A drosophila genetic resource of mutants to study mechanisms underlying human genetic diseases

Cell

Volumn 159, Issue 1, 2014, Pages 200-214

  Yamamoto, Shinya ^a,b,c   Jaiswal, Manish ^b,d   Charng, Wu Lin ^a,b   Gambin, Tomasz ^b,e   Karaca, Ender ^b   Mirzaa, Ghayda ^f,g   Wiszniewski, Wojciech ^b,h   Sandoval, Hector ^b   Haelterman, Nele A ^a   Xiong, Bo ^a   Zhang, Ke ^b   Bayat, Vafa ^a   David, Gabriela ^a   Li, Tongchao ^a   Chen, Kuchuan ^a   Gala, Upasana ^a   Harel, Tamar ^b,h   Pehlivan, Davut ^b   Penney, Samantha ^b,h   Vissers, Lisenka E L M ⁱ   De Ligt, Joep ⁱ   Jhangiani, Shalini N ^b   Xie, Yajing ^j   Tsang, Stephen H ^j   Parman, Yesim ^k   Sivaci, Merve ^l   Battaloglu, Esra ^l   Muzny, Donna ^b   Wan, Ying Wooi ^b,c   Liu, Zhandong ^b,c   Lin Moore, Alexander T ^c   Clark, Robin D ^m   Curry, Cynthia J ^n,o   Link, Nichole ^b   Schulze, Karen L ^b,d   Boerwinkle, Eric ^b,p   Dobyns, William B ^f,g,q   Allikmets, Rando ^j   Gibbs, Richard A ^b   Chen, Rui ^a,b   Lupski, James R ^b,h   Wangler, Michael F ^b,h   Bellen, Hugo J ^a,b,c,d   more..

^a BAYLOR COLLEGE OF MEDICINE   (United States)

^b BCM   (United States)

^c Jan and Dan Duncan Neurological Research Institute   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^e WARSAW UNIVERSITY OF TECHNOLOGY   (Poland)

^f UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^g SEATTLE CHILDREN S RESEARCH INSTITUTE   (United States)

^h TEXAS CHILDREN S HOSPITAL   (United States)

ⁱ RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^j Columbia University College of Physicians and Surgeons ^*  (United States)

^k ISTANBUL UNIVERSITY   (Turkey)

^l BOGAZICI UNIVERSITY   (Turkey)

^m LOMA LINDA UNIVERSITY MEDICAL CENTER   (United States)

ⁿ UNIVERSITY OF CALIFORNIA   (United States)

^o Genetic Medicine Central California/UCSF   (United States)

^p UNIVERSITY OF TEXAS   (United States)

^q UNIVERSITY OF WASHINGTON   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

MESYLIC ACID ETHYL ESTER;

ALLELE; APOPTOSIS; ARTICLE; ASYMMETRIC CELL DIVISION; CELL DEATH; CHEMICAL MUTAGENESIS; CHROMOSOME MUTATION; CONTROLLED STUDY; DROSOPHILA; DROSOPHILA OCELLILESS; DROSOPHILA SHIBIRE; EXOME; FEMALE; GENE FREQUENCY; GENE MUTATION; GENETIC CONSERVATION; GENETIC DISORDER; GENETIC RESOURCE; GENETIC SCREENING; GENOMICS; HEREDITARY MOTOR SENSORY NEUROPATHY; HUMAN; IN VIVO STUDY; INSECT GENETICS; MALE; MICROCEPHALY; MITOSIS; MOSAICISM; NERVOUS SYSTEM DEVELOPMENT; NERVOUS SYSTEM FUNCTION; NONHUMAN; PHENOTYPE; RNA INTERFERENCE; X CHROMOSOME; ANIMAL; DISEASE MODEL; DISEASES; DROSOPHILA MELANOGASTER; GENETICS; INHERITANCE;

ANIMALS; DISEASE; DISEASE MODELS, ANIMAL; DROSOPHILA MELANOGASTER; GENETIC TESTING; HUMANS; INHERITANCE PATTERNS; RNA INTERFERENCE; X CHROMOSOME;

EID: 84907561150     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2014.09.002     Document Type: Article

References (72)

