Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome-wide mapping of RNA:protein interactions of USP39 in HEK293T cells

ABSTRACT: Transcriptome-wide mapping of RNA:protein interactions of USP39 in HEK293T cells

PROVIDER: PRJNA954017 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24120317.fastq.gz	Fastqsanger.gz
	SRR24120318.fastq.gz	Fastqsanger.gz
	SRR24120319.fastq.gz	Fastqsanger.gz
	SRR24120320.fastq.gz	Fastqsanger.gz
	SRR24120321.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Transcriptome-wide mapping of RNA:protein interactions of USP39 in HEK293T cells

Project description:We performed USP39 iCLIP2 in HEK293T WT cells

2024-09-25 | GSE229330 | GEO

Role of USP39 in HeLa and HEK293T cells

Project description:Role of USP39 in HeLa and HEK293T cells

| PRJNA954021 | ENA

RNA sequencing of liver tissues from liver-specific Usp39 knockout (Usp39-HKO) mice

Project description:Regulation of alternative splicing (AS) is crucial for gene expression and enables a single transcript to yield multiple isoforms that increase transcriptome and proteome diversity. Dysregulated AS has been linked to the development of non-alcoholic fatty liver diseases (NAFLD). However, the splicing factors involved in hepatic homeostasis and their functional mechanisms remain to be further characterized. Here, we report that spliceosome component Usp39 plays a critical role in the regulation of hepatocyte lipid homeostasis. We found that Usp39 expression is downregulated in hepatic tissues of NAFLD and non-alcoholic steatohepatitis (NASH) subjects. We observed increased lipid accumulation, spontaneous steatosis and impaired autophagy, lipophagy in particular, in mice with hepatocyte-specific Usp39 deletion. Combined analysis of RIP-seq and RNA-seq data revealed that Usp39 regulates AS of several autophagy-related genes including Hsf1. More specifically, deletion of Usp39 resulted in alternative 5’ splice site selection of exon 6 in Hsf1 and consequently reduced expression. Hsf1 was also found to be downregulated in NAFLD/NASH mice and patients. Importantly, overexpression of Hsf1 restored lipophagy, attenuated lipid accumulation and alleviated NASH caused by Usp39 deficiency. Taken together, our findings indicate that Usp39-mediated AS is crucial for sustaining lipophagy and lipid homeostasis in the liver.

2023-09-24 | GSE213633 | GEO

The spliceosome component Usp39 controls B cell development by regulating immunoglobulin gene rearrangement

Project description:The spliceosome is a large ribonucleoprotein complex responsible for pre-mRNA splicing and genome stability maintenance. Disruption of the spliceosome activity may lead to developmental disorders and tumorigenesis. However, the physiological role that the spliceosome plays in B cell development and function is still poorly defined. Here, we demonstrate that ubiquitin-specific peptidase 39 (Usp39), a spliceosome component of the U4/U6.U5 tri-snRNP complex, is essential for B cell development. Ablation of Usp39 in B cell lineage blocks pre-pro-B to pro-B cell transition in the bone marrow, leading to a profound reduction of mature B cells in the periphery. We show that Usp39 specifically regulates immunoglobulin gene rearrangement in a spliceosome-dependent manner, which involves modulating chromatin interactions at the Igh locus. Moreover, our results indicate that Usp39-deletion reduces the pre-malignant B cells in Eμ-Myc transgenic mice and significantly improves their survival.

2022-02-08 | GSE173597 | GEO

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.

2021-04-20 | GSE157401 | GEO

Chromatin Immunoprecipitation(ChIP)-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. Since many RNA-binding proteins showed DNA-binding ability , we performed ChIP-seq in A2780 cells with Flag-USP39 overexpression in order to detect the bindng of USP39 to DNA and POLR2A was used as a positive control.

2021-09-05 | GSE157543 | GEO

RNA sequencing (RNA-SEQ) of USP39 knockdown by shRNA 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 regulatory mechanism of USP39 in ovarian cancer,we performed RNA-seq in A2780 cells with USP39 knock down compared with control in three repeat. HMGA2 was identified as USP39 target gene because of different expression and downregulated splicing efficiency.

2021-04-20 | GSE157365 | GEO

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA1108725 | ENA

Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

Project description:Exonuclease assisted mapping of protein-RNA interactions (ePRINT)

| PRJNA957458 | ENA

Single-cell mapping of regulatory DNA:Protein interactions

Project description:Single-cell mapping of regulatory DNA:Protein interactions

| PRJNA1259498 | ENA