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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq SS]

ABSTRACT: The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq SS]

PROVIDER: PRJNA548150 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9260630.fastq.gz	Fastqsanger.gz
	SRR9260631.fastq.gz	Fastqsanger.gz
	SRR9260632.fastq.gz	Fastqsanger.gz
	SRR9260625.fastq.gz	Fastqsanger.gz
	SRR9260626.fastq.gz	Fastqsanger.gz

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq SS]

Project description:This work shows that the exosome modulates the levels of LINE-1 retrotransposons, miRNAs, lncRNAs and specific mRNAs that encode developmental regulators or affect their expression. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation.

2019-07-11 | GSE132468 | GEO

The RNA exosome nuclease complex regulates human embryonic stem cell differentiation

Project description:The RNA exosome nuclease complex regulates human embryonic stem cell differentiation

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Project description:The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [RNA-Seq rescue_SS]

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

Project description:The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

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Project description:The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [HITS-CLIP]

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [PAR-iCLIP]

2019-07-11 | GSE132466 | GEO

The RNA exosome nuclease complex regulates human embryonic stem cell differentiation [HITS-CLIP]

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The RNA exosome nuclease complex regulates human embryonic stem cell differentiation.

Project description:A defining feature of embryonic stem cells (ESCs) is the ability to differentiate into all three germ layers. Pluripotency is maintained in part by a unique transcription network that maintains expression of pluripotency-specific transcription factors and represses developmental genes. While the mechanisms that establish this transcription network are well studied, little is known of the posttranscriptional surveillance pathways that degrade differentiation-related RNAs. We report that the surveillance pathway mediated by the RNA exosome nuclease complex represses ESC differentiation. Depletion of the exosome expedites differentiation of human ESCs into all three germ layers. LINE-1 retrotransposons and specific miRNAs, lncRNAs, and mRNAs that encode developmental regulators or affect their expression are all bound by the exosome and increase in level upon exosome depletion. The exosome restrains differentiation in part by degrading transcripts encoding FOXH1, a transcription factor crucial for mesendoderm formation. Our studies establish the exosome as a regulator of human ESC differentiation and reveal the importance of RNA decay in maintaining pluripotency.

| S-EPMC6683745 | biostudies-literature

RNA-seq of Schizosaccharomyces pombe nuclear RNA exosome mutants

Project description:Nuclear 3’ to 5’ nuclease RNA exosome plays a key role in quality control and processing of multiple protein-coding and non-coding transcripts made by RNA polymerase II. A mechanistic understanding of exosome function remains a challenge given the large number of RNA species and intervening RNA processing factors. Here we analysed changes in the poly(A)+ RNA proteins interactome provoked by mutations in three distinct subunits of the nuclear RNA exosome. Our data demonstrate a functional connection between Rrp6 and Mtl1 in controlling processing and levels of multiple protein-coding and non-coding transcripts. Furthermore, we show that exosome mutants accumulate components of U1 and U2 snRNPs and show depletion of NTC components from RNA suggesting that the stage prior to the activation of the spliceosome represents a critical quality control step. We have also identified potential new RNA binding factors involved in exosome regulation, including a zinc-finger protein called Mub1 that controls levels of selected transcripts encoding for proteins implicated in stress response. Collectively, our data have provided a global view of RNA metabolism alterations in exosome deficient cells and revealed RNA binding proteins that may act as novel exosome cofactors.

2020-04-17 | GSE148799 | GEO

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