Project description:This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected. SRA accession number: SRP003001.1 Sequencing of poly(A)+ RNA from S2R+ cells treated with either lacZ (control) or mago (experimental) dsRNA
Project description:DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
Project description:This study was designed to identify changes in gene expression resulting from depletion of Mago nashi (Mago), a core subunit of the exon junction complex. Drosophila S2R+ cells were treated with double-stranded RNA targeting either LacZ or Mago for 6 days. Poly(A)+ RNA was purified from each sample and sequenced using 54 bp reads on an Illumina Genome Analyzer II. Fold changes in expression were calculated for each gene as the ratio of the reads per kilobase per million reads (RPKM) for Mago relative to LacZ. In other experiments, we have shown that Mago is required for correct splicing of the MAP kinase gene and its depletion causes a large reduction in MAP kinase mRNA levels. MAP kinase is a large gene in heterochromatin. In this study, we find that heterochromatic genes are disproportionately down-regulated in Mago-depleted cells, and those with large introns are particularly likely to be affected. SRA accession number: SRP003001.1
Project description:ChIP of PolII in S2R+ cells depleted for EJC components or RnpS1 [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
Project description:ChIP of K4Me3 in Ctr condition and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]
