Project description:H3K27me3 profiles using Cleavage under targets and Release using nuclease (Cut&Run) in control and KD Drosophila melanogaster ovaries. We examined the impact on chromatin profiles in Drosophila melanogaster ovaries in which the lid, the Sin3a, the Snr1 or the mod(mdg4) gene have been selectively knocked down by tissue-specific shRNA expression. We additionally explored H3K27me3 and H3K9me3 in control and dhd mutant ovaries either carrying or not a transgene.
Project description:Alternative cleavage and polyadenylation (APA) is a mechanism generating multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here we used 3' Region Extraction And Deep Sequencing (3'READS) to systematically map cleavage and polyadenylation sites (PAS) in Drosophila and analyzsed APA in the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate. We found that about two thirds of mRNA genes in fly undergo APA and cis element analysis indicates that fly PASs are associated with downstream UGUG elements to a lesser degree than mammalian PASs. The head tissue tends to use distal PASs compared to the body, leading to preferential expression of long 3'UTR isoforms and transcripts using distal terminal exons. Gene Ontology analysis correlates brain-specific APA events with neuronal functions, indicating their functional relevance. We also found that the distance between the proximal and distal PASs and intron locations might play important roles for brain APA. Analysis of the RpII215 C4 mutant strain, reveals that a 50% decrease in transcriptional elongation rate leads to shortened 3'UTRs in the fly body, but not in the head. This correlates with an upregulation of Ssu72 specifically in RpII215 C4 bodies, suggesting that the mechanism underlying those observations involves another layer of regulation by RNAPII termination factors. By contrast, more significant activation of intronic PASs was observed in the head compared to the body when RNAPII speed is slow. Together, our results reveal that in Drosophila RNAPII elongation impacts on PAS choice in a context-specific manner.
Project description:To understand the function of gene CG7358 in Drosophila melanogaster, including indentification of those genes whose expression levels or alternative splicing are affected by CG7358.
Project description:We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Project description:We sequenced mRNA from head tissue of females and male of Drosophila melanogaster to identify genes differentially expressed between the sexes and sex-specific alternative splicing events. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Comparison of expression profiles in female and male head tissue from D. melanogaster
Project description:Thermal acclimation study on Drosophila melanogaster reared at 3 different temperatures (12, 25, and 31oC). The proteomic profiles of D. melanogaster under these different temperatures were analyzed and compared using label-free tandem mass spectrometry.
