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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

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

PROVIDER: PRJNA793872 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17413368_1.fastq.gz	Fastqsanger.gz
	SRR17413368_2.fastq.gz	Fastqsanger.gz
	SRR17413369_1.fastq.gz	Fastqsanger.gz
	SRR17413369_2.fastq.gz	Fastqsanger.gz
	SRR17413370_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

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.

2022-09-02 | GSE192950 | GEO

Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

Project description:Purpose:We used eCLIP experiment to analyze binding profile of SERBP1 and its relationship with G4. Result: we found 505 high-confidence SERBP1 binding sites in Hela cells, and the analysis of sequence revealed transcriptome-wide enrichment of PQS in SERBP1-binding regions

2020-10-27 | GSE156015 | GEO

Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

Project description:Enhanced crosslinking and immunoprecipitation of SERBP1 in Hela cells

| PRJNA656424 | ENA

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

Project description:Background 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. Methods 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 the transcriptome sequencing method (RNA-seq). RT-qPCR was conducted to assay SERBP1-regulated alternative splicing. Results 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. Conclusions 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.

| S-EPMC9536300 | biostudies-literature

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

Project description:In the associated paper, SERBP1 is shown to form granules in mitotic cells in a PKCɛ-dependent manner (M-bodies). We performed SERBP1 iCLIP in DLD1 cells that were either asynchronous or enriched for mitotic cells and after treatment with 2 hours of 500nM Blu577 or equivalent DMSO. We found that SERBP1 alters its positioning on rRNA in mitosis in a Blu577-dependent manner, identifying an alternative binding position that coincides with the formation of M-bodies. Mitotic enrichment was performed by single thymidine block, release in to G2 block with RO3306, and release and mitotic shake-off. The fastq files provided are demultiplexed, with adapters and barcodes trimmed and UMI sequences are found in the fastq headers.

2021-10-05 | E-MTAB-10830 | biostudies-arrayexpress

SERBP1 deacetylation inhibits ferroptosis to promote KSHV-induced cellular transformation by decaying lipoyltransferase 2 mRNA

Project description:Ferroptosis, a defensive strategy employed by the host to restrict pathogenic infections, has been implicated in the development and therapeutic responses of various types of tumors. However, the role of ferroptosis in KSHV-induced malignant tumors remains elusive. A steadily growing number of non-histone proteins have been identified as acetylation targets, their functions have yet to be revealed. In this study, we obtained a marked disparity in the landscape of acetylation between MM and KSHV-transformed MM (KMM) cells. SERBP1 deacetylation was upregulated in KMM cells and contributed to KSHV-induced cellular transformation by inhibiting ferroptosis. Mechanistically, KSHV-encoded viral interleukin-6 (vIL-6) hijacks SIRT3, a mitochondrial NAD+-dependent deacetylase, to interact with SERBP1 leading to the deacetylation of SERBP1. Deacetylated SERBP1 exhibits reduced binding to Lipt2 mRNA, which promotes Lipt2 mRNA degradation, resulting in ferroptosis inhibition. Our findings unveil a novel role of SERBP1 deacetylation in regulating ferroptosis and KSHV-induced cellular transformation and identify potential new therapeutic targets for KSHV infection and KSHV-induced cancers.

2023-08-22 | GSE241111 | GEO

Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells

Project description:Transcriptomics analysis of circular RNAs differentially expressed in apoptotic HeLa cells

| PRJNA515690 | ENA

Genomewide m6A mapping uncovers dynamic changes in the m6A epitranscriptome of cisplatin-treated apoptotic HeLa cells

Project description:We have performed a epitranscriptomics study in which we first tretaed DMSO as a negative control and cisplatin in HeLa cells. Total RNA was isolated from control as well as CP treated cells and apoptotic rate was determined by flow cytometry. Total RNAs were subjected to miCLIP to identify differentially m6A methylated RNAs. We then transcriptionally analyzed apoptotic genes which have differential m6A methylation in CP tretament by qPCR. Afterthat, candidate genes were examined at the level of translation by polysome fractioantion assay.

2022-10-28 | GSE188580 | GEO

Loss of LSM14b affects the meiosis process of mouse oocytes

Project description:Loss of LSM14b affects the meiosis process of mouse oocytes

| PRJNA814995 | ENA

A genetically-encoded crosslinker screen identifies SERBP1 as a PKC substrate influencing translation and cell division

Project description:The PKC-regulated genome protective pathway provides transformed cells a failsafe to successfully complete mitosis. Despite the necessary role for Aurora B in this programme, it is unclear whether its requirement is sufficient or if other PKC cell cycle targets are involved. To address this, we developed a trapping strategy using UV-photocrosslinkable amino acids encoded in the PKC kinase domain. The validation of the mRNA binding protein SERBP1 as a PKC substrate revealed a series of mitotic events controlled by the catalytic form of PKC. PKC represses protein translation, altering SERBP1 binding to the 40S ribosomal subunit and promoting the assembly of ribonucleoprotein granules containing SERBP1, termed M-bodies. Independent of Aurora B, SERBP1 is shown to be necessary for chromosome segregation and successful cell division, correlating with M-body formation. This requirement for SERBP1 demonstrates that Aurora B acts in concert with translational regulation in the PKC-controlled pathway exerting genome protection.

2021-12-09 | PXD029091 | Pride

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