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DAM ID sequencing of DAM fusion with Cdk9 in Control and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

ABSTRACT: DAM ID sequencing of DAM fusion with Cdk9 in Control and Mago knockdown [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

PROVIDER: PRJNA434225 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6729550_1.fastq.gz	Fastqsanger.gz
	SRR6729550_2.fastq.gz	Fastqsanger.gz
	SRR6729551_1.fastq.gz	Fastqsanger.gz
	SRR6729551_2.fastq.gz	Fastqsanger.gz
	SRR6729552_1.fastq.gz	Fastqsanger.gz

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DAM ID sequencing of DAM fusion with Cdk9 in Control and Mago knockdown [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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Effect of mago nashi depletion on gene expression in Drosophila S2R+ cells

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

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Dam(ID)-profiling in B cells

Project description:Both chromatin access, and binding of AID in B cells are of major scientific interest. Therefore DamID was setup in B cells. AID specific binding could not be identified. In contrast to binding, DAM profiling provide a upmost useful tool in defining chromatin access in vivo.

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Project description:MAGO proteins safeguard the plant male germline under environmental stress

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