Widespread regulation of gene expression by the histone acetyltransferase dTip60
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE13878 | GEO | 2010/01/19
SECONDARY ACCESSION(S): PRJNA110491
REPOSITORIES: GEO
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Project description:We used microarrays to detail the global gene expression changes following RNAi knock-down of dTip60 in Drosophila SL2 cells Experiment Overall Design: We compared SL2 cells treated with dTip60-RNAi with SL2 cells mock-treated with eGFP-RNAi to determine global gene expression changes by microarray analysis
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Project description:Profiling of changes in steady state RNA levels upon RNAi-mediated knockdown of the nucleosome remodeling ATPase ISWI in Drosophila SL2 cells. Quantitation of the corresponding proteomes has been performed to describe transcriptome-proteome relations. The analysis indicates a limited correlation of the two expression steps. Experiment Overall Design: Drosophila SL2 cells were incubated 7 days after treatment with 10 ug of dsRNA directed against GST or ISWI, respectively. 3 biological replicates per experimental conditions have been collected.
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Project description:Selenophosphate, which is the active donor of selenium in selenocysteine (Sec) biosynthesis is synthesized from selenite and ATP by an enzyme designated as selenophosphate synthetase (SPS).There are two isoforms of SPS in higher eukaryotes,SPS1 and SPS2. Initially, both SPS1 and SPS2 were thought to be involved in selenophosphate synthesis. However, it was subsequently shown that only SPS2 catalyzes selenophosphate synthesis. Although SPS1 is an essential gene in Drosophila, its function has not been determined. To identify transcriptional profile of SPS1 knockdown cells, which could offer valuable clues to identify molecular mechanism of SPS1, we introduced RNAi using its cognate double-stranded RNA into Drosophila SL2 cells, and then microarray analysis was carried out. Experiment Overall Design: In order to find primary or secondary target gene which is regulated by SPS1,Drosophila SL2 cells were harvested at day1, day3 and day5 after SPS1 knockown for RNA extraction and hybridization on Affymetrix microarrays.
2009-08-22 | E-GEOD-17685 | biostudies-arrayexpress
Project description:To evaluate the specificity of long dsRNAs used in high-throughput RNAi screens performed at the Drosophila RNAi Screening Center (DRSC), we performed a global analysis of their activity in 30 genome-wide screens completed at our facility. Surprisingly, our analysis predicts that dsRNAs containing ≥19 nucleotide perfect matches identified in silico to unintended targets may contribute to a significant false positive error rate arising from off-target effects. We confirmed experimentally that such sequences in dsRNAs lead to false positives and to the efficient knockdown of a cross-hybridizing transcript, raising a cautionary note when interpreting results based on the use of a single dsRNA per gene. Although a full appreciation of all causes of false positive errors remains to be determined, we suggest simple guidelines to help ensure high quality information from RNAi high-throughput screens Keywords: Specificity of long dsRNAs, Drosophila melanogaster, SL2 cell line, custom cDNA arrays, off-target effects, Drosophila RNAi Screening Center (DRSC)
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Project description:Although the functional role of chromatin marks at promoters in mediating cell-restricted gene expression has been well characterized, the role of intragenic chromatin marks is not well understood, especially in endothelial cell (EC) gene expression. Here, we characterized the histone H3 and H4 acetylation profiles of 19 genes with EC-enriched expression via locus-wide chromatin immunoprecipitation followed by ultra-high-resolution (5 bp) tiling array analysis in ECs versus non-ECs throughout their genomic loci. Importantly, these genes exhibit differential EC enrichment of H3 and H4 acetylation in their promoter in ECs versus non-ECs. Interestingly, VEGFR-2 and VEGFR-1 show EC-enriched acetylation across broad intragenic regions and are up-regulated in non-ECs by histone deacetylase inhibition. It is unclear which histone acetyltransferases (KATs) are key to EC physiology. Depletion of KAT7 reduced VEGFR-2 expression and disrupted angiogenic potential. Microarray analysis of KAT7-depleted ECs identified 263 differentially regulated genes, many of which are key for growth and angiogenic potential. KAT7 inhibition in zebrafish embryos disrupted vessel formation and caused loss of circulatory integrity, especially hemorrhage, all of which were rescued with human KAT7. Notably, perturbed EC-enriched gene expression, especially the VEGFR-2 homologs, contributed to these vascular defects. Mechanistically, KAT7 participates in VEGFR-2 transcription by mediating RNA polymerase II binding, H3 lysine 14, and H4 acetylation in its intragenic region. Collectively, our findings support the importance of differential histone acetylation at both promoter and intragenic regions of EC genes and reveal a previously underappreciated role of KAT7 and intragenic histone acetylation in regulating VEGFR-2 and endothelial function.
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