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Alternative splicing regulation of cell cycle genes by SPF45/SR140/CHERP complex controls cancer cell proliferation

ABSTRACT: SPF45, SR140 and CHERP were knock downed using lentiviral delivery of shRNAs in HeLa cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE180892 | GEO | 2021/07/30

REPOSITORIES: GEO

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CHERP controls alternative mRNA splicing in human cell line

Project description:Calcium Homeostasis Endoplasmic Reticulum Protein (CHERP) is co-localized with inositol 1,4,5-trisphosphate receptor (IP3R) in the endoplasmic reticulum or peri-nuclear part, and has been considered to have a role in intracellular calcium signaling. Recently, it has recognized that CHERP structurally carries nuclear localization signal and arginine/serine-dipeptide repeats like domain, and interacts with spliceosome. In this study, we showed that poly (A)+ RNA was accumulated in the nucleus on CHERP depletion. Using the global analysis, CHERP regulated alternative mRNA splicing events through the interaction with U2 snRNP and U2 snRNP related proteins. Our analysis indicated that intron retention was most frequently observed among five alternative splicing patterns in accordance with the accumulation of poly (A)+ RNA in the nucleus. Further, intron retention and cassette exon choice were influenced by the strength of 5’ or 3’ splice site, GC content, or intron length. In addition, CHERP depletion induced the abnormality of cell cycle progression at M phase and cell division. These results suggested that CHERP was involved in the regulation of alternative splicing.

2022-06-19 | GSE193399 | GEO

Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [RBM47 KD]

Project description:RBM47 is a RNA binding protein that is known to regulate alternative splicing. To study the genome wide regulatory role of RBM47 in alternative splicing and determine the potential function of RBM47 during EMT, we used lentiviral shRNAs to knockdown RBM47 in H358 cells and performed RNA-seq in biological triplicates. We used lentiviral based shRNAs to knockdown RBM47 in human H358 cells. We harvested total RNA and protein from RBM47 knockdown and control knockdown in biological triplicates. We made cDNA libraries for each replicate and subjected them to RNA-seq.

2016-04-05 | E-GEOD-75491 | biostudies-arrayexpress

Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [ESRP KD]

Project description:Epithelial specific splicing regulatory protein 1 and 2 (ESRP1 and ESRP2) are important regulators of alternative splicing during EMT. To study the alternative splicing events regulated by ESRP1/2 at a genome wide scale, we used lentiviral shRNAs to knockdown ESRP1/2 in H358 cells and performed RNA-seq in biological triplicates. We used lentiviral based shRNAs targeting ESRP1 and ESRP2 to knockdown both regulators in human H358 cells. We harvested total RNA and protein from ESRP1/2 knockdown and control knockdown in biological triplicates. We made cDNA libraries for each replicate and subjected them to RNA-seq.

2016-04-05 | E-GEOD-75489 | biostudies-arrayexpress

Alternative splicing regulation of cell cycle genes by SPF45/SR140/CHERP complex controls cancer cell proliferation

Project description:Alternative splicing regulation of cell cycle genes by SPF45/SR140/CHERP complex controls cancer cell proliferation

| PRJNA749954 | ENA

Alternative splicing signatures in apoptosis related genes of human HeLa cells with RNAi targeting p68 RNA helicase-DDX5

Project description:Alternative splicing profiling of apopotosis related genes in human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs targetting p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5) cloned into the pSuper expression vector compared to empty vector. Keywords: treated vs. untreated comparison; alternative splicing

2011-01-21 | GSE20010 | GEO

Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [RBM47 KD]

2016-04-05 | GSE75491 | GEO

Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [ESRP KD]

2016-04-05 | GSE75489 | GEO

CHERP controls alternative mRNA splicing in human cell line

Project description:CHERP controls alternative mRNA splicing in human cell line

| PRJNA796027 | ENA

PPIB-regulated alternative splicing of cell cycle genes contributes to the regulation of cell proliferation.

Project description:BackgroundPeptidylprolyl cis-trans isomerase B (PPIB) plays an important role in the process of inflammation through binding RNA, but the molecular pathogenesis is not yet clearly understood. The objective of this study was to investigate and verify the PPIB-regulated gene expressions and alternative splicing in Hela cells.MethodsWe examined the PPIB-regulated transcriptomes in HeLa cells using RNA-seq data. Differentially expressed genes, alternative splicing analysis were carried out. Functional enrichment analysis was used to define the enrichment of each term.ResultsWe found that PPIB knockdown successfully downregulated PPIB in Hela cells, which promoted cell proliferation (P < 0.001), but no significant effect on cell apoptosis. Ten alternative splicing genes regulated by PPIB were detected in Hela cells. The ten top Gene Ontology biological process analysis and functional pathways of the alternative splicing genes were screened and identified. The pathways where differentially expressed genes are most enriched were toll-like receptor 4 signaling pathways and other signaling pathways relating to inflammation and immune response. In addition, PPIB affects the alternative splicing of multiple genes, and the Gene Ontology-biological process analysis showed that genes significantly related to alternative splicing changes were mainly enriched in the cell cycle (P < 0.05).ConclusionPPIB regulates the alternative splicing of cell cycle-related genes to affect cell proliferation and regulate the occurrence and development of chronic inflammatory diseases such as Nasal polyps.

| S-EPMC9556483 | biostudies-literature

Alternative splicing regulation of cell-cycle genes by SPF45/SR140/CHERP complex controls cell proliferation.

Project description:The regulation of pre-mRNA processing has important consequences for cell division and the control of cancer cell proliferation, but the underlying molecular mechanisms remain poorly understood. We report that three splicing factors, SPF45, SR140, and CHERP, form a tight physical and functionally coherent complex that regulates a variety of alternative splicing events, frequently by repressing short exons flanked by suboptimal 3' splice sites. These comprise alternative exons embedded in genes with important functions in cell-cycle progression, including the G2/M key regulator FOXM1 and the spindle regulator SPDL1. Knockdown of either of the three factors leads to G2/M arrest and to enhanced apoptosis in HeLa cells. Promoting the changes in FOXM1 or SPDL1 splicing induced by SPF45/SR140/CHERP knockdown partially recapitulates the effects on cell growth, arguing that the complex orchestrates a program of alternative splicing necessary for efficient cell proliferation.

| S-EPMC8594467 | biostudies-literature

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