombination, Repetitive Sequences}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Bingham, P M and Kidwell, M G and Rubin, G M} } @article {982, title = {Cloning of DNA sequences from the white locus of D. melanogaster by a novel and general method.}, journal = {Cell}, volume = {25}, year = {1981}, month = {1981 Sep}, pages = {693-704}, abstract = {

We describe the isolation of a cloned DNA segment carrying unique sequences from the white locus of Drosophila melanogaster. Sequences within the cloned segment are shown to hybridize in situ to the white locus region on the polytene chromosomes of both wild-type strains and strains carrying chromosomal rearrangements whose breakpoints bracket the white locus. We further show that two small deficiency mutations, deleting white locus genetic elements but not those of complementation groups contiguous to white, delete the genomic sequences corresponding to a portion of the cloned segment. The strategy we have employed to isolate this cloned segment exploits the existence of an allele at the white locus containing a copy of a previously cloned transposable, reiterated DNA sequence element. We describe a simple, rapid method for retrieving cloned segments carrying a copy of the transposable element together with contiguous sequences corresponding to this allele. The strategy described is potentially general and we discuss its application to the cloning of the DNA sequences of other genes in Drosophila, including those identified only by genetic analysis and for which no RNA product is known.

}, keywords = {Animals, Bacteriophage lambda, Chromosome Mapping, Cloning, DNA Transposable Elements, Drosophila melanogaster, Genes, Genetic Linkage, Molecular, Nucleic Acid, Nucleic Acid Hybridization, Repetitive Sequences}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Bingham, P M and Levis, R and Rubin, G M} } @article {983, title = {Transposition of elements of the 412, copia and 297 dispersed repeated gene families in Drosophila.}, journal = {Cell}, volume = {17}, year = {1979}, month = {1979 Jun}, pages = {415-27}, abstract = {

The stability of elements of three different dispersed repeated gene families in the genome of Drosophila tissue culture cells has been examined. Different amounts of sequences homologous to elements of 412, copia and 297 dispersed repeated gene families are found in the genomes of D. melanogaster embryonic and tissue culture cells. In general the amount of these sequences is increased in the cell lines. The additional sequences homologous to 412, copia and 297 occur as intact elements and are dispersed to new sites in the cell culture genome. It appears that these elements can insert at many alternative sites. We also describe a DNA sequence arrangement found in the D. melanogaster embryo genome which appears to result from a transposition of an element of the copia dispersed repeated gene family into a new chromosomal site. The mechanism of insertion of this copia element is precise to within 90 bp and may involve a region of weak sequence homology between the site of insertion and the direct terminal repeats of the copia element.

}, keywords = {Animals, Base Sequence, Cells, Cultured, DNA, DNA Restriction Enzymes, Drosophila melanogaster, Genes, Genetic, Nucleic Acid Hybridization, Translocation}, issn = {0092-8674}, doi = {10.1186/gb-2007-8-7-r145}, author = {Potter, S S and Brorein, W J and Dunsmuir, P and Rubin, G M} } @article {984, title = {The nucleotide sequence of Saccharomyces cerevisiae 5.8 S ribosomal ribonucleic acid.}, journal = {The Journal of Biological Chemistry}, volume = {248}, year = {1973}, month = {1973 Jun 10}, pages = {3860-75}, keywords = {Autoradiography, Base Sequence, Chemical Phenomena, Chemistry, Coliphages, Drug Stability, Electrophoresis, Models, Oligonucleotides, Pancreas, Phosphorus Isotopes, Polyacrylamide Gel, Ribonucleases, Ribonucleotides, Ribosomal, RNA, Saccharomyces cerevisiae, Species Specificity, Structural}, issn = {0021-9258}, doi = {10.1186/gb-2007-8-7-r145}, author = {Rubin, G M} }