Transcription profiling of Drosophila imaginal disc cell line Cl.8+ stimulated with imaginal disc growth factor 2 (IDGF2)
ABSTRACT: Drosophila imaginal disc growth factors (IDGFs) comprise a small protein family of six members belonging to chitinase-like proteins (CLPs), which bind to, but do not cleave chitin or similar carbohydrates. IDGF2 is the prototypical member with known structure and reported to induce the proliferation of imaginal disc cells Cl.8+ in vitro. We characterized the effects of recombinant IDGF2 on tissue culture cells in vitro. We show that it is involved in cell protection from serum deprivation, as well as from the toxic effects of some xenobiotics and metabolites, when the cells are cultivated in serum-free medium conditions. Our results revealed that IDGF2 does not activate insulin pathway. Microarray-based gene expression analysis identified several IDGF2-dependent genes, including genes implicated in innate immune response, Wnt signaling and genes involved in the response to xenobiotics. Consistently, we observed that IDGF2 can be induced in vivo by aseptic or septic injury and high concentration of IDGF2 was detected in garland and pericardial nephrocytes. Our results suggest that IDGF2 is an important and abundant component of Drosophila hemolymph, which shows cytoprotective effects on insect cells in vitro and works as a modulator of multiple signaling pathways involved in morphogenesis, homeostasis and activation of innate immune response.
Project description:Drosophila imaginal disc growth factors (IDGFs) comprise a small protein family of six members belonging to chitinase-like proteins (CLPs), which bind to, but do not cleave chitin or similar carbohydrates. IDGF2 is the prototypical member with known structure and reported to induce the proliferation of imaginal disc cells Cl.8+ in vitro. We characterized the effects of recombinant IDGF2 on tissue culture cells in vitro. We show that it is involved in cell protection from serum deprivation, as well as from the toxic effects of some xenobiotics and metabolites, when the cells are cultivated in serum-free medium conditions. Our results revealed that IDGF2 does not activate insulin pathway. Microarray-based gene expression analysis identified several IDGF2-dependent genes, including genes implicated in innate immune response, Wnt signaling and genes involved in the response to xenobiotics. Consistently, we observed that IDGF2 can be induced in vivo by aseptic or septic injury and high concentration of IDGF2 was detected in garland and pericardial nephrocytes. Our results suggest that IDGF2 is an important and abundant component of Drosophila hemolymph, which shows cytoprotective effects on insect cells in vitro and works as a modulator of multiple signaling pathways involved in morphogenesis, homeostasis and activation of innate immune response.
Project description:Mutations that made the cells insensitive to the QS inhibition by C-30 were identified in mexR, a multi-drug resistance operon repressor. Gene expression of mexR mutant relative to wild-type at the presence of C-30 was examined. Strains: PA14_mexR and wildtype. Medium: OS minimal medium + 0.1% Adenosine as carbon source. Compounds: 50 µM C-30 added at OD600=0.25. Time: 2 hr. Temp: 37 ºC. Cell type: Planktonic Cells.
Project description:This dataset contains the gene expression signature in triplicates of Escherichia coli BW25113 growing exponentially on eight different environments: minimal medium supplemented with 5 g/L of Glucose, Galactose, Glycerol, Gluconate, Fructose, Pyruvate, Succinate or Acetate as the sole carbon source.
Project description:Analysis of gene expression levels of HER2-positive breast cancer cells exposed to the conditioned medium from adipocytes. The hypothesis tested in the present study was that adipocytes secrete factors that induce the resistance of cancer cells to antibody-dependent cellular cytotoxicity mediated by trastuzumab. The results provide insight into the genes that may be involved in the adipocyte-induced cancer resistance to trastuzumab treatment. BT474 cells or SKBR3 cells were exposed to the conditioned medium (CM) from differentiated hMADS (#hMADS) or to the control medium for 2 h. Total RNA was extracted and analyzed. The experiment was performed in triplicate.
Project description:Recent advances enabled by Hi-C technique have unraveled principles of chromosomal folding, which were since linked to many genomic processes. In particular, Hi-C revealed that chromosomes of animals are organized into Topologically Associating Domains (TADs), evolutionary conserved compact chromatin domains that influence gene expression. However, mechanisms that underlie partitioning of the genome into TADs remain poorly understood. To explore principals of TAD folding in Drosophila melanogaster, we performed Hi-C and PolyA+ RNA-seq in four cell lines of various origins (S2, Kc167, DmBG3-c2, and OSC). Contrary to previous studies, we find that regions between TADs (i.e. the inter-TADs and TAD boundaries) in Drosophila are only weakly enriched with the insulator protein dCTCF, while another insulator protein Su(Hw) is preferentially present within TADs. However, Drosophila inter-TADs harbor active chromatin and constitutively transcribed (housekeeping) genes. Accordingly, we find that binding of insulator proteins dCTCF and Su(Hw) predict TAD boundaries much worse than the active chromatin marks (in the minimal case, H3K4me3 and total RNA) do. Moreover, inter-TADs correspond to decompacted interbands of polytene chromosomes, whereas TADs mostly correspond to densely packed bands. Collectively, our results suggest that TADs are condensed chromatin domains depleted in active chromatin marks, separated by regions of active chromatin that cannot be organized into compact structures, possibly due to high levels of histone acetylation. Finally, we test this hypothesis by polymer simulations, and find that TAD partitioning can be explained by different modes of inter-nucleosomal interactions for active and inactive chromatin. Hi-C experiments, PolyA+ RNA profiling and mapping of chromosomal rearrangements in four Drosophila melanogaster cell lines.
