The Drosophila Tis11 protein and its effects on mRNA expression in flies
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Perry Blackshear
PROVIDER: E-GEOD-58937 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Insects generally express one tristetraprolin family member, proteins that in mammals promote mRNA decay. The Drosophila protein, Tis11, can promote mRNA decay in cells, and its deficiency in flies results in major changes in mRNA levels. Tis11 deficiency in Drosophila results in accumulation of potentialtarget transcripts. Tis11 can affect post- transcriptional gene expression in adult flies by regulating mRNA decay.
2014-10-23 | GSE58937 | GEO
Project description:In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs that suppress gene expression at the posttranscriptional level. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, targets ARE-containing reporter mRNAs for rapid degradation in SL2 cells. To identify Drosophila mRNA targets of Tis11, we performed genome-wide expression profiling after dsRNA-mediated depletion of endogenous Tis11 in SL2 cells. Furthermore, we studied the involvement of Tis11 in regulating the Drosophila immune response by profiling mRNA expression after LPS treatment, in the presence or absence of Tis11.
2011-03-25 | GSE28147 | GEO
Project description:Purpose: localized aberrant cell proliferation induced by activation of Yki in ISCs impairs muscle functions. To gain insight into the cross talk between intestine and muscle, we performed a transcriptomic analysis of thoracic muscles in ISC overproliferation flies. Methods: To extract total RNAs for RNA-Seq experiment, we used 10 thoraces dissected out from both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C. After assessing RNA quality with Agilent Bioanalyzer, mRNAs were enriched by poly-A pull-down. Then, sequencing libraries constructed with Illumina TruSeq RNA prep kit were sequenced using Illumina HiSeq2000 at the Columbia Genome Center (http://systemsbiology.columbia.edu/genome-center). We multiplexed samples in each lane, which yields targeted number of single-end 100 bp reads for each sample, as a fraction of 180 million reads for the whole lane. Sequence reads were mapped back to the Drosophila genome (flybase genome annotation version r5.51) using Tophat. With the uniquely mapped reads, we quantified gene expression levels using Cufflinks (FPKM values). Next, we performed data normalization on the read counts and applied a negative binomial statistical framework using the Bioconductor package DESeq to quantify differential expression between experimental and control data. Results: Gene list enrichment analysis of the downregulated muscle transcriptome by ISCs Yki overexpressioin revealed a striking enrichment of multiple metabolic processes impinging on carbohydrate metabolism, amino acid metabolism, metabolism of vitamins and cofactors, and metabolism of xenobiotics by cytochrome P450. Interestingly, target genes of Foxo, a transcription factor inhibited by insulin/IGF signaling, are enriched in the upregulated muscle transcriptome of ISCs Yki overepxression flies. In particular, induction of InR and Thor, well-characterized targets of Foxo, are validated with qPCR. Conclusions: Our study represents ISCs overproliferation induced by Yki overepxression remotedly regulates muscle function and gene expression probally via modulation of insulin signaling in muscle. Our results show that RNA-seq offers a comprehensive evaluation of signaling network and biological process in organ communication. Thoraces mRNA profiles of both esg-Gal4, tub-Gal80ts, UAS-GFP/+ (Con) and esg-Gal4, tub-Gal80ts, UAS-GFP/UAS-Yki-act (Yki) flies incubated for 8 days at 29°C were generated by deep sequencing, in replicate, using Illumina HiSeq2000.
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Project description:In mammalian cells, AU-rich elements (AREs) are well known regulatory sequences located in the 3' untranslated region (UTR) of many short-lived mRNAs that suppress gene expression at the posttranscriptional level. Tis11, a zinc finger RNA-binding protein homologous to mammalian tristetraprolin, targets ARE-containing reporter mRNAs for rapid degradation in SL2 cells. To identify Drosophila mRNA targets of Tis11, we performed genome-wide expression profiling after dsRNA-mediated depletion of endogenous Tis11 in SL2 cells. Furthermore, we studied the involvement of Tis11 in regulating the Drosophila immune response by profiling mRNA expression after LPS treatment, in the presence or absence of Tis11. SL2 cells were treated with either dsRNA against Tis11 or dsRNA against GFP (control). After 4 days of treatment with 12.5 microgram dsRNA / ml medium, total RNA was extracted and hybridized to Drosophila Genome 2.0 Arrays (Affymetrix, Cat. No. 900531). Where indicated, cells were treated with lipopolysaccharide (LPS, Sigma, O55:B5) at a concentration of 10 microgram / ml for 4 hours before lysis. All experiments were performed in 3 biological replicates.
