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Posttranscriptional mRNA expression changes in stress

ABSTRACT: Posttranscriptional mRNA expression changes in stress

PROVIDER: PRJEB9446 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR899353.fastq.gz	Fastqsanger.gz
	ERR899356.fastq.gz	Fastqsanger.gz
	ERR899358.fastq.gz	Fastqsanger.gz
	ERR899359.fastq.gz	Fastqsanger.gz
	ERR899360.fastq.gz	Fastqsanger.gz

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Posttranscriptional mRNA expression changes in stress

Project description:HEK T293 cells were treated with Anisomycin or the solvent control DMSO. Cells were fractionated and cytoplasmic and nuclear RNA were isolated. pre-mRNA-Seq was performed on stressed and unstressed nuclear RNA samples. mRNA-Seq was performed on stressed and unstressed cytoplasmic RNA samples. In addition, polyadenylation sites were globally mapped by applying the 3'T-fill method on the same stressed and unstressed cytoplasmic RNA samples.

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Coordinated posttranscriptional mRNA population dynamics during T-cell activation

Project description:Although RNA-binding proteins (RBPs) coordinate many key decisions during cell growth and differentiation, the dynamics of RNA–RBP interactions have not been extensively studied on a global basis. We immunoprecipitated endogenous ribonucleoprotein complexes containing HuR and PABP throughout a T-cell activation time course and identified the associated mRNA populations using microarrays. We used Gaussian mixture modeling as a discriminative model, treating RBP association as a discrete variable (target or not target), and as a generative model, treating RBP-association as a continuous variable (probability of association). We report that HuR interacts with different populations of mRNAs during T-cell activation. These populations encode functionally related proteins that are members of the Wnt pathway and proteins mediating T-cell receptor signaling pathways. Moreover, the mRNA targets of HuR were found to overlap with the targets of other posttranscriptional regulatory factors, indicating combinatorial interdependence of posttranscriptional regulatory networks and modules after activation. Applying HuR mRNA dynamics as a quantitative phenotype in the drug-gene-phenotype Connectivity Map, we identified candidate small molecule effectors of HuR and T-cell activation. We show that one of these candidates, resveratrol, exerts T-cell activation-dependent posttranscriptional effects that are rescued by HuR. Thus, we describe a strategy to systematically link an RBP and condition-specific posttranscriptional effects to small molecule drugs. Keywords: Timecourse, RIP, Immunoprecipitation, HuR, ELAVL1, PABP, T cell activation

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Pseudomonas aeruginosa GidA modulates the expression of catalases at the posttranscriptional level and plays a role in virulence

Project description:The expression of the antioxidant genes, katA and katB, in response to oxidative stress in Pseudomonas aeruginosa has recently been shown to be controlled at the translational level. Here, we demonstrate that the expression of katA and katB is also modulated by gidA at the posttranscriptional level.

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G3BP2B stress granules regulate mRNA expression under ER stress [Riboseq_Exp2]

Project description:G3BP2B stress granules regulate mRNA expression under ER stress [Riboseq_Exp2]

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G3BP2B stress granules regulate mRNA expression under ER stress [1]

Project description:G3BP2B stress granules regulate mRNA expression under ER stress [1]

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G3BP2B stress granules regulate mRNA expression under ER stress [2]

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G3BP2B stress granules regulate mRNA expression under ER stress [3]

Project description:G3BP2B stress granules regulate mRNA expression under ER stress [3]