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DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

ABSTRACT: DRB-4SU seq of Ctrl and Mago condition in 2 replicates with fragmentation [Promoter-proximal pausing mediated by the exon junction complex regulates splicing]

PROVIDER: PRJNA418417 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6292540_1.fastq.gz	Fastqsanger.gz
	SRR6292540_2.fastq.gz	Fastqsanger.gz
	SRR6292541_1.fastq.gz	Fastqsanger.gz
	SRR6292541_2.fastq.gz	Fastqsanger.gz
	SRR6292538_1.fastq.gz	Fastqsanger.gz

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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: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.

2019-01-22 | GSE106906 | GEO

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

2010-10-21 | GSE23997 | GEO

m6A RNA methylation regulates promoter proximal pausing of RNA Pol II (DRB-4sU-seq)

Project description:m6A RNA methylation regulates promoter proximal pausing of RNA Pol II (DRB-4sU-seq)

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Effect of mago nashi depletion on gene expression in Drosophila S2R+ cells

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MAGO

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

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Meiosis-associated argonaute (MAGO) proteins are necessary for meiosis in maize

Project description:Plants do not specify their germline until late in their life cycle. Hence, the plant germline is normally specified from terminally differentiated somatic cells, though the precise mechanism(s) are unknown. We have found that male gametogenesis in maize is associated with the accumulation of distinct 21-nt phased small-interfering RNAs (phasiRNAs) generated by meiosis-associated argonaute (MAGO) proteins. MAGO1 accumulates in the epidermis of pre-meiotic anthers while MAGO2 is found in developing meiocytes. We have found that MAGO proteins are required for meiocyte development as mutants display chromosomal defects and male infertility. Furthermore, we detect the heat stress-induced activation of a distinct class of Long terminal repeat retrotransposons in the male germline of MAGO mutants. Our data suggests that MAGO proteins and the reproductive phasiRNAs play important roles protecting the germline from transposable elements during environmental stress conditions.

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Effect of 4sU labeling concentrations on quantification bias in nucleotide conversion RNA-seq data

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Effect of transcription inhibitor DRB on gene expression under KRASG12V induction of SAEC

Project description:To investigate RNA expression sensitive to DRB, we induced KRASG12V in SAEC cells with or without DRB treatment. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different conditions.

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Effect of 4sU labeling durations on quantification bias in nucleotide conversion RNA-seq data

Project description:To investigate the effect of labeling durations on quantification bias in nucleotide conversion RNA-seq, we labeled NIH cells with 4sU. We then measured 4sU dropout in 4sU samples compared to 4sU naive samples.

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