Fly Base portals to human disease research using Drosophila Models

DMM Disease Models and Mechanisms

Volumn 9, Issue 3, 2016, Pages 245-252

  Millburn, Gillian H ^a   Crosby, Madeline A ^b   Gramates, L Sian ^b   Tweedie, Susan ^c   Gelbart, William ^d   Perrimon, Norbert ^d   Extavour, Cassandra ^d   Broll, Kris ^d   Dos Santos, Gilberto ^d   Emmert, David ^d   Falls, Kathleen ^d   Matthews, Beverley ^d   Gelbart, Susan Russo ^d   Schroeder, Andrew ^d   Tabone, Christopher ^d   Zhou, Pinglei ^d   Zytkovicz, Mark ^d   Brown, Nicholas ^d   Antonazzo, Giulia ^d   Attrill, Helen ^d   Costa, Marta ^d   Marygold, Steven ^d   Ponting, Laura ^d   Rey, Alix ^d   Staudt, Nicole ^d   Stefancsik, Raymund ^d   Urbano, Jose Maria ^d   Kaufman, Thomas ^d   Goodman, Joshua ^d   Grumbling, Gary ^d   Strelets, Victor ^d   Thurmond, Jim ^d   Cripps, Richard ^d   Werner Washburne, Maggie ^d   Baker, Phillip ^d   more..

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b HARVARD UNIVERSITY   (United States)

^c EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^d NONE

Author keywords

Disease model; Drosophila; Flybase; Online resource

Indexed keywords

ARTICLE; DISEASE MODEL; DISEASE ONTOLOGY; DROSOPHILA; FRUIT FLY MODEL; HUMAN; MEDICAL RESEARCH; MEDICAL TERMINOLOGY; NONHUMAN; PRIORITY JOURNAL; WEB BROWSER; AMYOTROPHIC LATERAL SCLEROSIS; ANIMAL; DISEASES; DROSOPHILA MELANOGASTER; GENETIC DATABASE; PATHOLOGY; PHYSIOLOGY;

AMYOTROPHIC LATERAL SCLEROSIS; ANIMALS; BIOMEDICAL RESEARCH; DATABASES, GENETIC; DISEASE; DISEASE MODELS, ANIMAL; DROSOPHILA MELANOGASTER; HUMANS;

EID: 84961755109     PISSN: 17548403     EISSN: 17548411     Source Type: Journal    
DOI: 10.1242/dmm.023317     Document Type: Article

References (40)

