Project description:The reversible posttranslational O-GlcNAc modification of serine or threonine residues of intracellular proteins is involved in many cellular events from signaling cascades to epigenetic and transcriptional regulation. O-GlcNAcylation is a conserved nutrient-dependent process involving two enzymes, O-GlcNAc Transferase (OGT) adding O-GlcNAc while O-GlcNAcase (OGA) removing it in a manner that’s protein and context dependent. O-GlcNAcylation is essential for epigenetic regulation of gene expression through its action on Polycomb and Trithorax and Compass complexes. However, the important role of O-GlcNAc on adult life and healthspan have been largely unexplored, mainly due the lack of available model systems. Cataloging the O-GlcNAc proteome has proven useful in understanding the biology of this modification in vivo. In this study, we leveraged a recently developed oga knockout fly mutant to identify the O-GlcNAcylated proteins in adult Drosophila melanogaster. The adult O-GlcNAc proteome revealed many proteins related to cell and organismal growth, development, differentiation, and epigenetics. We identified many O-GlcNAcylated proteins that serve a role in increased growth and decreased longevity, including HCF, SIN3A, LOLA, KISMET, ATX2, SHOT, and FOXO.
Project description:Due to the broad climate adaptation of perennial trees, phenological traits (e.g. chilling requirement-CR, bloom date-BD) exhibit complex inheritance patterns. Conceptually, these are adaptive responses to abiotic stress. As production depends on traits like CR, breeders have developed varieties that are phenotypically/genotypically matched to particular geographic/temperature zones. These genotypes are ideal for study of gene networks governing these climate-critical traits. Using genetic approaches, genome-wide association analyses, functional and comparative genomics in fruit and forest trees, we identified a foundational network of genetic activity (phenylpropanoid pathway) linking winter cold stress response to control of the endodormancy-ecodormancy transition (EET) and seed stratification. Our goal is to examine during endodormancy the allelic effects of genes controlling the production of stress related metabolic intermediates that regulate seed stratification, thus linking these two cold temperature responses. Our objective is to use a transcriptome sequencing approach to characterize genotypic effects on the phenylpropanoid gene network transcriptome during endodormancy and the EET. These adaptive genes and gene networks will be targets for knowledge based breeding strategies of fruit and forest trees to sustain and improve these resources to meet the challenges of rapid environmental change
Project description:This dataset is a part of a bigger work on RNA editing in D. melanogaster brain. We present Orbitrap spectra searched against a customized database of Drosophila proteome with introduction of variants provided by RNA editing. Tree files reflect 3 technical replicates.
Project description:This dataset is a part of a bigger work on RNA editing in D. melanogaster brain. We present Orbitrap spectra searched against a customized database of Drosophila proteome with introduction of variants provided by RNA editing. Three files reflect 3 technical replicates.
Project description:PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays. genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays.
Project description:PcG proteins are critical epigenetic regulators of development. Here we have determined genomic distributions of PHO, PHOL and SFMBT proteins in cultured Drosophila cells by hybridization of ChIP products with tiling microarrays.
Project description:Microarray analyses identified 713 genes whose expression increased or decrease by 1.5-fold with a P value <0.01 in response to exposure to JH for 3-12 hr. 497 were up-regulated, and 228 were down-regulated. 12 genes showed differentially regulated pattern that depended on the time of exposure to JH. 73 of these genes (57 genes up-regulated and 17 genes down-regulated) showed the presence of DR4 element in their promoter regions. We also screened the promoter regions of genes whose products are distributed in different cellular locations and various functional groups and found that the DR4 element is present in 275 out of 2850 genes screened. The distribution of DR4 element containing genes varied depending on both cellular location and gene function. The genes whose products are localized to the nucleus or cytoplasm showed higher proportion of DR4 element containing genes when compared to the genes coding for products localized to the membrane. Genes belonging to immune response and ligand activated receptor functional groups showed higher number of genes that contained DR4 elements when compared to the genes belonging to protein kinase or transmembrane receptor functional groups. The DR4 elements identified in the promoter regions of D. melanogaster genes bound to the nuclear proteins isolated from JH III-treated Drosophila L57 cells. In addition, the expression of DR4 element containing genes identified from various functional groups was induced by JH III in Drosophila mbn2 cells grown in the medium containing 1 µM JH III. Presence of DR4 element in JH-responsive genes is conserved across species. This study also demonstrates the feasibility of using genome-wide analysis for identification of genes regulated by various hormones and other signaling molecules. Keywords: Time course
Project description:We have conducted ChIP-Seq and RNA-Seq analyses in order to perform a comparative study between wing imaginal discs and eye imaginal discs from Drosophila melanogaster.
Project description:Microarray analyses identified 713 genes whose expression increased or decrease by 1.5-fold with a P value <0.01 in response to exposure to JH for 3-12 hr. 497 were up-regulated, and 228 were down-regulated. 12 genes showed differentially regulated pattern that depended on the time of exposure to JH. 73 of these genes (57 genes up-regulated and 17 genes down-regulated) showed the presence of DR4 element in their promoter regions. We also screened the promoter regions of genes whose products are distributed in different cellular locations and various functional groups and found that the DR4 element is present in 275 out of 2850 genes screened. The distribution of DR4 element containing genes varied depending on both cellular location and gene function. The genes whose products are localized to the nucleus or cytoplasm showed higher proportion of DR4 element containing genes when compared to the genes coding for products localized to the membrane. Genes belonging to immune response and ligand activated receptor functional groups showed higher number of genes that contained DR4 elements when compared to the genes belonging to protein kinase or transmembrane receptor functional groups. The DR4 elements identified in the promoter regions of D. melanogaster genes bound to the nuclear proteins isolated from JH III-treated Drosophila L57 cells. In addition, the expression of DR4 element containing genes identified from various functional groups was induced by JH III in Drosophila mbn2 cells grown in the medium containing 1 µM JH III. Presence of DR4 element in JH-responsive genes is conserved across species. This study also demonstrates the feasibility of using genome-wide analysis for identification of genes regulated by various hormones and other signaling molecules. Keywords: Time course We performed microarray analysis using RNA isolated form L57 cells that were exposed to 1 µM JH III for 0, 3, 6 and 12 hr and identified 497 genes that are induced by JH and 228 genes that are down-regulated by JH. Then, we searched the promoter regions of these genes and found that 57 out of these 497 JH induced genes, and 17 out of these 228 JH down-regulated genes had conserved DR4 element present in their promoters.