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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking

ABSTRACT: The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking

PROVIDER: PRJNA952202 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24064886.fastq.gz	Fastqsanger.gz
	SRR24063787.fastq.gz	Fastqsanger.gz
	SRR24064887.fastq.gz	Fastqsanger.gz
	SRR24063788.fastq.gz	Fastqsanger.gz
	SRR24064888.fastq.gz	Fastqsanger.gz

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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

Project description:Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3’ end anchored RNA sequencing, we mapped the alternative polyadenylation landscape (APA) following TGF-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3’UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a small subset of events including the length of its own transcript. Analysis of QKI CLIP-seq data identified the binding of QKI within 3’UTRs was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts are altered to produce predominantly shorter 3’UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.

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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PANQKI_HITS-CLIP]

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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

Project description:The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PANQKI_HITS-CLIP]

Project description:The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PANQKI_HITS-CLIP]

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The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking.

Project description:Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3' end anchored RNA sequencing, we mapped the alternative polyadenylation (APA) landscape following Transforming Growth Factor (TGF)-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3'UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a subset of events including the length of its own transcript. Analysis of QKI crosslinked immunoprecipitation (CLIP)-sequencing data identified the binding of QKI within 3' untranslated regions (UTRs) was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts is altered to produce predominantly shorter 3'UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.

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Coupling between alternative polyadenylation and alternative splicing is limited to terminal introns

Project description:Alternative polyadenylation has been implicated as an important regulator of gene expression. In some cases, alternative polyadenylation is known to couple with alternative splicing to influence last intron removal. However, it is unknown whether alternative polyadenylation events influence alternative splicing decisions at upstream exons. Knockdown of the polyadenylation factors CFIm25 or CstF64 was used as an approach in identifying alternative polyadenylation and alternative splicing events on a genome-wide scale. Although hundreds of alternative splicing events were found to be differentially spliced in the knockdown of CstF64, genes associated with alternative polyadenylation did not exhibit an increased incidence of alternative splicing. These results demonstrate that the coupling between alternative polyadenylation and alternative splicing is usually limited to defining the last exon. The striking influence of CstF64 knockdown on alternative splicing can be explained through its effects on UTR selection of known splicing regulators such as hnRNP A2/B1, thereby indirectly influencing splice site selection. We conclude that changes in the expression of the polyadenylation factor CstF64 influences alternative splicing through indirect effects. HeLa cell line was stably transfected with shRNA plasmids targeting CstF64. Total RNA was isolated from CstF64 KD cells and wild-type control cells using Trizol according to manufacturerâs protocols. Samples were deep sequenced in duplicate using the Illumina GAIIx system.

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