Transcript expression analysis of Drosophila melanogaster reveals sex-specific alternative splicing of qtc gene
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ABSTRACT:
PROVIDER: PRJNA748991 | ENA |
REPOSITORIES: ENA
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Project description:We used long-oligonucleotide microarrays to investigate whether alternative splicing in Drosophila is regulated in a sex-, stage-, or tissue-specific manner. To examine sex-specific splicing, we compared gene expression profiles of male and female pupae 12 hours after pupariation. To examine stage-specific splicing, we compared expression profiles of mixed-sex, 0-24 hour old embryos and mixed-sex, 12 hour old pupae. To examine tissue-specific splicing, we compared expression profiles of adult male heads and abdomens 24-48 hours after eclosion. To examine tissue-specific splicing, we compared expression profiles of adult male heads and abdomens at 24-48 hours after eclosion. Keywords: tissue-specific expression profiles
2007-06-22 | GSE5190 | GEO
Project description:We used long-oligonucleotide microarrays to investigate whether alternative splicing in Drosophila is regulated in a sex-, stage-, or tissue-specific manner. To examine sex-specific splicing, we compared gene expression profiles of male and female pupae 12 hours after pupariation. To examine stage-specific splicing, we compared expression profiles of mixed-sex, 0-24 hour old embryos and mixed-sex, 12 hour old pupae. To examine tissue-specific splicing, we compared expression profiles of adult male heads and abdomens 24-48 hours after eclosion. To examine tissue-specific splicing, we compared expression profiles of adult male heads and abdomens at 24-48 hours after eclosion. Keywords: tissue-specific expression profiles Drosophila isogenic line WI89 was used. Mixed-sex, mixed-stage embryos were harvested from plates on which females had been allowed to oviposit for 24 hours. To obtain synchronized cohorts of pupae, male and female white prepupae were collected at 0-1 hour after pupariation and aged for 12 hours at 25C. Mixed-sex pupal samples were generated by mixing equal amount of male and female pupal RNA. Adult heads and abdomens were dissected from 24-48 hour old males. mRNA was isolated and labeled without amplification.
2010-06-10 | E-GEOD-5190 | biostudies-arrayexpress
Project description:Many multi-exon genes are subject to alternative splicing, which is thought to increase phenotypic complexity by allowing a single locus to produce multiple functionally distinct proteins. However, genetic and developmental variation in alternative splicing has never been examined systematically. We therefore undertook a genome-wide analysis of sex- and genotypic-specific splicing in Drosophila in conjunction with sex- and line-specific transcription. Keywords: microarray, sexual dimorphism, alternative splicing, genetical genomics, genetic variation
2006-06-06 | GSE4976 | GEO
Project description:Sex-specific and lineage-specific alternative splicing in primates
| PRJNA119135 | ENA
Project description:Here, we report transcriptome analysis in different tissues of Drosophila melanogaster, enriched with qtc transcripts.
2021-07-27 | GSE180626 | GEO
Project description:Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution. Keywords: Gene Regulation Study Examination of gene expression levels in livers from three primate species (human, chimpanzee, and rhesus macaque), using 3 male and 3 female samples from each species.
2009-12-01 | E-GEOD-17274 | biostudies-arrayexpress
Project description:Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here we used recently-developed RNA sequencing protocols, which side-step this limitation, to assess intra- and inter-species variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNAseq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates. These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution. Keywords: Gene Regulation Study
2009-12-01 | GSE17274 | GEO
Project description:In Drosophila female development is governed by a single RNA-binding protein, Sex lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Functional Sxl protein is only synthesized in female flies. Its expression is established in the pre-cellular, female embryo by an X-chromosome counting mechanism and maintained by a positive feedback loop with Sxl controlling alternative splicing of its own transcript. In male flies this feedback loop is not activated, keeping Sxl expression in the ‘off’ state. But what protects males against accidental triggering of the self-sustaining feedback loop and Sxl protein production snowballing out of control? Here we identify Sister of sex lethal (Ssx) as a protein that antagonizes Sxl in autoregulatory splicing by competition for the same RNA elements. Male flies mutant for ssx exhibit a low level of productive Sxl mRNA splicing and in cultured Drosophila cells, Sxl-induced changes in alternative splicing can be reverted by the expression of Ssx. In sum, this demonstrates that Ssx helps to establish a stable, male-specific gene expression pattern by protecting male flies against triggering Sxl expression.
2019-01-15 | GSE98188 | GEO
Project description:In Drosophila female development is governed by a single RNA-binding protein, Sex lethal (Sxl), that controls the expression of key factors involved in dosage compensation, germline homeostasis and the establishment of female morphology and behaviour. Functional Sxl protein is only synthesized in female flies. Its expression is established in the pre-cellular, female embryo by an X-chromosome counting mechanism and maintained by a positive feedback loop with Sxl controlling alternative splicing of its own transcript. In male flies this feedback loop is not activated, keeping Sxl expression in the ‘off’ state. But what protects males against accidental triggering of the self-sustaining feedback loop and Sxl protein production snowballing out of control? Here we identify Sister of sex lethal (Ssx) as a protein that antagonizes Sxl in autoregulatory splicing by competition for the same RNA elements. Male flies mutant for ssx exhibit a low level of productive Sxl mRNA splicing and in cultured Drosophila cells, Sxl-induced changes in alternative splicing can be reverted by the expression of Ssx. In sum, this demonstrates that Ssx helps to establish a stable, male-specific gene expression pattern by protecting male flies against triggering Sxl expression.
2019-01-15 | GSE98187 | GEO
Project description:Alternative splicing is a critical determinant of genome complexity and by implication, is assumed to engender proteomic diversity. This notion has not been experimentally tested in a targeted, quantitative manner. Here, we have developed an integrative approach to ask whether dynamic perturbations in mRNA splicing patterns that follow depletion of the core spliceosome factor PRPF8 alter the composition of the proteome. We integrate RNA-sequencing (to comprehensively report intron retention, differential transcript usage and gene expression) with a newly developed data-independent acquisition (DIA) method, SWATH-MS (Sequential Window Acquisition of all THeoretical spectra – mass spectrometry), to capture an unbiased and quantitative snapshot of constitutive and alternative splicing events at the protein level. Whereas intron retention is accompanied by decreased protein abundance, dynamic alterations in differential transcript usage and gene expression alter protein abundance proportionally to transcript levels. Our findings exemplify how RNA splicing exerts a pervasive effect linking isoform expression in the human transcriptome with proteomic diversity, and provide a toolkit for studying its perturbation in human diseases.
2017-08-02 | PXD003278 | Pride