Project description:Generation of oligodendrocytes (OLs) is a sophisticated multistep process, mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell (hESC) differentiation into OLs, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag (TMT) based proteomics approach. Findings: Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human OL lineage differentiation. The proteome profile of OL lineage cells revealed 378 proteins that were specifically up-regulated only in one differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Our results highlighted the eminence of the planar cell polarity (PCP) signaling and autophagy (particularly macroautophagy) in the progression of OL lineage differentiation
Project description:We profiled nucleosome occupancy of different developmental stages in C. elegans. Mononucleosomal DNA was sequenced by Illumina paired-end sequencing. We used embryos, germlineless adults, germ line containing adults, and XO hermaphrodites at L3 larval stage. RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf After MNase digestion of chromatin, we purified mononucleosomal DNA and used Illumina paired-end sequencing. Mapping was done in embryo (strain N2), germlineless adults (strain JK1107), germ line containing adults (strain DH245),and XO hermaphrodites (strain TY2205) at L3 larval stage. For each experimental replicate RNA abundance is determined by microarray analysis. We also digested naked DNA with MNase.
Project description:DNA microarray analysis revealed that the genes related to cell cycle regulation were significantly induced at non- and sub-lethal concentrations (i.e., 0.05-6 µM), while the common feature of heavy metal toxicity such as oxidative damage and following increase in glutathione, heat shock proteins, and metallothionein were confirmed at high concentrations (i.e., 6-40 µM). The concentration dependent modulation of gene expression (induction of cell cycle genes, induction of cell cycle arrest genes and apoptotic genes) following exposure to arsenic was further supported by acceleration of cell proliferation, ROS generation, and cytotoxicity. Furthermore, three cell cycle genes (i.e., CDC25B, UBE2C, and PTTG1) were proposed as marker genes of inorganic arsenic exposure. Those results indicated the potential pro-carcinogenic actions of inorganic arsenic occur in environmentally relevant exposures (as low as 0.07 µM). In this study, we examined the gene expression alteration in HepG2 cells exposed to arsenic trioxide (5 nM to 40 µM as As2O3 for 48 hours) by DNA microarray with 8795 human genes. HepG2 cells were also exposed to ε-caprolactam as a reference of non carcinogen since it is the only chemical categorized in IARC’s group 4 (Probably Not Carcinogenic). MQ water was used as control. For replicate, three dishes were prepared for each sample and individually treated in parallel.
Project description:Copper is an essential cofactor for many enzymes but at high concentrations it is toxic for the cell. Copper ion concentrations ≥50 µM inhibited growth of Corynebacterium glutamicum. The transcriptional response to 20 µM Cu2+ was studied using DNA microarrays and revealed 26 genes that showed a ≥3-fold increased mRNA level, including cg3280-cg3289. Several genes in this genomic region code for proteins presumably involved in the adaption to copper-induced stress, e. g. a multicopper oxidase and a copper-transport ATPase. In addition, this region includes the copRS genes (previously named cgtRS9) which encode a two-component signal transduction system composed of the histidine kinase CopS and the response regulator CopR. Deletion of the copRS genes increased the sensitivity of C. glutamicum towards copper ions, but not to other heavy metal ions. Using comparative transcriptome analysis of the ΔcopRS mutant and the wild type in combination with electrophoretic mobility shift assays and reporter gene studies the CopR regulon and the DNA-binding motif of CopR were identified. Evidence was obtained that CopR binds only to the intergenic region between cg3285 and cg3286 in the genome of C. glutamicum and activates expression of the divergently oriented gene clusters cg3285-cg3280 and cg3286-cg3289. Altogether, our data suggest that CopRS is the key regulatory system in C. glutamicum for the extracytoplasmic sensing of elevated copper ion concentrations and for induction of a set of genes capable of diminishing copper stress. Four or five biological replicates of each experiment were performed. Experiment 1: Transcriptome comparison of wild type grown with 1.25 µM or with 21.25 µM CuSO4; Exp. 2: WT vs. copRS deletion mutant grown with 21.25 µM CuSO4; For analysis via DNA microarrays, the RNA was isolated from exponentially growing cells cultivated in CgXII medium containing glucose as carbon source and either 1.25 uM CuSO4 or 21.25 uM CuSO4.
Project description:Mycelium from the rice blast fungus Magnaporthe oryzae was grown in both rich medium and under nutrient limiting conditions. Genes were identified that were more highly expressed in one condition as compared to the other. Samples were taken from mycelium grown in both complete medium and in glucose minimal medium. One replicate for each sample.