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PubMed2003

The zinc finger-associated domain of the Drosophila transcription factor grauzone is a novel zinc-coordinating protein-protein interaction module.

About one-third of the more than 300 C2H2 zinc finger proteins of Drosophila contain a conserved sequence motif, the zinc finger-associated domain (ZAD). Genes that encode ZAD proteins are specific for and expanded in the genomes of insects. Only three ZAD-encoding gene functions are established, and the role of ZAD is unknown. Here we present the crystal structure of the ZAD of Grauzone (ZAD(Grau)), a Drosophila transcription factor that specifically controls the maternal Cdc20-like APC subunit Cortex. ZAD forms an atypical treble-clef-like zinc-coordinating fold. Head-to-tail arrangement of two ZAD(Grau) molecules in the crystals suggests dimer formation, an observation supported by crosslinking and dynamic light scattering. The results indicate that ZAD provides a novel protein-protein interaction module that characterizes a large family of insect transcription factors.

Amino Acid Motifs↗
PubMed2025

3D chromatin structures precede genome activation in Drosophila embryogenesis.

3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These high-resolution contact maps reveal fine-scale features such as loops and boundaries delineating topologically associating domains. Notably, we observe that 3D chromatin structures form prior to zygotic genome activation and persist during successive mitotic cycles. Integrative analysis with 149 public chromatin immunoprecipitation sequencing (ChIP-seq) datasets identifies four classes of chromatin structuring elements, including a distinct group enriched for GAGA-associated factor (GAF) and Zelda binding, associated with developmental-gene regulation. These elements are mitotically retained and exhibit sequence and structure similarity between D. melanogaster and D. virilis. We propose that 3D chromatin organization in the pre-cellular embryo facilitates deployment of developmentally regulated genes during Drosophila embryogenesis.

Animals↗
PubMed2025

Saturating the eQTL map in Drosophila: Genome-wide patterns of cis and trans regulation of transcriptional variation in outbred populations.

Most genetic polymorphisms associated with complex traits are found in non-coding regions of the genome. Characterizing their effect presents a formidable challenge, and expression quantitative trait locus (eQTLs) mapping has been a key approach to do so. As comprehensive eQTL maps are available only for a few species, here we developed the Drosophila outbred synthetic population (Dros-OSP) and used it to characterize the landscape of transcriptional regulation in Drosophila melanogaster. We collected head and body transcriptomes and genomes from 1,286 outbred flies and mapped local and distant eQTLs for 98% of the genes. We characterized the network organization of the transcriptome across tissues and described the properties of local and distal eQTLs in terms of genetic diversity, heritability, connectivity, and pleiotropy. These results provide new insights into the genetic basis of transcriptional regulation in the fruit fly and offer a new mapping resource that will expand the possibilities currently available for the Drosophila community.

Animals↗
PubMed2005

Multiple Promoter Targeting Sequences exist in Abdominal-B to regulate long-range gene activation.

In complex genomes, insulators set up chromatin domain boundaries and protect promoters from inappropriate activation by enhancers from neighboring genes. The Drosophila Abdominal-B locus uses insulator elements to organize its large regulatory region into several body segment-specific chromatin domains. This organization leads to a problem in enhancer-promoter communication, that is, how do distal enhancers activate the Abd-B promoter when there are several insulators in between? This issue is partially resolved by the Promoter Targeting Sequence, which can overcome the enhancer blocking effect of an insulator. In this study, we describe a new Promoter Targeting Sequence, PTS-6, from the Abd-B 3' regulatory region. PTS-6, comprised of approximately 200 bp, was found to bypass both homologous Abdominal-B insulators, such as Fab-7 and Fab-8, and a heterologous insulator, suHw. Most importantly, it also overcomes a combination of two insulators such as Fab-7/Fab-8. Thus, PTS-6 could, in principle, target remote enhancers that are separated from the Abd-B promoter by multiple insulators. In addition, PTS-6 selectively targets the distal enhancer to only one transgenic promoter, and it strongly facilitates Abd-B enhancers. These results suggest that promoter targeting is necessary for long-range enhancer-promoter communication in Abd-B, and PTS elements could be a common occurrence in large, complex genetic loci.

Animals↗
PubMed2006

The UBX-regulated network in the haltere imaginal disc of D. melanogaster.

