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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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Similar Datasets

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

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

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]

| PRJNA641661 | ENA

FUS reads histone H3K36me3 to regulate alternative polyadenylation [RIP-seq]

Project description:FUS reads histone H3K36me3 to regulate alternative polyadenylation [RIP-seq]

| PRJNA875417 | ENA

RIP-seq experiment to evaluate the role of methylation of the spliceosome component LSM4 in the regulation of alternative splicing

Project description:The RIP-seq experiment was designed to look for the direct targets of LSM4 U6snRNP component. For this plants were grown in Murashige and Skoog (MS) plates in continuous light (LL) for 12 days and were vacuum-infiltrated with 1% formaldehyde for 15 min followed by quenching with 125 mM glycine. A whole-cell extract was prepared in RIP-lysis buffer. The extract was pre-cleared with Sepharose beads and subjected to immunoprecipitation with GFP-Trap beads (Chromotek). After extensive washing with RIP washing buffer, co-precipitated RNAs were extracted with Trizol (Invitrogen) and treated with DNase (Promega). Libraries were prepared and sequenced at the Max Planck-Genome-Centre Cologne (MP-GC).

2023-05-31 | E-MTAB-12369 | biostudies-arrayexpress

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