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Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

ABSTRACT: Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

PROVIDER: PRJNA630447 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11688435.fastq.gz	Fastqsanger.gz
	SRR11688436.fastq.gz	Fastqsanger.gz
	SRR11688437.fastq.gz	Fastqsanger.gz
	SRR11688438.fastq.gz	Fastqsanger.gz
	SRR11688439.fastq.gz	Fastqsanger.gz

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Nascent RNA-seq of human AID-NeonGreen-Tpr tagged DLD-1 cells after loss of Tpr nucleoporin

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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Gene expression profiling of human DLD-1 cells after block of CRM1 receptor with Leptomycin B inhibitor.

Project description:We used RNA-seq approach to define a contribution of mammalian export receptor CRM1 (Chromosomal Maintenance 1 or Exportin 1) into Tpr-dependent export of RNA molecules from the nucleus to the cytoplasm. Basket nucleoporin Tpr was AID-tagged and depleted through Auxin Induced Degradation system. Loss of Tpr led to rapid changes in gene expression profile, and gene expression changes were compared to GANP, NXF1, RanGAP1 (GSE132363) and CRM1 loss and inhibition, respectively. Altogether, we found a minimal subset of RNAs that are controlled both by Tpr nucleoporin and CRM1 receptor.

2020-06-15 | GSE148560 | GEO

Gene expression profiling of human DLD-1 cells after instant depletion of basket nucleoporins

Project description:We used RNA-seq approach to distinguish roles of basket nucleoporins Nup153, Nup50, and Tpr in transcription and nucleocytoplasmic trafficking. AID-mediated depletion of BSK-NUPs caused rapid and drastic changes in transcriptomic profiles within two hours of auxin addition. Changes upon Tpr nucleoporin loss were distinct from Nup153 and Nup50, but similar to changes upon loss of export factor NXF1 and GANP subunit of the TREX-2 mRNA export complex. Altogether, we demonstrated a unique role of Tpr nucleoporin in regulating genes expression through mRNA export.

2020-06-04 | GSE132363 | GEO

Total proteome analysis of DLD-1 cells expressing various degrons

Project description:Total Proteome analysis of various AID degron-bearing DLD-1 cells ( Nup96, Nup62, Nup188, TPR, Nup93, GANP, PCID2, Nup153, Nup160, Nup205) before and after addition of Auxin for 4-8 h.

2023-03-31 | PXD039407 | Pride

Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

Project description:Nascent RNA sequencing (PRO-seq) after rapid degradation of AID-tagged ZNF143

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TPR Knockdown Frac-Seq

Project description:TPR Knockdown Frac-Seq

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ZC3HC1 has functions distinct from TPR and is dispensable for TPR localization to the nuclear basket

Project description:Background: The nuclear basket is a ‘fishtrap’-like structure on the nucleoplasmic face of the nuclear pore complex which has been implicated in diverse functions including RNA export, heterochromatin organisation, and mitosis. Recently, a novel component of the nuclear basket, ZC3HC1, has been described. The localisation of ZC3HC1 to nuclear pores has been reported to occur reciprocally with TPR, a major structural component of the nuclear basket. Methods and Results: Using immunofluorescence and RNA sequencing, here we show that in human fibroblasts, although ZC3HC1 localisation to nuclear pores is TPR-dependent, TPR localises to pores regardless of the presence of ZC3HC1. We demonstrate that knockdown of TPR and ZC3HC1 produce distinct transcriptional profiles. Conclusions: Our results suggest that there is little overlap in function between these two nuclear basket proteins

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TPR Knockdown Frac-Seq

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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