Hox proteins have been proposed to act at multiple levels within regulatory hierarchies and to directly control the expression of a plethora of target genes. However, for any specific Hox protein or tissue, very few direct in vivo-regulated target genes have been identified. Here, we have identified target genes of the Hox protein Ultrabithorax (UBX), which modifies the genetic regulatory network of the wing to generate the haltere, a modified hindwing. We used whole-genome microarrays and custom arrays including all predicted transcription factors and signaling molecules in the Drosophila melanogaster genome to identify differentially expressed genes in wing and haltere imaginal discs. To elucidate the regulation of selected genes in more detail, we isolated cis-regulatory elements (CREs) for genes that were specifically expressed in either the wing disc or haltere disc. We demonstrate that UBX binds directly to sites in one element, and these sites are critical for activation in the haltere disc. These results indicate that haltere and metathoracic segment morphology is not achieved merely by turning off the wing and mesothoracic development programs, but rather specific genes must also be activated to form these structures. The evolution of haltere morphology involved changes in UBX-regulated target genes, both positive and negative, throughout the wing genetic regulatory network.

Animals↗
PubMed2006

Conservation patterns in different functional sequence categories of divergent Drosophila species.

We have explored the distributions of fully conserved ungapped blocks in genome-wide pair-wise alignments of recently completed species of Drosophila: D. melanogaster, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis, and D. mojavensis. Based on these distributions we have found that nearly every functional sequence category possesses its own distinctive conservation pattern, sometimes independent of the overall sequence conservation level. In the coding and regulatory regions, the ungapped blocks were longer than in introns, UTRs, and nonfunctional sequences. At the same time, the blocks in the coding regions carried a 3N + 2 signature characteristic of synonymous substitutions in the third-codon position. Larger block sizes in transcription regulatory regions can be explained by the presence of conserved arrays of binding sites for transcription factors. We also have shown that the longest ungapped blocks, or "ultraconserved" sequences, are associated with specific gene groups, including those encoding ion channels and components of the cytoskeleton. We discuss how restraining conservation patterns may help in mapping functional sequence categories and improve genome annotation.

Animals↗
PubMed2006

A dicistronic gene pair within a cluster of "EF-hand" protein genes in the genomes of Drosophila species.

Androcam is a Drosophila melanogaster calmodulin-related protein that functions specifically in the testis. We show that the Acam gene is part of a cluster of three intronless genes arranged in a head-to-tail manner. The additional genes also encode calmodulin-related proteins with testis-specific transcription. Acam and the 5'-most gene (gene1) generate monocistronic transcripts. Surprisingly, the central gene (gene2) is transcribed only as a dicistronic transcript with Acam. A similar cluster is found in D. yakuba. In D. pseudoobscura, the cluster contains four genes: two Acam-type genes downstream of a single gene related to both gene1 and gene2 and a fourth weakly related gene. Nevertheless, the D. pseudoobscura cluster also generates a dicistronic transcript from a gene pair analogous to the gene2-Acam pair. A cotranscribed gene1/2-Acam gene pair may be the founding feature of this locus. Although Acam protein is present in D. melanogaster and D. pseudoobscura testes, cognate proteins for the gene1/2-type ORFs are not detectable by immunoblotting and mass spectrometry techniques.

Animals↗
PubMed2006

Conserved family of glycerol kinase loci in Drosophila melanogaster.

Glycerol kinase (GK) is an enzyme that catalyzes the formation of glycerol 3-phosphate from ATP and glycerol, the rate-limiting step in glycerol utilization. We analyzed the genome of the model organism Drosophila melanogaster and identified five GK orthologs, including two loci with sequence homology to the mammalian Xp21 GK protein. Using a combination of sequence analysis and evolutionary comparisons of orthologs between species, we characterized functional domains in the protein required for GK activity. Our findings include additional conserved domains that suggest novel nuclear and mitochondrial functions for glycerol kinase in apoptosis and transcriptional regulation. Investigation of GK function in Drosophila will inform us about the role of this enzyme in development and will provide us with a tool to examine genetic modifiers of human metabolic disorders.

Amino Acid Sequence↗
PubMed2006

Mapping Drosophila genomic aberration breakpoints with comparative genome hybridization on microarrays.

