With the vast amount of genomic sequence from a wide variety of organisms, the next major challenge in genomics is to identify and assemble complete protein sets for each. At the Berkeley Drosophila Genome Project (BDGP) we are actively generating a comprehensive cDNA resource, the Drosophila Gene Collection (DGC) that will contain at least one cDNA for each of the ~14,000 annotated protein-coding genes. Our cDNA collection has greatly accelerated progress towards a comprehensive transcript map of all Drosophila genes and is being used to determine gene expression patterns in the embryo. Presently, 9,020 cDNA clones representing two-thirds of the currently annotated genes comprise the DGC Gold Collection, which is a set of full-length cDNAs that are free of nonsense and missense mutations. We have used a little over half of the Gold cDNA clones to construct two collections of universal donor clones, one with and one without the native stop codon. We propose to extend these collections with the existing and anticipated additional clones in the DGC Gold set these collections are and will continue to be the primary source of high quality Drosophila melanogaster open reading frames (ORFs) that are easily transferred into a number of different expression vectors. Further, we plan to use the donor clones to make three sets of expression clones. Two are designed for use in tissue culture cells, one epitope-tagged for protein purification studies and the other untagged for gain-of-function screens to complement ongoing RNAi screens. The third is designed to produce transgenic flies with epitope-tagged proteins for in vivo studies of expression, localization and purification of endogenous complexes. The clones are available without restrictions to all researchers.
Our goals are to obtain a more detailed understanding of the complete set of proteins that are encoded by the Drosophila genome and to provide resources for functional genomics and proteomics to the research community. These clone resources will be used to further our understanding of conserved genes, pathways and cellular differentiation in higher eukaryotes with broad implications for improvements in human health.
| Guruharsha, K G; Hori, Kazuya; Obar, Robert A et al. (2014) Proteomic analysis of the Notch interactome. Methods Mol Biol 1187:181-92 |
| Rhee, David Y; Cho, Dong-Yeon; Zhai, Bo et al. (2014) Transcription factor networks in Drosophila melanogaster. Cell Rep 8:2031-2043 |
| Özkan, Engin; Carrillo, Robert A; Eastman, Catharine L et al. (2013) An extracellular interactome of immunoglobulin and LRR proteins reveals receptor-ligand networks. Cell 154:228-39 |
| Enuameh, Metewo Selase; Asriyan, Yuna; Richards, Adam et al. (2013) Global analysis of Drosophila Cys?-His? zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants. Genome Res 23:928-40 |
| Guruharsha, K G; Obar, Robert A; Mintseris, Julian et al. (2012) Drosophila protein interaction map (DPiM): a paradigm for metazoan protein complex interactions. Fly (Austin) 6:246-53 |
| Hens, Korneel; Feuz, Jean-Daniel; Isakova, Alina et al. (2011) Automated protein-DNA interaction screening of Drosophila regulatory elements. Nat Methods 8:1065-70 |
| Guruharsha, K G; Rual, Jean-Francois; Zhai, Bo et al. (2011) A protein complex network of Drosophila melanogaster. Cell 147:690-703 |
| Yu, Charles; Wan, Kenneth H; Hammonds, Ann S et al. (2011) Development of expression-ready constructs for generation of proteomic libraries. Methods Mol Biol 723:257-72 |