1. Bassett, A. R. and Liu, J.-L. (2014). CRISPR/Cas9 and genome editing in Drosophila. J. Genet. Genomics 41, 7-19.
2. Bassett, A. R., Tibbit, C., Ponting, C. P. and Liu, J.-L. (2013). Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system. Cell Rep. 4, 220-228.
3. Bellen, H. J., Levis, R. W., Liao, G., He, Y., Carlson, J. W., Tsang, G., Evans- Holm, M., Hiesinger, P. R., Schulze, K. L., Rubin, G. M. et al. (2004). The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 167, 761-781.
4. Bellen, H. J., Levis, R. W., He, Y., Carlson, J. W., Evans-Holm, M., Bae, E., Kim, J., Metaxakis, A., Savakis, C., Schulze, K. L. et al. (2011). The Drosophila gene disruption project: progress using transposons with distinctive site specificities. Genetics 188, 731-743.
5. Beumer, K. J. and Carroll, D. (2014). Targeted genome engineering techniques in Drosophila. Methods 68, 29-37.
6. Boutros, M., Kiger, A. A., Armknecht, S., Kerr, K., Hild, M., Koch, B., Haas, S. A., Heidelberg Fly, Array Consortium, Paro, R. and Perrimon, N. (2004). Genomewide RNAi analysis of growth and viability in Drosophila cells. Science 303, 832-835.
7. Buszczak, M., Paterno, S., Lighthouse, D., Bachman, J., Planck, J., Owen, S., Skora, A. D., Nystul, T. G., Ohlstein, B., Allen, A. et al. (2007). The Carnegie protein trap library: A versatile tool for Drosophila developmental studies. Genetics 175, 1505-1531.
8. Dietzl, G., Chen, D., Schnorrer, F., Su, K.-C., Barinova, Y., Fellner, M., Gasser, B., Kinsey, K., Oppel, S., Scheiblauer, S. et al. (2007). A genome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448, 151-156.
9. dos Santos, G., Schroeder, A. J., Goodman, J. L., Strelets, V. B., Crosby, M. A., Thurmond, J., Emmert, D. B., Gelbart, W. M. and the FlyBase Consortium. (2015). FlyBase: introduction of the Drosophila melanogasterRelease 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res. 43, D690-D697.
10. Ejsmont, R. K. and Hassan, B. A. (2014). The little fly that could: Wizardry and artistry of Drosophila genomics. Genes 5, 385-414.
11. Feany, M. B. and Bender, W. W. (2000). A Drosophila model of Parkinson's disease. Nature 404, 394-398.
12. Flockhart, I. T., Booker, M., Hu, Y., McElvany, B., Gilly, Q., Mathey-Prevot, B., Perrimon, N. and Mohr, S. E. (2012). FlyRNAi.org-the database of the Drosophila RNAi screening center: 2012 update. Nucleic Acids Res. 40, D715-D719.
13. Gratz, S. J., Cummings, A. M., Nguyen, J. N., Hamm, D. C., Donohue, L. K., Harrison, M. M., Wildonger, J. and O'Connor-Giles, K. M. (2013). Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics 194, 1029-1035.
14. Gray, K. A., Yates, B., Seal, R. L., Wright, M. W. and Bruford, E. A. (2015). Genenames.org: The HGNC resources in 2015. Nucleic Acids Res. 43, D1079-D1085.
15. Hu, Y., Flockhart, I., Vinayagam, A., Bergwitz, C., Berger, B., Perrimon, N. and Mohr, S. E. (2011). An integrative approach to ortholog prediction for diseasefocused and other functional studies. BMC Bioinformatics 12, 357.
16. Jackson, G. R., Salecker, I., Dong, X., Yao, X., Arnheim, N., Faber, P. W., MacDonald, M. E. and Zipursky, S. L. (1998). Polyglutamine-expanded human huntingtin transgenes induce degeneration of Drosophila photoreceptor neurons. Neuron 21, 633-642.
17. Jaiswal, M., Sandoval, H., Zhang, K., Bayat, V. and Bellen, H. J. (2012). Probing mechanisms that underlie human neurodegenerative diseases in Drosophila. Annu. Rev. Genet. 46, 371-396.
18. Kibbe, W. A., Arze, C., Felix, V., Mitraka, E., Bolton, E., Fu, G., Mungall, C. J., Binder, J. X., Malone, J., Vasant, D. et al. (2015). Disease Ontology 2015 update: An expanded and updated database of human diseases for linking biomedical knowledge through disease data. Nucleic Acids Res. 43, D1071-D1078.
19. Kishita, Y., Tsuda, M. and Aigaki, T. (2012). Impaired fatty acid oxidation in a Drosophila model of mitochondrial trifunctional protein (MTP) deficiency. Biochem. Biophys. Res. Commun. 419, 344-349.
20. Kondo, S. and Ueda, R. (2013). Highly improved gene targeting by germlinespecific Cas9 expression in Drosophila. Genetics 195, 715-721.
21. Li, Y. R., King, O. D., Shorter, J. and Gitler, A. D. (2013). Stress granules as crucibles of ALS pathogenesis. J. Cell Biol. 201, 361-372.
