Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptional profiling of Caenorhabditis elegans nematodes bearing overexpression of NPP-16/CeNUP50 variants.

ABSTRACT: Deregulated nutrient sensing and metabolism are hallmarks of aging, whereas hormetic nutrient stress extends the lifespan and health span across species. As the only gateway governing nucleocytoplasmic trafficking, the nuclear pore complex (NPC) is critical for most fundamental cellular processes and becomes dysfunctional with age. However, the complexity of NPC composition and structure makes granular determination of the age-related role of specific nucleoporins challenging. Here we demonstrated that NUP50, a nuclear basket protein induced by AMP-activated protein kinase (AMPK) in a post-transcriptional and evolutionarily conserved way, is required for the metabolic rewiring and longevity of hormetic nutrient stress in Caenorhabditis elegans. Of interest, NUP50 sufficiently promotes transcriptomic alteration for lipid catabolism activation, extending lifespan independent of nuclear transport, but through its intrinsically disordered region (IDR) that binds to the promoter of catabolic genes. Our findings uncover a conserved nucleoporin as a metabolic switch bridging energy sensing, metabolic adaptation, and aging regulation by mediating transcription directly.

ORGANISM(S): Caenorhabditis elegans

PROVIDER: GSE268357 | GEO | 2025/03/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

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

The nucleoporin Nup50 activates the Ran guanyl-nucleotide exchange factor RCC1 to promote NPC assembly at the end of mitosis

Project description:During mitotic exit, thousands of nuclear pore complexes (NPCs) assemble concomitant with the nuclear envelope to build a transport-competent nucleus. Here, we show that Nup50 plays a crucial role in NPC assembly independent of its well-established function in nuclear transport. RNAi-mediated downregulation in cells or immunodepletion of Nup50 protein in Xenopus egg extracts interferes with NPC assembly. We define a conserved central region of 46 residues in Nup50 that is crucial for Nup153 and MEL28/ELYS binding, and for NPC interaction. Surprisingly, neither NPC interaction nor binding of Nup50 to importin /, the GTPase Ran, or chromatin is crucial for its function in the assembly process. Instead, an N-terminal fragment of Nup50 can stimulate the Ran GTPase guanyl-nucleotide exchange factor RCC1 and NPC assembly, indicating that Nup50 acts via the Ran system in NPC reformation at the end of mitosis. In support of this conclusion, Nup50 mutants defective in RCC1 binding and stimulation cannot replace the wild-type protein in in vitro NPC assembly assays, while excess RCC1 can compensate the loss of Nup50.

2021-11-03 | PXD028701 | Pride

The canonical helixes of Nup50c drive its interaction with Nup82 at nuclear basket in plants

Project description:The nuclear basket (NB) as essential peripheral parts of nuclear pore complex (NPC), plays crucial roles in mRNA surveillance and transport, chromatin organization, and regulation of gene expression. However, the architectural and functional understanding of plant NB remains largely unknown. Using proximity labeling technology we identified a novel paralog of plant Nup50, designated Nup50c. Nup50c is predominantly located at the NB and interacts with plant-specific NB component Nup82. The C terminal region of Nup82 is responsible for the interaction with the canonical helixes of Nup50c and tethering it to the NPC.

2024-10-14 | PXD056763 |

Docking a flexible basket onto the core of the nuclear pore complex

Project description:The nuclear basket attaches to the nucleoplasmic side of the nuclear pore complex (NPC), coupling transcription to mRNA quality control and export. The basket expands the functional repertoire of a subset of NPCs in S. cerevisiae by drawing a unique RNA/protein interactome. Yet, how the basket docks onto the NPC core remains unknown. By integrating AlphaFold-powered interaction screens, electron microscopy and membrane-templated reconstitution, we uncovered a membrane-anchored tripartite junction between basket and NPC core. The basket subunit Nup60 harbours three adjacent short linear motifs (SLiMs) which connect Mlp1, a parallel homodimer consisting of coiled-coil segments interrupted by flexible hinges, and the Nup85 subunit of the Y-complex. We reconstituted the Y-complex•Nup60•Mlp1 assembly on a synthetic membrane and validated the protein interfaces in vivo. Our study explains how a SLiM-based protein junction can substantially reshape NPC structure and function, advancing our understanding of compositional and conformational NPC heterogeneity.

