Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE149890 | GEO | 2020/06/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

| PRJNA630447 | ENA

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.

2020-10-02 | GSE135537 | GEO

Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity

Project description:The nuclear pore complex (NPC) has dual roles in nucleocytoplasmic transport and chromatin organisation. In many eukaryotes the coiled coil Mlp/Tpr proteins of the NPC nuclear basket have specific roles in interactions with chromatin and defining specialised regions of active transcription, while Mlp2 associates with the mitotic spindle in a cell-cycle dependent manner. We previously identified two putative Mlp-related proteins in African trypanosomes, TbNup110 and TbNup92, the latter of which associates with the spindle. We now provide evidence for independent ancestry for TbNup92/TbNup110 and Mlp/Tpr proteins. However, TbNup92 is required for correct chromosome segregation, with knockout cells exhibiting microaneuploidy and low fidelity telomere segregation. Further, TbNup92 is intimately associated with the mitotic spindle and spindle anchor site, but apparently has minimal roles in the control of gene transcription, indicating that TbNup92 lacks major barrier activity. TbNup92 therefore acts as a functional analog of Mlp/Tpr proteins, and together with the lamina analog NUP-1, represents a cohort of novel proteins operating at the nuclear periphery of trypanosomes, uncovering complex evolutionary trajectories for the NPC and nuclear lamina. Whole transcriptome comparison between parental and TbNup92? cells

2014-04-03 | E-GEOD-56436 | biostudies-arrayexpress

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

Distinct Basket Nucleoporins roles in Nuclear Pore Function and Gene Expression

Project description:Nuclear pore complexes (NPCs) are important for cellular functions beyond nucleocytoplasmic trafficking, including genome organization and gene expression. This multi-faceted nature and the slow turnover of NPC components complicates investigations of how individual nucleoporins act in these diverse processes. To address this question, we used an Auxin-Induced Degron (AID) system to distinguish roles of basket nucleoporins Nup153, Nup50 and Tpr. Here, we provide MS data for the Nuclear Pore-enriched fraction of human DLD-1 cells, expressing CRISPR-engeneered degron, fused with the endogenous locus of corresponding basket NUPs, in the absence or presence of Auxin.

2020-06-30 | PXD020075 | Pride

Nuclear pore complex evolution: A trypanosome Mlp analog functions in chromosomal segregation but lacks transcriptional barrier activity

2014-04-03 | GSE56436 | GEO

Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

Project description:To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain.

2022-06-11 | GSE205717 | GEO

RNA degradation in proliferating and differentiated C2C12 muscle precursor cells analyzed on Affymetrix exon arrays

Project description:Steady-state RNA levels are a result of RNA synthesis and degradation. The importance of transcription-factor mediated induction or repression of mRNA synthesis is well established, but the role and mechanisms of RNA degradation are less well understood. We globally evaluated the RNA decay rates in proliferating and differentiated mouse myoblasts on whole-genome Affymetrix exon arrays, allowing for the assessment of directionality of RNA degradation and the detection of splice variant-specific differences in RNA decay rates. We found large differences in decay rates. mRNAs coding for proteins involved in signal transduction and transcriptional regulation have shortest half lives, whereas mRNAs coding for DNA replication enzymes and muscle contraction proteins are among the most stable. Many genes differentially expressed between proliferating and differentiated myoblasts demonstrate major differences in RNA decay rates. Quantitative PCR experiments confirmed the higher stability of transcripts with increased expression levels. RNA degradation has no apparent preferential directionality. RNA degradation appears to affect the ratio of different splice variants. For example, Itga7 isoforms with higher abundance in differentiated than in proliferating cells are more stable in differentiated cells, despite the sharing of a common 3’ untranslated region. Thus, where it was previously thought that the abundance of different splice isoforms was mainly controlled by tissue-specific splicing factors, we now demonstrate that isoforms may be produced at comparable levels but degraded with different efficiencies, depending on the differentiation status of the cells. Our results indicate that control of RNA degradation rates contributes significantly to the differentiation stage-dependent differences in abundance of transcripts and splice variants. Keywords: total RNA expression profiling; cultured cells

2010-09-22 | GSE14387 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data