1. C. Asencio, I.F. Davidson, R. Santarella-Mellwig, T.B. Ly-Hartig, M. Mall, M.R. Wallenfang, I.W. Mattaj, and M. Gorjánácz Coordination of kinase and phosphatase activities by Lem4 enables nuclear envelope reassembly during mitosis Cell 150 2012 122 135
2. M.N. Bainbridge, W. Wiszniewski, D.R. Murdock, J. Friedman, C. Gonzaga-Jauregui, I. Newsham, J.G. Reid, J.K. Fink, M.B. Morgan, and M.C. Gingras Whole-genome sequencing for optimized patient management Sci. Transl. Med. 3 2011 re3
3. M.J. Bamshad, J.A. Shendure, D. Valle, A. Hamosh, J.R. Lupski, R.A. Gibbs, E. Boerwinkle, R.P. Lifton, M. Gerstein, M. Gunel Centers for Mendelian Genomics The Centers for Mendelian Genomics: a new large-scale initiative to identify the genes underlying rare Mendelian conditions Am. J. Med. Genet. A. 158A 2012 1523 1525
4. V. Bayat, I. Thiffault, M. Jaiswal, M. Tétreault, T. Donti, F. Sasarman, G. Bernard, J. Demers-Lamarche, M.J. Dicaire, and J. Mathieu Mutations in the mitochondrial methionyl-tRNA synthetase cause a neurodegenerative phenotype in flies and a recessive ataxia (ARSAL) in humans PLoS Biol. 10 2012 e1001288
5. H.J. Bellen, C. Tong, and H. Tsuda 100 years of Drosophila research and its impact on vertebrate neuroscience: a history lesson for the future Nat. Rev. Neurosci. 11 2010 514 522
6. P.V. Benos, M.K. Gatt, L. Murphy, D. Harris, B. Barrell, C. Ferraz, S. Vidal, C. Brun, J. Demaille, and E. Cadieu From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies Genome Res. 11 2001 710 730
7. E. Bier Drosophila, the golden bug, emerges as a tool for human genetics Nat. Rev. Genet. 6 2005 9 23
8. J. Bischof, R.K. Maeda, M. Hediger, F. Karch, and K. Basler An optimized transgenesis system for Drosophila using germ-line-specific phiC31 integrases Proc. Natl. Acad. Sci. USA 104 2007 3312 3317
9. C. Bökel EMS screens: from mutagenesis to screening and mapping Methods Mol. Biol. 420 2008 119 138
10. J. Ceron, C. González, and F.J. Tejedor Patterns of cell division and expression of asymmetric cell fate determinants in postembryonic neuroblast lineages of Drosophila Dev. Biol. 230 2001 125 138
11. W.L. Charng, S. Yamamoto, and H.J. Bellen Shared mechanisms between Drosophila peripheral nervous system development and human neurodegenerative diseases Curr. Opin. Neurobiol. 27C 2014 158 164
12. R.K. Cook, M.E. Deal, J.A. Deal, R.D. Garton, C.A. Brown, M.E. Ward, R.S. Andrade, E.P. Spana, T.C. Kaufman, and K.R. Cook A new resource for characterizing X-linked genes in Drosophila melanogaster: systematic coverage and subdivision of the X chromosome with nested, Y-linked duplications Genetics 186 2010 1095 1109
13. C.F. Cullen, A.L. Brittle, T. Ito, and H. Ohkura The conserved kinase NHK-1 is essential for mitotic progression and unifying acentrosomal meiotic spindles in Drosophila melanogaster J. Cell Biol. 171 2005 593 602
14. K. Emoto Signaling mechanisms that coordinate the development and maintenance of dendritic fields Curr. Opin. Neurobiol. 22 2012 805 811
15. C. Gonzaga-Jauregui, T. Lotze, L. Jamal, S. Penney, I.M. Campbell, D. Pehlivan, J.V. Hunter, S.L. Woodbury, G. Raymond, and A.M. Adesina Mutations in VRK1 associated with complex motor and sensory axonal neuropathy plus microcephaly JAMA Neurol. 70 2013 1491 1498
16. E.W. Green, G. Fedele, F. Giorgini, and C.P. Kyriacou A Drosophila RNAi collection is subject to dominant phenotypic effects Nat. Methods 11 2014 222 223
17. N. Haelterman, L. Jiang, S. Li, V. Bayat, B. Ugur, K.L. Tan, K. Zhang, D. Bei, B. Xiong, and W.L. Charng Large-scale identification of chemically induced mutations in Drosophila melanogaster Genome Res. 24 2014 1707 1718
18. A. Hamosh, N. Sobreira, J. Hoover-Fong, V.R. Sutton, C. Boehm, F. Schiettecatte, and D. Valle PhenoDB: a new web-based tool for the collection, storage, and analysis of phenotypic features Hum. Mutat. 34 2013 566 571
19. L. Huang, X. Xiao, S. Li, X. Jia, P. Wang, X. Guo, and Q. Zhang CRX variants in cone-rod dystrophy and mutation overview Biochem. Biophys. Res. Commun. 426 2012 498 503
20. H. Jafar-Nejad, H.K. Andrews, M. Acar, V. Bayat, F. Wirtz-Peitz, S.Q. Mehta, J.A. Knoblich, and H.J. Bellen Sec15, a component of the exocyst, promotes notch signaling during the asymmetric division of Drosophila sensory organ precursors Dev. Cell 9 2005 351 363
21. M. Jaiswal, H. Sandoval, K. Zhang, V. Bayat, and H.J. Bellen Probing mechanisms that underlie human neurodegenerative diseases in Drosophila Annu. Rev. Genet. 46 2012 371 396
22. A.M. Kaindl, S. Passemard, P. Kumar, N. Kraemer, L. Issa, A. Zwirner, B. Gerard, A. Verloes, S. Mani, and P. Gressens Many roads lead to primary autosomal recessive microcephaly Prog. Neurobiol. 90 2010 363 383
23. E. Karaca, S. Weitzer, D. Pehlivan, H. Shiraishi, T. Gogakos, T. Hanada, S.N. Jhangiani, W. Wiszniewski, M. Withers, I.M. Campbell Baylor Hopkins Center for Mendelian Genomics Human CLP1 mutations alter tRNA biogenesis, affecting both peripheral and central nervous system function Cell 157 2014 636 650
24. B. Lehner Genotype to phenotype: lessons from model organisms for human genetics Nat. Rev. Genet. 14 2013 168 178
25. T.S. Liao, G.B. Call, P. Guptan, A. Cespedes, J. Marshall, K. Yackle, E. Owusu-Ansah, S. Mandal, Q.A. Fang, and G.L. Goodstein An efficient genetic screen in Drosophila to identify nuclear-encoded genes with mitochondrial function Genetics 174 2006 525 533
26. X. Liu, X. Jian, and E. Boerwinkle dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions Hum. Mutat. 32 2011 894 899
27. B. Lu, and H. Vogel Drosophila models of neurodegenerative diseases Annu. Rev. Pathol. 4 2009 315 342
28. J.R. Lupski, J.W. Belmont, E. Boerwinkle, and R.A. Gibbs Clan genomics and the complex architecture of human disease Cell 147 2011 32 43
29. J.R. Lupski, C. Gonzaga-Jauregui, Y. Yang, M.N. Bainbridge, S. Jhangiani, C.J. Buhay, C.L. Kovar, M. Wang, A.C. Hawes, and J.G. Reid Exome sequencing resolves apparent incidental findings and reveals further complexity of SH3TC2 variant alleles causing Charcot-Marie-Tooth neuropathy Genome Med 5 2013 57
30. S.J. Marygold, P.C. Leyland, R.L. Seal, J.L. Goodman, J. Thurmond, V.B. Strelets, R.J. Wilson FlyBase consortium FlyBase: improvements to the bibliography Nucleic Acids Res. 41 Database issue 2013 D751 D757
31. K.L. McGary, T.J. Park, J.O. Woods, H.J. Cha, J.B. Wallingford, and E.M. Marcotte Systematic discovery of nonobvious human disease models through orthologous phenotypes Proc. Natl. Acad. Sci. USA 107 2010 6544 6549
32. S.E. Mohr RNAi screening in Drosophila cells and in vivo Methods 68 2014 82 88
33. J.L. Mummery-Widmer, M. Yamazaki, T. Stoeger, M. Novatchkova, S. Bhalerao, D. Chen, G. Dietzl, B.J. Dickson, and J.A. Knoblich Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi Nature 458 2009 987 992
34. G.G. Neely, A. Hess, M. Costigan, A.C. Keene, S. Goulas, M. Langeslag, R.S. Griffin, I. Belfer, F. Dai, and S.B. Smith A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene Cell 143 2010 628 638
35. T.P. Newsome, B. Asling, and B.J. Dickson Analysis of Drosophila photoreceptor axon guidance in eye-specific mosaics Development 127 2000 851 860
