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Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RIP-seq)

ABSTRACT: Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RIP-seq)

PROVIDER: PRJNA633561 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11808545_1.fastq.gz	Fastqsanger.gz
	SRR11808545_2.fastq.gz	Fastqsanger.gz
	SRR11808546_1.fastq.gz	Fastqsanger.gz
	SRR11808546_2.fastq.gz	Fastqsanger.gz
	SRR11808547_1.fastq.gz	Fastqsanger.gz

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Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RIP-seq)

Project description:Poly (A) binding protein interacting protein 1 (PAIP1) has been shown to causally contribute to the development and progression of cancer. However, the biological function of PAIP1 in tumorigenesis remains largely unexplored. Here, we used RNA immunoprecipitation to map the interactions between PAIP1 and RNA on a genome wide level. A genome wide analysis showed that PAIP1 binding is specifically enriched in exon, intron and 3’ untranslated regions. The genes bound by PAIP1 were strongly associated with cancer-related pathways and we found that PAIP1 knockdown mediates the statistically significant regulation of alternative splice events. These data suggest that PAIP1 may influence alternative splicing and, using a VEGF-A minigene, we showed that overexpression of PAIP1 inhibits the expression of exon 6. Further analysis of PAIP1 showed that interacting proteins participate in splice factors, spliceosomes and exon junction complex assembly. Our work has demonstrated that PAIP1 has specific RNA binding properties that help to coordinate the isoform-specific expression of coding genes. These genes are associated with cancer, which suggests that PAIP1 is an important regulator of key cancer processes.

2022-05-05 | GSE150780 | GEO

Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RNA-Seq)

2022-05-05 | GSE150779 | GEO

Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing

Project description:Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing

| PRJNA633557 | ENA

Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RNA-Seq)

Project description:Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing (RNA-Seq)

| PRJNA633559 | ENA

Identification of the RNA-protein interactions of PAIP1, which plays a novel role in alternative mRNA splicing

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

2022-05-05 | GSE150781 | GEO

PAIP1 promote the progress of liver cancer via regulating expression of immune and inflammatory response associated genes

Project description:Poly(A) binding protein interacting protein 1 (PAIP1) is a translation regulator and also regulate the decay of mRNA. PAIP1 has also been reported to be a marker of increased invasive potential of liver cancer. However, the underlying molecular mechanism of PAIP1 in liver cancer is still unclear. Here, the gene expression profile of HepG2 cells transfected with PAIP1 shRNA (shPAIP1) was compared with cells transfected with empty vector (shCtrl). The results showed that shPAIP1 extensively affects the transcriptional level of 893 genes in HepG2 cells. In particular, GO analysis showed that a large number of up-regulated genes were annotated with terms including cell cycle and WNT receptor signaling pathway. The down-regulated genes were enriched in some pathways including immune response and inflammatory response. qPCR confirmed that PAIP1 knockdown significantly negatively or positively affected the expression of selected DEGs including interleukin-10 signaling pathway genes in HepG2 cells. Expression analysis of TCGA revealed that PAIP1 had positive correlations with IL1R2 and PTAFR in liver tumor tissue, respectively. Our results demonstrated that PAIP1 was not only a translation regulator, but also a transcription regulator in liver cancer. Thus, our study provides important cues for further study on the regulatory mechanism of PAIP1 in liver cancer

2023-03-12 | GSE185866 | GEO

CPEB3 regulates neuron-specific alternative splicing and involves neurogenesis gene expression [RIP-seq]

Project description:CPEB3 regulates neuron-specific alternative splicing and involves neurogenesis gene expression [RIP-seq]

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RNA helicase DDX5 maintains cardiac function by regulating CamkIIδ alternative splicing [RIP-seq]

Project description:RNA helicase DDX5 maintains cardiac function by regulating CamkIIδ alternative splicing [RIP-seq]

| PRJNA1044024 | ENA

Transcriptome analysis of control (y w) and Paip1 mutant third instar larval wing imaginal discs

Project description:We report the genome-wide RNA profiling of third instar larval wing imaginal discs upon Paip1 mutation

2023-07-31 | GSE146531 | GEO

DEK binds to pre-mRNAs and regulated alternative splicing of Hippo signaling genes in HeLa cell [RIP-seq]

Project description:Purpose: Explore how DEK genome widely bind RNA and affect the alternative splicing in cancer Methods: DEK was overexpressed by transfecting HeLa cells with a DEK-overexpressing plasmid and RNA_seq was used to analyze gene expression profile and splicing pattern of DEK overexpression and control cells. Then, an improved RIP-seq was conducted to explore genome-widely binding characteristic of DEK in HeLa cell. Bioinformatics analysis and qPCR/RIP-PCR were performed to identify and validate the bound and regulated targets of DEK, respectively Results:The results showed DEK overexpression did not affect transcript level expression of those high expressed genes (with FPKM > 1), but splicing pattern of 411 genes (RASGs) was regulated by DEK in HeLa cells, which were enriched in Hippo signaling pathway. Moreover, DEK broadly bind the RNA of a total of 11, 112 genes, with a biased binding the GGUAA motifs at the CDS and intronic regions Conclusions: our results indicated DEK could broadly bind and regulate the pre-mRNA splicing process, which provide new insights of mechanisms that DEK functions in various biological processes including cancer

2025-03-19 | GSE141566 | GEO

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