Chromosomal aberrations are genetic "reagents" that are commonly used in Drosophila research. Stocks containing chromosomes carrying large deletions of DNA (deficiency stocks, designated Df) as well as stocks carrying an extra copy of a chromosomal region (duplication stocks, designated Dp) are essential for a variety of genetic analyses. The extent of what is deleted or duplicated has typically been determined cytologically by salivary gland polytene chromosome squashes, which identify the edges of the aberration (so-called breakpoints) of each Df or Dp at low resolution. The margin of error for this technique can be quite high, however, because it is dependent on the quality of the squash and the experience of the scientist interpreting the data. Comparative genome hybridization on microarrays provides a precise molecular method to identify which regions of the genome are deleted or duplicated in these stocks by examining a change in chromosomal ploidy across the whole genome. Furthermore, this technique allows genetic data obtained with these strains to be placed in a molecular genomic context.

Animals↗
PubMed2001

A chemosensory gene family encoding candidate gustatory and olfactory receptors in Drosophila.

A novel family of candidate gustatory receptors (GRs) was recently identified in searches of the Drosophila genome. We have performed in situ hybridization and transgene experiments that reveal expression of these genes in both gustatory and olfactory neurons in adult flies and larvae. This gene family is likely to encode both odorant and taste receptors. We have visualized the projections of chemosensory neurons in the larval brain and observe that neurons expressing different GRs project to discrete loci in the antennal lobe and subesophageal ganglion. These data provide insight into the diversity of chemosensory recognition and an initial view of the representation of gustatory information in the fly brain.

Animal Structures↗
PubMed1995

The relationship between the flamenco gene and gypsy in Drosophila: how to tame a retrovirus.

For a long time, retroviruses have been considered to be restricted to vertebrates. However, the genome of insects contains elements like gypsy in Drosophila melanogaster that are strikingly similar to vertebrate proviruses of retroviruses, which were considered to be transposable elements. Recent results indicate that gypsy has infective properties and is therefore a retrovirus, the first to be identified in invertebrates. It is normally repressed by a host gene called flamenco, which apparently controls the transposition and infective properties of gypsy. This provides an exceptional experimental model to investigate the genetic relationships between retroviruses and their hosts.

Alleles↗
PubMed1998

Imprinted control of gene activity in Drosophila.

Genetic imprinting is defined as a reversible, differential marking of genes or chromosomes that is determined by the sex of the parent from whom the genetic material is inherited [1]. Imprinting was first observed in insects where, in some species, most notably among the coccoids (scale insects and allies), the differential marking of paternally and maternally transmitted chromosome sets leads to inactivation or elimination of paternal chromosomes [2]. Imprinting is also widespread in plants and mammals [3,4], in which paternally and maternally inherited alleles may be differentially expressed. Despite imprinting having been discovered in insects, clear examples of parental imprinting are scarce in the model insect species Drosophila melanogaster. We describe a case of imprint-mediated control of gene expression in Drosophila. The imprinted gene - the white+ eye-color gene - is expressed at a low level when transmitted by males, and at a high level when transmitted by females. Thus, in common with coccoids, Drosophila is capable of generating an imprint, and can respond to that imprint by silencing the paternal allele.

Animals↗
PubMed2001

Aedes aegypti peroxidase gene characterization and developmental expression.

The functions of insect peroxidases include detoxification, stabilization of extracellular matrices, and possible involvement in insect immunity. The current study describes the isolation of a peroxidase gene, AePox, and its cDNA from the mosquito, Aedes aegypti. AePox codes for a protein that is homologous to various heme-peroxidases from vertebrates and invertebrates, with highest identity to Drosophila melanogaster peroxidase (62%). Sequence comparison identified several functionally and structurally conserved domains in the mosquito peroxidase, including a heme environment, a calcium binding site, and five possible disulfide bridges. These results imply that AePOX may likely have a similar structure and catalytic mechanism as those described for the mammalian myeloperoxidase superfamily. Expression studies demonstrate that AePox is transcribed in mosquito larvae and pupae, but not in adults, in ovaries, or in early embryos. However, AePOX protein is present in all mosquito stages and possibly has a maturation process that is similar to that of human myeloperoxidase. Unlike most human peroxidases, the AePox gene contains a TATA box and an ecdysone response element (EcRE).

Aedes↗
PubMed2003

Exploring the salivary gland transcriptome and proteome of the Anopheles stephensi mosquito.