36. C. Nüsslein-Volhard, and E. Wieschaus Mutations affecting segment number and polarity in Drosophila Nature 287 1980 795 801
37. M.A. Oortveld, S. Keerthikumar, M. Oti, B. Nijhof, A.C. Fernandes, K. Kochinke, A. Castells-Nobau, E. van Engelen, T. Ellenkamp, and L. Eshuis Human intellectual disability genes form conserved functional modules in Drosophila PLoS Genet. 9 2013 e1003911
38. J.C. Pastor-Pareja, and T. Xu Dissecting social cell biology and tumors using Drosophila genetics Annu. Rev. Genet. 47 2013 51 74
39. M.A. Rujano, L. Sanchez-Pulido, C. Pennetier, G. le Dez, and R. Basto The microcephaly protein Asp regulates neuroepithelium morphogenesis by controlling the spatial distribution of myosin II Nat. Cell Biol. 15 2013 1294 1306
40. A. Saj, Z. Arziman, D. Stempfle, W. van Belle, U. Sauder, T. Horn, M. Dürrenberger, R. Paro, M. Boutros, and G. Merdes A combined ex vivo and in vivo RNAi screen for notch regulators in Drosophila reveals an extensive notch interaction network Dev. Cell 18 2010 862 876
41. S. Saksena, and S.D. Emr ESCRTs and human disease Biochem. Soc. Trans. 37 2009 167 172
42. A.E. Schaffer, V.R. Eggens, A.O. Caglayan, M.S. Reuter, E. Scott, N.G. Coufal, J.L. Silhavy, Y. Xue, H. Kayserili, and K. Yasuno CLP1 founder mutation links tRNA splicing and maturation to cerebellar development and neurodegeneration Cell 157 2014 651 663
43. E.R. Vandendries, D. Johnson, and R. Reinke orthodenticle is required for photoreceptor cell development in the Drosophila eye Dev. Biol. 173 1996 243 255
44. K.J. Venken, Y. He, R.A. Hoskins, and H.J. Bellen P[acman]: a BAC transgenic platform for targeted insertion of large DNA fragments in D. melanogaster Science 314 2006 1747 1751
45. K.J. Venken, E. Popodi, S.L. Holtzman, K.L. Schulze, S. Park, J.W. Carlson, R.A. Hoskins, H.J. Bellen, and T.C. Kaufman A molecularly defined duplication set for the X chromosome of Drosophila melanogaster Genetics 186 2010 1111 1125
46. T. Wang, and C. Montell Phototransduction and retinal degeneration in Drosophila Pflugers Arch. 454 2007 821 847
47. J.K. White, A.K. Gerdin, N.A. Karp, E. Ryder, M. Buljan, J.N. Bussell, J. Salisbury, S. Clare, N.J. Ingham, C. Podrini Sanger Institute Mouse Genetics Project Genome-wide generation and systematic phenotyping of knockout mice reveals new roles for many genes Cell 154 2013 452 464
48. S. Yamamoto, and E.S. Seto Dopamine dynamics and signaling in Drosophila: an overview of genes, drugs and behavioral paradigms Exp. Anim. 63 2014 107 119
49. M.N. Bainbridge, M. Wang, Y. Wu, I. Newsham, D.M. Muzny, J.L. Jefferies, T.J. Albert, D.L. Burgess, and R.A. Gibbs Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities Genome Biol. 12 2011 R68
50. K. Blochlinger, R. Bodmer, L.Y. Jan, and Y.N. Jan Patterns of expression of cut, a protein required for external sensory organ development in wild-type and cut mutant Drosophila embryos Genes Dev. 4 1990 1322 1331
51. G.B. Call, J.M. Olson, J. Chen, N. Villarasa, K.T. Ngo, A.M. Yabroff, S. Cokus, M. Pellegrini, E. Bibikova, and C. Bui Genomewide clonal analysis of lethal mutations in the Drosophila melanogaster eye: comparison of the X chromosome and autosomes Genetics 177 2007 689 697
52. C. Chabu, and C.Q. Doe Dap160/intersectin binds and activates aPKC to regulate cell polarity and cell cycle progression Development 135 2008 2739 2746
53. D. Challis, J. Yu, U.S. Evani, A.R. Jackson, S. Paithankar, C. Coarfa, A. Milosavljevic, R.A. Gibbs, and F. Yu An integrative variant analysis suite for whole exome next-generation sequencing data BMC Bioinformatics 13 2012 8
