Nature Genetics
36, 288 - 292 (2004)
Published online: 22 February 2004; | doi:10.1038/ng1312
Systematic generation of high-resolution deletion coverage of the Drosophila melanogaster genomeAnnette L Parks1, 4, Kevin R Cook2, 4, Marcia Belvin1, 4, Nicholas A Dompe1, Robert Fawcett1, Kari Huppert1, 3, Lory R Tan1, Christopher G Winter1, Kevin P Bogart2, Jennifer E Deal2, Megan E Deal-Herr2, Deanna Grant1, Marie Marcinko1, 3, Wesley Y Miyazaki1, Stephanie Robertson1, Kenneth J Shaw1, Mariano Tabios1, Valentina Vysotskaia1, Lora Zhao1, Rachel S Andrade2, Kyle A Edgar1, Elizabeth Howie1, Keith Killpack1, Brett Milash1, 3, Amanda Norton1, Doua Thao1, Kellie Whittaker1, Millicent A Winner2, 3, Lori Friedman1, Jonathan Margolis1, Matthew A Singer1, 3, Casey Kopczynski1, 3, Daniel Curtis1, 3, Thomas C Kaufman2, Gregory D Plowman1, Geoffrey Duyk1
& Helen L Francis-Lang11
Exelixis, 170 Harbor Way, South San Francisco, California 94083-0511, USA. 2
Bloomington Drosophila Stock Center, Department of Biology, Indiana University, 1001 E. Third St. Bloomington, Indiana 47405-3700, USA. 3
Present addresses: Department of Molecular Biology and Pharmacology, Washington University School of Medicine, Campus Box 8103, 660 S. Euclid Ave., St Louis, Missouri 63110, USA (K.H.); Scripps Research Institute, 10550 N. Torrey Pines, SP 145, La Jolla, California 92037, USA (M.M.); Huntsman Cancer Institute, 2000 Circle of Hope, University of Utah, Salt Lake City, Utah 84132, USA (B.M.); Department of Medicine, University of Louisville, Baxter II, Room 334, 570 S. Preston St., Louisville, Kentucky 40202, USA (M.A.W.); Chemicon International, 28820 Single Oak Drive, Temecula, California, 92590, USA (M.A.S.); Ercole Biotech, 7030 Kit Creek Road, P.O. Box 12295, Research Triangle Park, North Carolina 27709, USA (C.K.); Novartis Institutes for BioMedical Research, Developmental & Molecular Pathways, 100 Technology Square, Office 5653, Cambridge, Massachusetts 02139, USA (D.C.). 4
These authors contributed equally to this work.
Correspondence should be addressed to Kevin R Cook kcook@bio.indiana.eduIn fruit fly research, chromosomal deletions are indispensable tools for mapping mutations, characterizing alleles and identifying interacting loci. Most widely used deletions were generated by irradiation or chemical mutagenesis. These methods are labor-intensive, generate random breakpoints and result in unwanted secondary mutations that can confound phenotypic analyses. Most of the existing deletions are large, have molecularly undefined endpoints and are maintained in genetically complex stocks. Furthermore, the existence of haplolethal or haplosterile loci makes the recovery of deletions of certain regions exceedingly difficult by traditional methods, resulting in gaps in coverage. Here we describe two methods that address these problems by providing for the systematic isolation of targeted deletions in the D. melanogaster genome. The first strategy used a P element−based technique to generate deletions that closely flank haploinsufficient genes and minimize undeleted regions. This deletion set has increased overall genomic coverage by 5−7%. The second strategy used FLP recombinase and the large array of FRT-bearing insertions described in the accompanying paper1 to generate 519 isogenic deletions with molecularly defined endpoints. This second deletion collection provides 56% genome coverage so far. The latter methodology enables the generation of small custom deletions with predictable endpoints throughout the genome and should make their isolation a simple and routine task.
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