Expression of baculovirus P35 prevents cell death in Drosophila

The baculovirus P35 protein functions to prevent apoptotic death of infected cells. We have expressed P35 in the developing embryo and eye of the fly Drosophila melanogaster. P35 eliminates most, if not all, normally occurring cell death in these tissues, as well as X-irradiation-induced death. Excess pupal eye cells that are normally eliminated by apoptosis develop into pigment cells when their death is prevented by P35 expression. Our results suggest that one mechanism by which viruses prevent the death of the host cell is to block a cell death pathway that mediates normally occurring cell death. Identification of molecules that interact biochemically or genetically with P35 in Drosophila should provide important insights into how cell death is regulated

Global analyses of mRNA translational control during early Drosophila embryogenesis

The polysomal profiles of over 15,000 transcripts during the first ten hours after egg laying have been determined

Computational identification of Drosophila microRNA genes

BACKGROUND: MicroRNAs (miRNAs) are a large family of 21-22 nucleotide non-coding RNAs with presumed post-transcriptional regulatory activity. Most miRNAs were identified by direct cloning of small RNAs, an approach that favors detection of abundant miRNAs. Three observations suggested that miRNA genes might be identified using a computational approach. First, miRNAs generally derive from precursor transcripts of 70-100 nucleotides with extended stem-loop structure. Second, miRNAs are usually highly conserved between the genomes of related species. Third, miRNAs display a characteristic pattern of evolutionary divergence. RESULTS: We developed an informatic procedure called 'miRseeker', which analyzed the completed euchromatic sequences of Drosophila melanogaster and D. pseudoobscura for conserved sequences that adopt an extended stem-loop structure and display a pattern of nucleotide divergence characteristic of known miRNAs. The sensitivity of this computational procedure was demonstrated by the presence of 75% (18/24) of previously identified Drosophila miRNAs within the top 124 candidates. In total, we identified 48 novel miRNA candidates that were strongly conserved in more distant insect, nematode, or vertebrate genomes. We verified expression for a total of 24 novel miRNA genes, including 20 of 27 candidates conserved in a third species and 4 of 11 high-scoring, Drosophila-specific candidates. Our analyses lead us to estimate that drosophilid genomes contain around 110 miRNA genes. CONCLUSIONS: Our computational strategy succeeded in identifying bona fide miRNA genes and suggests that miRNAs constitute nearly 1% of predicted protein-coding genes in Drosophila, a percentage similar to the percentage of miRNAs recently attributed to other metazoan genomes

Comparative Genomics of the Eukaryotes

A comparative analysis of the genomes ofDrosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae—and the proteins they are predicted to encode—was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease

P1 interneurons promote a persistent internal state that enhances inter-male aggression in Drosophila

How brains are hardwired to produce aggressive behavior, and how aggression circuits are related to those that mediate courtship, is not well understood. A large-scale screen for aggression-promoting neurons in Drosophila identified several independent hits that enhanced both inter-male aggression and courtship. Genetic intersections revealed that P1 interneurons, previously thought to exclusively control male courtship, were responsible for both phenotypes. The aggression phenotype was fly-intrinsic, and required male-specific chemosensory cues on the opponent. Optogenetic experiments indicated that P1 activation promoted aggression vs. wing extension at low vs. high thresholds, respectively. High frequency photostimulation promoted wing extension and aggression in an inverse manner, during light ON and OFF, respectively. P1 activation enhanced aggression by promoting a persistent internal state, which could endure for minutes prior to social contact. Thus P1 neurons promote an internal state that facilitates both aggression and courtship, and can control these social behaviors in a threshold-dependent manner

A molecular analysis of three unstable alleles in drosophila : (transposable elements, mutable alleles, white locus)

We have determined the structure of several unstable mutant alleles of the white locus in Drosophila melanogaster. The white ivory (w[superscript i]) allele is a moderately unstable allele, which gave rise to the highly unstable white-crimson (w[superscript C]) allele. We have determined that the w[superscript i] mutation is due to the duplication of 2.9 kilobases (kb) of DNA within the white locus, and that reversion of w[superscript i] to wild type usually occurs by simple loss of one copy of the duplication. We have also analyzed two highly unstable alleles of the white locus, we and white dominant zeste-like (w[superscript DZL]) and have shown that both are insertion mutations. The w[superscript C] mutation results from the insertion of 10 kb of DNA into the w[superscript i] duplication, and the w[superscript DZL] mutation results from the insertion of 13 kb of DNA at or near the right end of the white locus. The w[superscript C] and w[superscript DZL] insertions are structurally related, but not identical, and are related to a previously characterized family of transposable elements, the fold back(FB) elements. The we insertion consists of a single FB elementwith a low eopy number sequence between the moderately repetitive terminal inverted repeats. The wDZL insertion contains two FB elements which flank a single copy sequence in the middle of the insertion. Reversion of w[superscript C] to w[superscript i] is mediated by an apparently precise excision event, while reversion of w[superscript DZL] to wild type occurs by an imprecise excision of the insertion. We suggest that structural differences in the two insertions may account for these different modes of reversion.Mary Collins, Robert Levis, Roger Karess, and Gerald M. Rubin, Department of Embryology Carnegie Institute of Washington, 115 West University Parkway, Baltimore, Maryland

Global analysis of patterns of gene expression during Drosophila embryogenesis

Embryonic expression patterns for 6,003 (44%) of the 13,659 protein-coding genes identified in the Drosophila melanogaster genome were documented, of which 40% show tissue-restricted expression

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

BACKGROUND: The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. RESULTS: We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. CONCLUSIONS: Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity