TPR Knockdown Frac-Seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA559187 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9922630.fastq.gz | Fastqsanger.gz | |||
| SRR9922640.fastq.gz | Fastqsanger.gz | |||
| SRR9922650.fastq.gz | Fastqsanger.gz | |||
| SRR9922660.fastq.gz | Fastqsanger.gz | |||
| SRR9922670.fastq.gz | Fastqsanger.gz |
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Project description:To identify changes in splicing patterns following WTAP and TPR knockdown, RNA-sequencing was performed on breast cancer cells transfected with siRNAs targeting WTAP or TPR.
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Project description:How splicing regulates the nuclear export of mRNAs has been a source of much debate. While splicing has been shown to enhance nuclear export, it has remained unclear whether mRNAs generated from intronless genes use specific machinery to promote their export. Here we investigate the role of the major nuclear pore basket protein, TPR, in regulating mRNA and lncRNA nuclear export. We provide evidence that TPR is required for the nuclear export of mRNAs and lncRNAs that are generated from intronless or intron-poor genes. In contrast, TPR is not required for the nuclear retention of mRNAs that have retained introns, or unused 5’ splice site motifs. In summary, our study provides one of the first examples of a factor that is specifically required for the nuclear export of intronless mRNAs.
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Project description:Total RNA-seq of siRNA-mediated WTAP and TPR knockdown
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Project description:We used SLAM-seq approach to define a contribution of RNA synthesis into RNA abundance changes after Tpr loss. Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in rates of RNA synthesis. The majority of transcripts were downregulated. Analysis of RNA-seq and SLAM-seq indicated that the changes in RNA abundance of most of Tpr-dependent up- and downregulated genes resulted from increased or decreased rates of RNA synthesis, respectively.
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Project description:Frac-Seq Analysis of ZFC3H1 Knockdown U2OS Cells
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Project description:Nowadays, fibroblast growth factor receptor 1 (FGFR1) inhibitors are considered as an effective kinase inhibitor for 8p11 myeloproliferative syndrome (EMS) treatment. However, targeting FGFR1 alone may not be sufficient in EMS patients with TPR-FGFR1 rearrangement. In this study, we established TPR FGFR1 expressing Baf3 cells and performed RNA-Seq analysis. RNA-Seq analysis revealed that genes associated with TPR-FGFR1 expression mainly participated in the epidermal growth factor receptor (EGFR) pathway (|FC| > 1.80, P < 0.05). Gene set enrichment analysis (GSEA) identified significant enrichment in the PI3K/AKT pathways. We found that EGFR is another activation pathway for AKT in TPR-FGFR1-expressing Baf3 cells. Moreover, we found that treatment with FGFR1 inhibitors alone could completely inhibit FGFR1 phosphorylation, but could not completely inhibit AKT, which is the downstream molecule of FGFR1. Compared to FGFR1 inhibitors alone, co-treatment with PD-166866 (FGFR1 inhibitor) and MK-2206 (AKT inhibitor) could simultaneously inhibit the phosphorylation of FGFR1 and AKT. In addition, FACS results indicated that the combination therapy of PD-168866 and MK-2206 significantly increased the rate of cells apoptosis than monotherapy of PD-166866 (P < 0.0001). Collectively, the data obtained in the present study provides strong evidence for dual targeting therapy of FGFR1 and AKT in EMS patients with TPR-FGFR1 rearrangement, offering a new direction for EMS treatment.
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Project description:BioID performed in HeLa cells for the TPR domain of The O-GlcNAc Transferase and eGFP (negative control). Used to determine TPR interactors and the TPR interactome in HeLa cells. Three biological replicates were performed, with each replicate having an experimental (TPR-BirA*) and negative (eGFP-BirA*) condition, and each condition was split into four fractions during in-gel digest for mass spectrometry.
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Project description:Nucleocytoplasmic O-linked N-acetylglucosamine (O-GlcNAc) is an essential post-translational modification that is installed to thousands of protein substrates by O-GlcNAc transferase (OGT). Substrate selection by OGT and its isoforms is primarily mediated by the tetratricopeptide repeat (TPR) domain, yet the impact of truncations to the TPR domain on substrate and glycosite selection remains unresolved. Here, we report the effects of TPR truncations on the substrate and glycosite selection of OGT against the model protein GFP-JunB and the surrounding O-GlcNAc proteome in U2OS cells. Truncation of the TPR domain of OGT maintains glycosyltransferase activity but alters subcellular localization in cells. Examination of the glycoproteome across the TPR truncations revealed the broadest substrate activity from the canonical nucleocytoplasmic OGT, with the greatest changes in O-GlcNAc occurring on proteins associated with mRNA splicing processes. Glycosite analysis revealed alterations to the O-GlcNAc consensus sequence globally and differential glycosite selectivity on GFP-JunB as a function of the OGT TPR isoform. This dataset provides a foundation to analyze how perturbations to the TPR domain and expression of OGT isoforms affects the glycosylation of substrates, which will be critical for future protein engineering of OGT, the biology of OGT isoforms, and diseases associated with the TPR domain of OGT.
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Project description:OGT’s tetratricopeptide(TPR) domain is important in substrate recognition, but there is little information on how changing the TPR domain impacts its cellular functions. Here, we investigate how altering OGT’s TPR domain impacts cell growth after the endogenous enzyme is deleted. We find that disrupting the TPR residues required for OGT dimerization leads to faster cell growth, whereas truncating the TPR domain slows cell growth.We also find that OGT requires eight of its 13 TPRs to sustain cell viability. OGT-8, like the nonviable shorter OGT variants, is mislocalized and has reduced Ser/Thr glycosylation activity; moreover, its interactions with most of wild-type OGT’s binding partners are broadly attenuated.
2024-05-06 | PXD052018 | Pride