54. R.K. Cook, S.J. Christensen, J.A. Deal, R.A. Coburn, M.E. Deal, J.M. Gresens, T.C. Kaufman, and K.R. Cook The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome Genome Biol. 13 2012 R21
55. P. Danecek, A. Auton, G. Abecasis, C.A. Albers, E. Banks, M.A. DePristo, R.E. Handsaker, G. Lunter, G.T. Marth, S.T. Sherry 1000 Genomes Project Analysis Group The variant call format and VCFtools Bioinformatics 27 2011 2156 2158
56. G. Dennis Jr., B.T. Sherman, D.A. Hosack, J. Yang, W. Gao, H.C. Lane, and R.A. Lempicki DAVID: Database for Annotation, Visualization, and Integrated Discovery Genome Biol. 4 2003 3
57. C.L. Freund, Q.L. Wang, S. Chen, B.L. Muskat, C.D. Wiles, V.C. Sheffield, S.G. Jacobson, R.R. McInnes, D.J. Zack, and E.M. Stone De novo mutations in the CRX homeobox gene associated with Leber congenital amaurosis Nat. Genet. 18 1998 311 312
58. E. Gallardo, K.G. Claeys, E. Nelis, A. García, A. Canga, O. Combarros, V. Timmerman, P. De Jonghe, and J. Berciano Magnetic resonance imaging findings of leg musculature in Charcot-Marie-Tooth disease type 2 due to dynamin 2 mutation J. Neurol. 255 2008 986 992
59. J.G. Heuer, K. Li, and T.C. Kaufman The Drosophila homeotic target gene centrosomin (cnn) encodes a novel centrosomal protein with leucine zippers and maps to a genomic region required for midgut morphogenesis Development 121 1995 3861 3876
60. V.B. Kitiratschky, D. Nagy, T. Zabel, E. Zrenner, B. Wissinger, S. Kohl, and H. Jägle Cone and cone-rod dystrophy segregating in the same pedigree due to the same novel CRX gene mutation Br. J. Ophthalmol. 92 2008 1086 1091
61. T. Lee, and L. Luo Mosaic analysis with a repressible cell marker for studies of gene function in neuronal morphogenesis Neuron 22 1999 451 461
62. H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
63. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
64. D.L. Lindsley, and G.G. Zimm The Genome of Drosophila melanogaster 1992 Academic Press San Diego
65. E.M. O'Neill, I. Rebay, R. Tjian, and G.M. Rubin The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway Cell 78 1994 137 147
66. A.L. Parks, K.R. Cook, M. Belvin, N.A. Dompe, R. Fawcett, K. Huppert, L.R. Tan, C.G. Winter, K.P. Bogart, and J.E. Deal Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genome Nat. Genet. 36 2004 288 292
67. E. Silva, J.M. Yang, Y. Li, S. Dharmaraj, O.H. Sundin, and I.H. Maumenee A CRX null mutation is associated with both Leber congenital amaurosis and a normal ocular phenotype Invest. Ophthalmol. Vis. Sci. 41 2000 2076 2079
68. A. Untergasser, I. Cutcutache, T. Koressaar, J. Ye, B.C. Faircloth, M. Remm, and S.G. Rozen Primer3 - new capabilities and interfaces Nucleic Acids Res. 40 2012 e115
69. M.W. Wright, T.A. Eyre, M.J. Lush, S. Povey, and E.A. Bruford HCOP: the HGNC comparison of orthology predictions search tool Mamm. Genome 16 2005 827 828
70. B. Xiong, V. Bayat, M. Jaiswal, K. Zhang, H. Sandoval, W.L. Charng, T. Li, G. David, L. Duraine, and Y.Q. Lin Crag is a GEF for Rab11 required for rhodopsin trafficking and maintenance of adult photoreceptor cells PLoS Biol. 10 2012 e1001438
71. S. Yamamoto, W.L. Charng, N.A. Rana, S. Kakuda, M. Jaiswal, V. Bayat, B. Xiong, K. Zhang, H. Sandoval, and G. David A mutation in EGF repeat-8 of Notch discriminates between Serrate/Jagged and Delta family ligands Science 338 2012 1229 1232
72. S. Züchner, M. Noureddine, M. Kennerson, K. Verhoeven, K. Claeys, P. De Jonghe, J. Merory, S.A. Oliveira, M.C. Speer, and J.E. Stenger Mutations in the pleckstrin homology domain of dynamin 2 cause dominant intermediate Charcot-Marie-Tooth disease Nat. Genet. 37 2005 289 294