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Homo sapiens

ABSTRACT: RNAseq to identify TGF-beta and EGF regulated alternative splicing in Hela cells

PROVIDER: PRJNA290799 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2130060_1.fastq.gz	Fastqsanger.gz
	SRR2130060_2.fastq.gz	Fastqsanger.gz
	SRR2130070_1.fastq.gz	Fastqsanger.gz
	SRR2130070_2.fastq.gz	Fastqsanger.gz
	SRR2130061_1.fastq.gz	Fastqsanger.gz

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Direct regulation of alternative splicing by SMAD3 through interaction with PCBP1 is essential for the tumor-promoting role of TGF-beta

Project description:To assess the global impact of TGF-beta on alternative splicing, we conducted RNA-seq of total RNAs isolated from various lines of HeLa cells that were generated for this study and treated without or with TGF-beta and EGF. Using rMAT tool from the RNA-Seq data and annotation of transcripts in GTF format, we identified differential alternative splicing events between untreated and treated cell lines. Our study shows that the TGF-beta-mediated alternative splicing affects the protein products of a large number of genes enriched in pathways critical for EMT, cykeskeleton organization, and adherens junction signaling. PCBP1 was required for the most, if not all, alternative splicing events detected. SRA accession number: SRP061634, BioProject ID PRJNA290799. RNAs from Hela cells were treated with TGF-Î² and EGF, in triplicates and sequenced on HiSeq2000 with 2 samples pooled into one lane with Illumina TruSeq v3 chemistry.

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Direct regulation of alternative splicing by SMAD3 through interaction with PCBP1 is essential for the tumor-promoting role of TGF-beta

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Role of TGF-β signaling in hypoxia-induced alternative splicing in breast cancer cells

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The Akt-SRPK-SR axis constitutes a major pathway in transducing EGF signaling to regulate alternative splicing in the nucleus

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SERBP1 affects the apoptotic level by regulating the expression and alternative splicing of cellular and metabolic process genes in HeLa cells

Project description:RNA-binding proteins (RBPs) have important roles in orchestrating posttranscriptional regulation and modulating many tumorigenesis events. SERBP1 has been recognized as an important regulator in multiple cancers, while it remains unclear whether SERBP1-regulated gene expression at the transcriptome-wide level is significantly correlated with tumorigenesis.We overexpressed SERBP1 in HeLa cells and explored whether SERBP1 overexpression (SERBP1-OE) affects the proliferation and apoptosis of HeLa cells. We analyzed the transcriptome-wide gene expression changes and alternative splicing changes mediated by SERBP1-OE using transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing.SERBP1-OE induced the apoptosis of HeLa cells. The downregulated genes were strongly enriched in the cell proliferation and apoptosis pathways according to the GO analysis, including FOS, FOSB, PAK6 and RAB26. The genes undergoing at least one SERBP1-regulated alternative splicing event were enriched in transcriptional regulation, suggesting a mechanism of the regulation of gene expression, and in pyruvate and fatty acid metabolic processes critical for tumorigenesis events. The SERBP1-regulated alternative splicing of ME3, LPIN3, CROT，PDP1, SLC27A1 and ALKBH7 was validated by RT-qPCR analysis.We for the first time demonstrated the cellular function and molecular targets of SERBP1 in HeLa cells at transcriptional and post-transcriptional levels. The SERBP1-regulated gene expression and alternative splicing networks revealed by this study provide important information for exploring the functional roles and regulatory mechanisms of SERBP1 in cancer development and progression.

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