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Project description:Microarray data of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Nimblegen 12-plex array platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #. PolyA+ mRNA was isolated in triplicate to quadruplicate from 5 day old adult female or male whole flies. Female and male mRNA were labeled with Cy3 or Cy5 dyes separately and hybridized to Drosophila 12-plex Nimblegen arrays.
2012-04-02 | E-GEOD-31386 | biostudies-arrayexpress
Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the Illumina platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies).
2012-04-03 | E-GEOD-31549 | biostudies-arrayexpress
Project description:we show that Tis11, an Adenine-uridine Rich Element (ARE) binding protein that promotes mRNA degradation, is required to re-establish basal proliferation rates of adult Drosophila intestinal stem cells (ISC) after a regenerative episode. We find that Tis11 limits ISC proliferation specifically after proliferation has been stimulated in response to heat stress or infection, and show that Tis11 expression and activity are increased in ISCs during tissue repair. Based on stem cell transcriptome analysis and RNA immunoprecipitation, we propose that Tis11 activation represents an integral part of a negative feedback mechanism that limits the expression of key components of several signaling pathways that control ISC function and proliferation. Our results identify Tis11 mediated mRNA decay as an evolutionarily conserved mechanism of re-establishing basal proliferation rates of stem cells in regenerating tissues.
2017-09-05 | GSE97216 | GEO
Project description:RNA-Seq reads of DrosDel deficiency (Df/+) and parental strain diploid flies along with spike-in controls was performed on the SOLiD platform. Samples are named in this dataset according to the following sample naming scheme: tissue_genotype shorthand_sex_biological replicate #_platform_technical replicate. We sequenced mRNA from pools of female or male DrosDel and w1118 (parental strain for the Df/+ flies). The same sample was sequenced across two flow cells on the SOLiD platform.
2012-04-03 | E-GEOD-31401 | biostudies-arrayexpress
Project description:The ZFP36L3 protein is a rodent-specific, placenta- and yolk sac-specific member of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins. These proteins bind to AU-rich elements in target mRNAs, and promote their deadenylation and decay. Mice deficient in ZFP36L3 exhibited decreased neonatal survival rates, but no apparent morphological changes in the placenta or surviving offspring. Zfp36l3 is paternally imprinted, with profound parent-of-origin effects on gene expression. RNASeq of KO placental mRNA revealed many significantly affected transcripts, some of which exhibited decreased decay rates in differentiated trophoblast stem cells derived from KO blastocysts. The type 1 transferrin receptor mRNA was unexpectedly decreased in KO placentas, despite an increase in its stability. This receptor is critical for placental iron uptake from the maternal circulation, and its decrease was accompanied by decreased iron stores in the KO fetus, suggesting that this intrauterine deficiency might have deleterious consequences in later life.
2016-05-05 | GSE66138 | GEO
Project description:The ZFP36L3 protein is a rodent-specific, placenta- and yolk sac-specific member of the tristetraprolin (TTP) family of CCCH tandem zinc finger proteins. These proteins bind to AU-rich elements in target mRNAs, and promote their deadenylation and decay. Mice deficient in ZFP36L3 exhibited decreased neonatal survival rates, but no apparent morphological changes in the placenta or surviving offspring. Zfp36l3 is paternally imprinted, with profound parent-of-origin effects on gene expression. RNASeq of KO placental mRNA revealed many significantly affected transcripts, some of which exhibited decreased decay rates in differentiated trophoblast stem cells derived from KO blastocysts. The type 1 transferrin receptor mRNA was unexpectedly decreased in KO placentas, despite an increase in its stability. This receptor is critical for placental iron uptake from the maternal circulation, and its decrease was accompanied by decreased iron stores in the KO fetus, suggesting that this intrauterine deficiency might have deleterious consequences in later life.
2016-05-05 | GSE66137 | GEO