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RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

ABSTRACT: Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a major challenge to identify the cancer-specific splicing variants. Here we demonstrated that splicing factor PQBP1 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of PQBP1 is associated with poor prognosis. To gain global insights into PQBP1-RNA binding property, RNA immunoprecipitation sequencing (RIP-seq) and SpyTag-based CLIP (SpyCLIP) were performed to analysis the interaction between PQBP1 and the target RNA.

ORGANISM(S): Homo sapiens

PROVIDER: GSE223090 | GEO | 2024/05/01

REPOSITORIES: GEO

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SpyTag-based CLIP (SpyCLIP) sequencing of PQBP1 in ovarian cancer cells

Project description:Dysregulated expression of splicing factors has important roles in cancer development and progression. However, it remains a major challenge to identify the cancer-specific splicing variants. Here we demonstrated that splicing factor PQBP1 is commonly overexpressed in high-grade serous ovarian carcinoma (HGSOC) and high level of PQBP1 is associated with poor prognosis. To gain global insights into PQBP1-RNA binding property, RNA immunoprecipitation sequencing (RIP-seq) and SpyTag-based CLIP (SpyCLIP) were performed to analysis the interaction between PQBP1 and the target RNA.

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RNA Immunoprecipitation(RIP)-seq of Flag-USP39 in ovarian cancer cells

Project description:High-grade serous ovarian carcinoma is the most lethal type of gynecologic malignancy.Emerging evidences have suggested the vital roles of splicing factor in the human cancers. RNA splicing pathways was found excessive activated in HGSOC. USP39 was one of overexpressed splicing factor in HGSOC. However, the biological function and concrete regulatory mechanism of USP39 in ovarian cancer remain unclear. In this study, we investigate the oncogenic roles of the splicing factor USP39 in HGSOC through facilitated the growth speed and invasion of ovarian cancer cells.Elevated USP39 expression levels, based on immunohistochemistry staining, were associated with poor survival in HGSOC patients. In order to investigate the binding peaks of USP39 in ovarian cancer,we performed RIP-seq in A2780 cells with Flag-USP39 overexpression.

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RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

Project description:RNA immunoprecipitation sequencing (RIP-seq) of PQBP1 in ovarian cancer cells

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Next-generation sequencing identifies mRNAs targets that experience significant changes in alternative splicing upon PQBP1 knockdown in mouse embryonic cortical neurons

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RNA sequencing (RNA-seq) of PQBP1 knockdown in ovarian cancer cells

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PQBP1-associated proteins spectrums in HEK-293 cells

Project description:Our study shows that deletion of the alternative splicing regulator PQBP1 in striatal progenitors resulted in defective striatal development due to impaired neurogenesis of spiny projection neurons (SPNs). Therefore, we further reveal that PQBP1 associated with components in splicing machinery by LC-MS/MS. These findings identify PQBP1 as a novel regulator in balancing striatal progenitor proliferation and differentiation.

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Project description:To investigate the comprehensive function of PQBP1 in the regulation of RNA splicing, we established Dox-inducible PQBP1 knockdown HEY cell line. We then performed transcript expression profiling analysis using data obtained from long-read nanopore-seq of PQBP1 knockdown and control HEY cells (three biological replications of each sample).

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