22. Lü cking, C. B., Dü rr, A., Bonifati, V., Vaughan, J., De Michele, G., Gasser, T., Harhangi, B. S., Meco, G., Denèfle, P., Wood, N. W. et al. (2000). Association between early-onset Parkinson's disease and mutations in the parkin gene. N. Engl. J. Med. 342, 1560-1567.
23. McGary, K. L., Park, T. J., Woods, J. O., Cha, H. J., Wallingford, J. B. and Marcottea, E. M. (2010). Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proc. Natl. Acad. Sci. USA 107, 6544-6549.
24. Mohr, S. E., Hu, Y., Kim, K., Housden, B. E. and Perrimon, N. (2014). Resources for functional genomics studies in Drosophila melanogaster. Genetics 197, 1-18.
25. Morin, X., Daneman, R., Zavortink, M. and Chia, W. (2001). A protein trap strategy to detect GFP-tagged proteins expressed from their endogenous loci in Drosophila. Proc. Natl. Acad. Sci. USA 98, 15050-15055.
26. Mounkes, L. C., Jones, R. S., Liang, B.-C., Gelbart, W. and Fuller, M. T. (1992). A Drosophila model for xeroderma pigmentosum and Cockayne's syndrome: haywire encodes the fly homolog of ERCC3, a human excision repair gene. Cell 71, 925-937.
27. Nagarkar-Jaiswal, S., Lee, P.-T., Campbell, M. E., Chen, K., Anguiano-Zarate, S., Gutierrez, M. C., Busby, T., Lin, W.-W., He, Y., Schulze, K. L. et al. (2015). A library of MiMICs allows tagging of genes and reversible, spatial and temporal knockdown of proteins in Drosophila. Elife 4, e05338.
28. Ni, J.-Q., Zhou, R., Czech, B., Liu, L.-P., Holderbaum, L., Yang-Zhou, D., Shim, H.-S., Tao, R., Handler, D., Karpowicz, P. et al. (2011). A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat. Methods 8, 405-407.
29. Pagliarini, D. J., Calvo, S. E., Chang, B., Sheth, S. A., Vafai, S. B., Ong, S.-E., Walford, G. A., Sugiana, C., Boneh, A., Chen, W. K. et al. (2008). A mitochondrial protein compendium elucidates complex I disease biology. Cell 134, 112-123.
30. Phillips, J. P., Tainer, J. A., Getzoff, E. D., Boulianne, G. L., Kirby, K. and Hilliker, A. J. (1995). Subunit-destabilizing mutations in Drosophila copper/zinc superoxide dismutase: neuropathology and a model of dimer dysequilibrium. Proc. Natl. Acad. Sci. USA 92, 8574-8578.
31. Ren, X., Sun, J., Housden, B. E., Hu, Y., Roesel, C., Lin, S., Liu, L.-P., Yang, Z., Mao, D., Sun, L. et al. (2013). Optimized gene editing technology for Drosophila melanogaster using germ line-specific Cas9. Proc. Natl. Acad. Sci. USA 110, 19012-19017.
32. Sebo, Z. L., Lee, H. B., Peng, Y. and Guo, Y. (2014). A simplified and efficient germline-specific CRISPR/Cas9 system for Drosophila genomic engineering. Fly 8, 52-57.
33. Søndergaard, L. (1993). Homology between the mammalian liver and the Drosophila fat body. Trends Genet. 9, 193.
34. Stapleton, M., Carlson, J., Brokstein, P., Yu, C., Champe, M., George, R., Guarin, H., Kronmiller, B., Pacleb, J., Park, S. et al. (2002). A Drosophila fulllength cDNA resource. Genome Biol. 3, research0080.1-research0080.8.
35. Wang, C., Lu, R., Ouyang, X., Ho, M.W. L., Chia, W., Yu, F. and Lim, K.-L. (2007). Drosophila overexpressing parkin R275W mutant exhibits dopaminergic neuron degeneration and mitochondrial abnormalities. J. Neurosci. 27, 8563-8570.
36. Warrick, J. M., Paulson, H. L., Gray-Board, G. L., Bui, Q. T., Fischbeck, K. H., Pittman, R. N. and Bonini, N. M. (1998). Expanded polyglutamine protein forms nuclear inclusions and causes neural degeneration in Drosophila. Cell 93, 939-949.
37. Waterhouse, R. M., Tegenfeldt, F., Li, J., Zdobnov, E. M. and Kriventseva, E. V. (2013). OrthoDB: A hierarchical catalog of animal, fungal and bacterial orthologs. Nucleic Acids Res. 41, D358-D365.
38. West, A., Periquet, M., Lincoln, S., Lü cking, C. B., Nicholl, D., Bonifati, V., Rawal, N., Gasser, T., Lohmann, E., Deleuze, J.-F. et al. (2002). Complex relationship between Parkin mutations and Parkinson disease. Am. J. Med. Genet. 114, 584-591.
39. Yu, Z., Ren, M., Wang, Z., Zhang, B., Rong, Y. S., Jiao, R. and Gao, G. (2013). Highly efficient genome modifications mediated by CRISPR/Cas9 in Drosophila. Genetics 195, 289-291.
40. Zhang, K., Li, Z., Jaiswal, M., Bayat, V., Xiong, B., Sandoval, H., Charng, W.-L., David, G., Haueter, C., Yamamoto, S. et al. (2013). The C8ORF38 homologue Sicily is a cytosolic chaperone for a mitochondrial complex I subunit. J. Cell Biol. 200, 807-820.