Anopheles stephensi is the main urban mosquito vector of malaria in the Indian subcontinent, and belongs to the same subgenus as Anopheles gambiae, the main malaria vector in Africa. Recently the genome and proteome sets of An. gambiae have been described, as well as several protein sequences expressed in its salivary glands, some of which had their expression confirmed by amino terminal sequencing. In this paper, we randomly sequenced a full-length cDNA library of An. stephensi and performed Edman degradation of polyvinylidene difluoride (PVDF)-transferred protein bands from salivary homogenates. Twelve of 13 proteins found by aminoterminal degradation were found among the cDNA clusters of the library. Thirty-three full-length novel cDNA sequences are reported, including a novel secreted galectin; the homologue of anophelin, a thrombin inhibitor; a novel trypsin/chymotrypsin inhibitor; an apyrase; a lipase; and several new members of the D7 protein family. Most of the novel proteins have no known function. Comparison of the putatively secreted and putatively housekeeping proteins of An. stephensi with An. gambiae proteins indicated that the salivary gland proteins are at a faster evolutionary pace. The possible role of these proteins in blood and sugar feeding by the mosquito is discussed. The electronic tables and supplemental material are available at http://www.ncbi.nlm.nih.gov/projects/Mosquito/A_stephensi_sialome/ .

Amino Acid Sequence↗
PubMed2003

A catalogue of Anopheles gambiae transcripts significantly more or less expressed following a blood meal.

The recent assembly of the Anopheles gambiae genome included the sequencing of ~80,000 EST from blood fed (BF) and non-blood fed (NBF) adult female mosquitoes to help find the exons and introns in the mosquito genome. These two EST libraries provided an insight into the differential gene expression resulting from the metabolically intense task of converting the massive blood meal into eggs. Previously, 168 genes have been identified to be either significantly more or significantly less transcribed after the blood meal [Science 298 (2002) 129]. Presently, 435 transcripts are described; these are grouped in supplemental tables by probable function to facilitate public access to these data and to help in designing postgenome experiments in the biology of Anopheles gambiae. The electronic tables and supplemental material are available at http://www.ncbi.nlm.nih.gov/projects/Mosquito/Ag-ESTs.

Animals↗
PubMed2006

Genetic architecture of variation in sex-comb tooth number in Drosophila simulans.

The sex comb on the forelegs of Drosophila males is a secondary sexual trait, and the number of teeth on these combs varies greatly within and between species. To understand the relationship between the intra- and interspecific variation, we performed quantitative trait locus (QTL) analyses of the intraspecific variation in sex-comb tooth number. We used five mapping populations derived from two inbred Drosophila simulans strains that were divergent in the number of sex-comb teeth. Although no QTLs were detected on the X chromosome, we identified four QTLs on the second chromosome and three QTLs on the third chromosome. While identification and estimated effects of the second-chromosome QTLs depend on genetic backgrounds, significant and consistent effects of the two third-chromosome QTLs were found in two genetic backgrounds. There were significant epistatic interactions between a second-chromosome QTL and a third-chromosome QTL, as well as between two second-chromosome QTLs. The third-chromosome QTLs are concordant with the locations of the QTLs responsible for the previously observed differences in sex-comb tooth number between D. simulans and D. mauritiana.

Animals↗
PubMed2006

Microsatellites reveal extensive geographical, ecological and genetic contacts between invasive and indigenous whitefly biotypes in an insular environment.

Human-mediated bioinvasions provide the opportunity to study the early stages of contact between formerly allopatric, divergent populations of a species. However, when invasive and resident populations are morphologically similar, it may be very difficult to assess their distribution in the field, as well as the extent of ecological overlap and genetic exchanges between invasive and resident populations. We here illustrate the use of data obtained from a set of eight microsatellite markers together with Bayesian clustering methods to document invasions in a group of major tropical pests, Bemisia tabaci, which comprises several morphologically indistinguishable biotypes with different agronomic impacts. We focus on the island of La Réunion, where an invasive biotype (B) has recently been introduced and now interacts with the resident biotype (Ms). The temporal and spatial distribution, host-plant range and genetic structure of both biotypes are investigated. We showed (i) that, without prior information, clustering methods separate two groups of individuals that can safely be identified as the B and Ms biotypes; (ii) that the B biotype has invaded all regions of the island, and showed no signs of genetic founder effect relative to the Ms biotype; (iii) that the B and Ms biotypes coexist in sympatry throughout most of their geographical ranges, although they tend to segregate into different host plants; and finally (iv) that asymmetrical and locus-specific introgression occurs between the two biotypes when they are in syntopy.

Animals↗