RIP-seq analysis of Usp39 binding sites in mouse AML12 cell line
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA881956 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR21622576_1.fastq.gz | Fastqsanger.gz | |||
| SRR21622576_2.fastq.gz | Fastqsanger.gz | |||
| SRR21622577_1.fastq.gz | Fastqsanger.gz | |||
| SRR21622577_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
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 | GSE213629 | GEO
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
Project description:MATR3-binding RNAs in AML12 cells [RIP-Seq]
| PRJNA823726 | ENA
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
Project description:RNA-binding proteins (RBPs) and non-coding RNAs orchestrate post-transcriptional processes through the recognition of specific sites on targeted transcripts. Thus, understanding the connection between binding to specific sites and active regulation of the whole transcript is essential. Many immunoprecipitation techniques have been developed that identify either whole transcripts or binding sites of RBPs on each transcript using cell lysates. However, none of these methods simultaneously measures the strength of each binding site, and quantifies binding to whole transcripts. In this study, we compare current procedures and present Digestion Optimized (DO)-RIP-seq, a simple method that locates and quantifies RBP binding sites using a continuous metric. We have used the RBP HuR/ELAVL1 to demonstrate that DO-RIP-seq can quantify HuR binding sites with high coverage across the entire human transcriptome, thereby generating metrics of relative RNA binding strength. We demonstrate that this quantitative enrichment of binding sites is proportional to the relative in vitro binding strength for these sites. Also, we used DO-RIP-seq to quantify and compare HuR's binding to whole transcripts, thus allowing for seamless integration of binding site data with whole transcript measurements. Finally, we demonstrate that DO-RIP-seq is useful for identifying functional mRNA target sets, and binding sites where combinatorial interactions between HuR and AGO-microRNAs regulate the fate of the transcripts. Our data indicate that DO-RIP-seq will be useful for quantifying RBP binding events that regulate dynamic biological processes.
2016-10-13 | GSE87887 | GEO
Project description:We performed RNA binding protein immunoprecipitation (RIP) assay with anti-IgG/anti-MATR3 antibody. The RNA libraries were constructed using rib-off and strand-specific kits. Next-generation sequencing (NGS) were performed to analyze MATR3-binding RNAs.
2023-06-28 | GSE200244 | GEO
Project description:RNA Immunoprecipitation(RIP)-seq of Flag-USP39 in ovarian cancer cells
| PRJNA661211 | ENA
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
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
Project description:RNA splicing and protein degradation systems allow the functional adaptation of the proteome in response to changing cellular contexts. However, the regulatory mechanisms connecting these processes remain poorly understood. Here, we show that impaired spliceosome assembly caused by USP39 deficiency leads to a pathogenic splicing profile characterized by the use of cryptic 5′ splice sites. To explore the interactions of USP39 and the effect of its depletion in HeLa cells, we performed complexome profiling of nuclear lysates. We observed most USP39 stably integrated into the tri-snRNP complex and there is almost no free nuclear protein. More importantly, the relative abundance of tri-snRNP spliceosome complex was impaired in USP39-depleted cells. As previous reports indicated, USP39 is a regulator of tri-snRNP stability and its depletion decreased the levels of assembled U4/U6.U5 complexes.
2024-09-25 | PXD050738 | Pride