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Deletions, commonly referred to as deficiencies by Drosophila geneticists, are valuable tools for mapping genes and for genetic pathway discovery via dose-dependent suppressor and enhancer screens. More recently, it has become clear that deviations from normal gene dosage are associated with multiple disorders in a range of species including humans. While we are beginning to understand some of the transcriptional effects brought about by gene dosage changes and the chromosome rearrangement breakpoints associated with them, much of this work relies on isolated examples. We have systematically examined deficiencies of the left arm of chromosome 2 and characterize gene-by-gene dosage responses that vary from collapsed expression through modest partial dosage compensation to full or even over compensation. We found negligible long-range effects of creating novel chromosome domains at deletion breakpoints, suggesting that cases of gene regulation due to altered nuclear architecture are rare. These rare cases include trans de-repression when deficiencies delete chromatin characterized as repressive in other studies. Generally, effects of breakpoints on expression are promoter proximal (~100bp) or in the gene body. Effects of deficiencies genome-wide are in genes with regulatory relationships to genes within the deleted segments, highlighting the subtle expression network defects in these sensitized genetic backgrounds., Competing Interests: The authors have declared that no competing interests exist.

Animal transcriptomes are dynamic, with each cell type, tissue and organ system expressing an ensemble of transcript isoforms that give rise to substantial diversity. Here we have identified new genes, transcripts and proteins using poly(A)+ RNA sequencing from Drosophila melanogaster in cultured cell lines, dissected organ systems and under environmental perturbations. We found that a small set of mostly neural-specific genes has the potential to encode thousands of transcripts each through extensive alternative promoter usage and RNA splicing. The magnitudes of splicing changes are larger between tissues than between developmental stages, and most sex-specific splicing is gonad-specific. Gonads express hundreds of previously unknown coding and long non-coding RNAs (lncRNAs), some of which are antisense to protein-coding genes and produce short regulatory RNAs. Furthermore, previously identified pervasive intergenic transcription occurs primarily within newly identified introns. The fly transcriptome is substantially more complex than previously recognized, with this complexity arising from combinatorial usage of promoters, splice sites and polyadenylation sites.

The sequencing of the genomes of 12 Drosophila species has created an opportunity for much in the way of comparative molecular analyses amongst these species. To aid that endeavor, we have made several transformation vectors based on the piggyBac transposon with 3xP3-EGFP and -ECFP transgenic markers that should be useful for mutagenesis and establishing the GAL4/UAS system in these species. We have tested the ability of mini-white to be used as a marker for insertional mutagenesis, and have observed mini-white derived pigmentation of the testes sheath in a subset of lines from D. pseudoobscura and D. virilis. We have incorporated a source of piggyBac transposase into nine Drosophila species, and have demonstrated the functionality of these transposase lines for mobilization of marked inserts in vivo. Additionally, we tested the ability of a D. melanogaster nanos enhancer element to drive expression of GAL4 in D. melanogaster, D. simulans, D. erecta, D. yakuba, D. pseudoobscura, and D. virilis. The efficacy of the nos-Gal4 transgene was determined by measuring the response of UAS-EGFPtub in all six species. Our results show that D. melanogaster nos-Gal4 drives expression in other species, to varying degrees, in similar spatiotemporal domains in the ovaries, testes, and embryos as seen in D. melanogaster. However, expression levels are variable, demonstrating the possible need to use species-specific promoters in some cases. In summary, we hope to provide a set of guidelines and basic tools, based upon this work, for both insertional mutagenesis and GAL4/UAS system-based experiments in multiple species of Drosophila.

Thelytokous parthenogenesis (female progeny only) in animals is believed to arise initially in unfertilized eggs produced by bisexual females via the fusion of two haploid nuclei following meiosis, to produce diploid female progeny. The transition from sexual to parthenogenetic mechanisms of reproduction requires that the egg replace the paternal contributions of a haploid genetic complement and the basal body, which is thought to be essential for centrosome formation. The transitional facultative parthenogenetic stage is usually associated with a high rate of failed or abortive development, but the molecular and mechanistic reasons for this failure remain unclear. We show that a facultative parthenogenetic strain of Drosophila mercatorum produces a high percentage of unfertilized eggs competent to restore diploidy and form centrosomes de novo following meiosis. The female meiotic products replicate and divide by an acentrosomal mechanism in most oocytes and cytoplasmic centrosomes form in 35% of the oocytes. However, after pronuclear replication the cytoplasmic centrosomes must "capture" two haploid nuclei in order to restore diploidy. In practice, this process frequently fails due to centrosome-mediated capture events of single or more than two haploid nuclei, as well as multiple nuclear capture events in a single embryo when excess free centrosomes are not inactivated following formation of the first zygotic nucleus. Additionally, as development proceeds, many of the centrosomes that initiate syncytial development do not remain functional, possibly due to centrosome maturation defects, and later stages of syncytial development fail. The combined effect of the high error rate associated with nuclear capture and the failure of centrosome maturation during later developmental prevents successful parthenogenesis in most of the eggs that initiate development. This shows that the high rate of failed development associated with the transition from sexual to parthenogenetic reproduction is limited by the low probability of the formation of a diploid zygotic nucleus with the correct complement of centrosomes in D. mercatorum.

Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved.

Loci on the third chromosome of Drosophila melanogaster that affect an index of wing shape were mapped, using recombinant isogenic lines, with transposable elements as markers. Many genes with small subequal effects are dispersed along the whole chromosome. Their alleles act nearly additively in heterozygotes. They have small correlated effects on leg shape, but no detectable effects on halteres. Small negative net interactions occur over most of the chromosome. The data set of 519 recombinant isogenic lines can be explained reasonably well by two models. One model posits an indefinitely large number of loci with no interactions. The other model posits 11 loci with additive effects whose sum equals the total phenotypic range and with large positive and negative interactions that nearly cancel each other.

The protein product of the cystic fibrosis (CF) gene, termed the cystic fibrosis transmembrane conductance regulator (CFTR), is known to function as an apical chloride channel at the surface of airway epithelial cells. It has been proposed that CFTR has additional intracellular functions and that there is altered processing of mutant forms. In examining these functions we found a stable form of CFTR with slow turnover in surface membrane preparations from CF and non-CF immortalized airway epithelial cell lines. The methods used to study the turnover of CFTR were pulse/chase experiments utilizing saturation labeling of [35S] Met with chase periods of 5-24 h in the presence of 8 mM Met and cell fractionation techniques. Preparations of morphologically identifiable surface membranes were compared to total cell membrane preparations containing intracellular membranes. Surface membrane CFTR had lower turnover defined by pulse/chase ratios than that of the total cell membrane preparations. Moreover, mutant CFTR was stable in the surface membrane fraction with little degradation even after a 24 h chase, whereas wild-type CFTR had a higher pulse/chase ratio at 24 h. In the presence of 50 microM castanospermine, which is an inhibitor of processing alpha-glucosidases, a more rapid turnover of mutant CFTR was found in the total cell membrane preparation, whereas wild-type CFTR had a lower response. The results are compatible with a pool of CFTR in or near the surface membranes which has an altered turnover in CF and a glycosylation-dependent alteration in the processing of mutant CFTR.

The glycoprotein (GP) IIb/IIIa heterodimer functions as a receptor for fibrinogen, von Willebrand factor, and fibronectin on activated platelets; it is dysfunctional in the bleeding diathesis Glanzmann's thrombasthenia. This receptor is a member of the integrin family, which includes homologous membrane receptors involved in a number of different cell-cell and cell-matrix adhesive interactions. Knowledge of the sequence and organization of the GPIIb and GPIIIa genes will help in understanding evolutionary relationships and functional homologies of this family of adhesion protein receptors and will facilitate analysis of molecular defects responsible for thrombasthenia. Using the GPIIb cDNA as a probe, we have isolated overlapping genomic clones encompassing the entire coding region, the 5'- and 3'-untranslated sequences, and the immediate flanking regions for the GPIIb gene. The gene spans approximately 17.2 kilobases (kb); all but approximately 2.6 kb of intronic DNA sequence has been determined. The GPIIb gene contains 30 exons whose demarcations do not correlate with previously suggested functional domains. Two intron/exon borders have the rare GC splice donor sequence instead of the consensus GT sequence. There are at least seven complete and three partial AluI sequence repeats within the intron sequences. RNase protection, S1 nuclease analysis, and primer extension studies using human erythroleukemia (HEL) cell RNA and platelet RNA map a major transcription start site 32 base pairs (bp) 5' to the beginning of the coding region; however, there are no canonical consensus TATA or CAAT boxes in the region immediately 5' to the proposed cap site. The immediate 5'-flanking sequence of rodent GPIIb demonstrates complete identity near the proposed cap site with its human counterpart, but again, no TATA or CAAT boxes are apparent.