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MRNAseq of Drosophila S2 cells after knockdown of EJC components

ABSTRACT: mRNAseq of Drosophila S2 cells after knockdown of EJC components

PROVIDER: PRJEB29045 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2822670.fastq.gz	Fastqsanger.gz
	ERR2822671.fastq.gz	Fastqsanger.gz
	ERR2822672.fastq.gz	Fastqsanger.gz
	ERR2822673.fastq.gz	Fastqsanger.gz
	ERR2822674.fastq.gz	Fastqsanger.gz

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mRNAseq of Drosophila S2 cells after knockdown of EJC components

Project description:This study used Drosophila melanogaster S2 cells treated with siRNA against the EJC components mago or eIF4A3, or a non-targeting control siRNA (three samples per condition). mRNA-seq libraries were prepared from the samples and the data was used to examine 'RS-exons' - exons which reconstitute a 5' splice site when they are spliced to the upstream exon. In contrast to mammalian cells, RS-exons are not recursively spliced out from Drosophila transcripts after perturbation of the EJC.

2018-10-15 | E-MTAB-7271 | biostudies-arrayexpress

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Project description:mRNAseq of Drosophila S2 cells after knockdown of EJC components

2019-05-15 | E-MTAB-7271 | ExpressionAtlas

Transcriptional profiling of EJC depletion by RNA-Seq using the SOLiD platform (Applied Biosystems)

Project description:Signaling pathways are controlled by a vast array of post-translational mechanisms. By contrast, little is known regarding the mechanisms that regulate the expression of their core components. We conducted an RNAi screen in Drosophila for factors modulating RAS/MAPK signaling and identified the Exon Junction Complex (EJC) as a novel key element of this pathway. The EJC binds the exon-exon junctions of mRNAs, and thus far, has been linked exclusively to post-splicing events. Here, we report that the EJC is required for proper splicing of mapk transcripts by a mechanism that apparently controls exon definition. Moreover, whole transcriptome and RT-PCR analyses of EJC-depleted cells revealed that the splicing of long intron-containing genes, which includes mapk, is sensitive to EJC activity. These results identify a role for the EJC in the splicing of a subset of transcripts and suggest that RAS/MAPK signaling depends on the regulation of MAPK levels by the EJC. Transcriptome sequencing (RNA-Seq) of Drosophila S2 cells to monitor the effect of EJC depletion on the cellular mRNA expression profile. Each treatment (dsRNA knockdown of MAGO (CG9401), dsRNA knockdown of eIF4AIII (CG7483)) was done in biological duplicate and each sample was sequenced separately on a quad slide on the SOLiD 3.0 platform. The reference samples were treated with a dsRNA targeted to GFP.

2010-10-19 | E-GEOD-24012 | biostudies-arrayexpress

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:Promoter-proximal pausing of RNA polymerase II (Pol II) is a widespread transcriptional regulatory step across metazoans. Here we find that the nuclear exon junction complex (pre-EJC) is a critical and conserved regulator of this process. Depletion of pre-EJC subunits leads to a global decrease in Pol II pausing and to premature entry into elongation. This effect occurs, at least in part, via non-canonical recruitment of pre-EJC components at promoters. Failure to recruit the pre-EJC at promoters results in increased binding of the positive transcription elongation complex (P-TEFb) and in enhanced Pol II release. Notably, restoring pausing is sufficient to rescue exon skipping and the photoreceptor differentiation defect associated with depletion of pre-EJC components in vivo. We propose that the pre-EJC serves as an early transcriptional checkpoint to prevent premature entry into elongation, ensuring proper recruitment of RNA processing components that are necessary for exon definition.

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RNA-seq of Drosophila S2 cells after RNAi knock-down of signal transduction components

Project description:We performed RNAi knockdown experiments on 15 different signal transduction components in Drosophila S2 cells and prepared RNA libraries from the poly-adenylated fraction of the RNA. SOLiD sequencing of strand-specific, barcoded transcriptome libraries yielded expression profiles allowing us to extract common pathway signatures and indicated that Cka may function as novel regulator in Ras/MAPK signaling

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Project description:RNAi of signal transduction components in Drosophila S2 cells

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The Cellular EJC Interactome Reveals Higher-Order mRNP Structure and an EJC-SR Protein Nexus

Project description:To uncover exon junction complex (EJC) deposition sites on cellular mRNAs, RNA footprints of EJC immuo-purified from HEK293 cells were deep sequenced. The analysis of these data revealed that major “canonical” EJC occupancy site in vivo lies 24 nucleotides upstream of exon junctions (-24 position) and that the majority of exon junctions carry an EJC. Unexpectedly, we find that many sites further upstream of -24 position are also enriched in these EJC footprints. These "non-canonical" sites are binding sites of EJC-interacting proteins with a subset being occupied by SR proteins. Thus, an EJC-SR protein nexus exists within spliced mRNPs and is revealed here.

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Project description:EJC ipaRt: Transcriptome-wide definition of stable EJC RNA interactions in cytoplasm of adult flies

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