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

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

PROVIDER: PRJNA633557 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11808541_1.fastq.gz	Fastqsanger.gz
	SRR11808541_2.fastq.gz	Fastqsanger.gz
	SRR11808542_1.fastq.gz	Fastqsanger.gz
	SRR11808542_2.fastq.gz	Fastqsanger.gz
	SRR11808543_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 (RIP-seq)

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

| PRJNA633561 | 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

Modeling of the U1 snRNP assembly pathway in alternative splicing in human cells using Petri nets

Project description:The investigation of spliceosomal processes is currently a topic of intense research in molecular biology. In the molecular mechanism of alternative splicing, a multi-protein–RNA complex – the spliceosome – plays a crucial role. To understand the biological processes of alternative splicing, it is essential to comprehend the biogenesis of the spliceosome. In this paper, we propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1. Using Petri nets, we describe its highly ordered assembly that takes place in a stepwise manner.

2024-10-31 | MODEL2410300001 | BioModels

Genomewide analysis of U1C-dependent alternative splicing

Project description:To investigate whether U1C plays a role in splicing regulation in human system, we performed siRNA-mediated knockdown of U1C in HeLa cells and analyzed alternative splicing patterns by high-throughput RNA sequencing (RNAseq) RNAseq performed with poly(A)+ selected total RNA from U1C-knockdown and control-treated HeLa cells

2013-09-30 | E-GEOD-42485 | biostudies-arrayexpress

Heat stress induced alternative splicing in a species-dependent manner

Project description:Patterns of alternative splicing during heat stress in Arabidopsis thaliana and Boechera depauperata indicate complex and species-specific interactions between differential expression and alternative splicing.

2018-03-21 | GSE107820 | GEO

Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation.

Project description:Splicing factor SRSF10 is known to function as a sequence-specific splicing activator. Here, we used RNA-seq coupled with bioinformatics analysis to identify the extensive splicing network regulated by SRSF10 in chicken cells. We found that SRSF10 promoted both exon inclusion and exclusion. Functionally, many of SRSF10-verified alternative exons are linked to pathways of stress and apoptosis. Importantly, reconstituted SRSF10 in knockout cells recovered wild-type splicing patterns and considerably rescued the stress-related defects. Together, our results provide mechanistic insight into SRSF10-regulated alternative splicing events in vivo and demonstrate that SRSF10 plays a crucial role in cell survival under stress conditions. RNA-seq for wide type (WT) and SRSF10-deficient (KO) chicken DT40 cells

2014-01-22 | E-GEOD-53354 | biostudies-arrayexpress

Genomewide analysis of U1C-dependent alternative splicing

2013-09-30 | GSE42485 | GEO

Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB

Project description:This SuperSeries is composed of the following subset Series: GSE23513: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (HJAY) GSE23514: Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB (Exon array) Refer to individual Series

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