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RNA-Seq, Ribo-Seq and iCLIP of P19 cells overexpressing SRSF7

ABSTRACT: RNA-Seq, Ribo-Seq and iCLIP of P19 cells overexpressing SRSF7

PROVIDER: PRJNA598362 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10502429.fastq.gz	Fastqsanger.gz
	SRR10502430.fastq.gz	Fastqsanger.gz
	SRR10502431.fastq.gz	Fastqsanger.gz
	SRR10502432.fastq.gz	Fastqsanger.gz
	SRR10502433.fastq.gz	Fastqsanger.gz

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Transcriptome-wide mapping of RNA:protein interactions of SRSF7 variants in P19 cells by iCLIP and piCLIP

Project description:We used P19 cells that overexpress GFP-tagged SRSF7 by 3.4-fold and expression-matched SRSF7 mutants that either lack a functional Zinc-knuckle domain or a part of their RS-domain and compared the extent and pattern of binding to mRNAs. For this we performed iCLIP using anti-GFP antibodies. We also performed iCLIP from monosomal and polysomal fractions. In addition we performed iCLIP using anti-SRSF7 antibodies to compare the binding patterns of SRSF7-GFP, endogenous SRSF7 protein and its truncated SRSF7_RRM variant.

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Project description:We used P19 cells that overexpress GFP-tagged SRSF7 by 3.4-fold.

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RNA-Seq and Ribo-Seq of P19 WT and SRSF7-GFP overexpressing cells

Project description:RNA-Seq and Ribo-Seq of P19 WT and SRSF7-GFP overexpressing cells

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RNA-Seq, Ribo-Seq and iCLIP of P19 cells overexpressing SRSF7

Project description:This SuperSeries is composed of the SubSeries listed below.

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iCLIP mapping of coilin-RNA interactions in HeLa and P19 cells

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Project description:Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3’ untranslated regions (3’UTRs). APA regulates stage- and tissue-specific gene expression by affecting the stability, subcellular localization and translation rate of transcripts. We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained, however, unknown. Here, we combined iCLIP, RNA-Seq and 3’-end sequencing to find that both proteins bind upstream of proximal PASs (pPASs), yet they exert opposite effects on 3’UTR length. We show that SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, thereby generating short 3’UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, and hypo-phosphorylation contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3’UTRs by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon reduced expression of SRSF3, CFIm levels strongly decrease and 3’UTRs are globally shortened. In SRSF3-regulated transcripts, CFIm and FIP1 bind upstream of dPASs and promote their usage. Surprisingly, both factors are also recruited to pPASs under conditions where their usage is blocked, suggesting the formation of inactive cleavage complexes. Thus, we identify SRSF3 as a novel regulator of CFIm activity, provide evidence that CFIm inhibits pPAS usage and show that small differences in the domain architecture of SR proteins confer opposite effects on PAS selection.

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