2024-07-11 | PXD052015 | Pride

GBPL3 is a novel component of the nuclear pore complex and functionally connects the nuclear basket with the nucleoskeleton in plants

Project description:The nuclear basket (NB) is an essential structure of the nuclear pore complex (NPC). It serves as a dynamic and multi-functional platform that participates in various critical nuclear processes, including cargo transport, molecular docking, and gene expression regulation. However, the compositional and functional mechanisms are not completely understood, particularly in plants. Here, we identified a guanylate-binding protein (GBP)-like GTPase (GBPL3) as a novel NPC basket component in Arabidopsis. Using fluorescence and immunoelectron microscopy, we found that GBPL3 is enriched in the nuclear rim and localizes to the nuclear pore. Proximity labeling proteomics and protein-protein interaction assays revealed that GBPL3 is predominantly distributed at the NPC basket and physically associated with NB nucleoporins as well as many chromatin remodelers, transcription apparatus, and regulators, and the RNA splicing and processing machinery, suggesting a conserved function of the nuclear basket in transcription regulation as reported in yeasts and animals. Moreover, we found that GBPL3 physically interacts with the nucleoskeleton via its disordered coiled-coil regions. Simultaneous loss of GBPL3 with any one of all the four Arabidopsis nucleoskeleton genes CRWNs led to distinct development- and stress-related phenotypes, ranging from seedling lethality to leaf lesions, concomitant aberrant transcription of stress-related genes. Our results indicate that GBPL3 is a bona fide component of the plant NPC and physically and functionally connects the nuclear basket with different components of the nucleoskeleton, which is required for the coordination of plant development and stress responses.

2022-08-25 | PXD032906 | Pride

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

Functional interaction of chromatin with nucleoporins in Drosophila

Project description:Nuclear pore complexes (NPCs) mediate transport across the nuclear envelope. In yeast, they have also been proposed to interact with active genes, attracting or retaining them at the nuclear periphery. However, some NPC components (nucleoporins) in higher eukaryotes are also found in the nucleoplasm, with so far unknown function. Therefore, we have functionally distinguished between nucleoporin-chromatin interactions at the NPC and within the nucleoplasm in Drosophila. For this we analyzed genomic interactions of full-length nucleoporins Nup98, Nup50 and Nup62 and nucleoplasmic and NPC-tethered forms of Nup98. We found that nucleoporins predominantly interacted with transcriptionally active genes inside the nucleoplasm. A smaller set of non-active genes interacted with the NPC. We identified a direct role for nucleoplasmic Nup98 in stimulating gene expression, as genes downregulated upon Nup98 depletion were activated upon nucleoplasmic Nup98 overexpression and showed strong nucleoplasmic Nup98 interaction. Thus, nucleoporins stimulate gene expression away from the NPC by interacting with genes inside the nucleoplasm.

2010-03-01 | GSE19307 | 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

Interactome of Sec13 paralogs in Paradiplonema papillatum

Project description:The acquisition of new functions is frequently the result of gene duplication and is a major driver of evolutionary complexity. The β-propeller protein Sec13 plays roles in at least three distinct processes by virtue of being a component of the COPII endoplasmic reticulum export vesicle coat, the nuclear pore complex (NPC) and the Seh1-associated (SEA)/GATOR nutrient-sensing complex, suggesting that regulatory mechanisms coordinating these cellular activities may operate via Sec13. COPII, SEA and the NPC are ancient features of eukaryotic cells. We analyzed the Sec13 interactome in diplonemids, widespread marine protists, and found that Sec13 functions are divided between two paralogs, Sec13a and Sec13b. Sec13a interacts with COPII and the NPC, but by contrast Sec13b interacts with Sec16 and components of the SEA/GATOR complex. Hence, we infer that Sec13a is responsible for NPC functions and canonical anterograde transport activities while Sec13b acts within nutrient and autophagy-related pathways. Furthermore, duplication of Sec13 is near universal across the Euglenozoa, providing a potent exemplar of paralogy expansion and functional diversification.

2023-06-14 | PXD037122 | Pride

Y-complex nucleoporins independently contribute to nuclear pore assembly and gene regulation in neuronal progenitors

Project description:From their essential function in building up the nuclear pore complexes, nucleoporins have expanded roles beyond nuclear transport. Hence, their contribution to chromatin organization and gene expression has set them as critical players in development and pathologies. We previously reported that Nup133 and Seh1, two components of the Y-complex subunit of the nuclear pore scaffold, are dispensable in mouse embryonic stem cells but required for their survival during neuroectodermal differentiation. Here, a transcriptomic analysis revealed that Nup133 regulates a subset of genes at early stages of neuroectodermal differentiation, including Lhx1 and Nup210L, encoding a newly validated nucleoporin. These genes were also misregulated in Nup133∆Mid neuronal progenitors, in which NPC basket assembly is impaired, as previously observed in pluripotent cells. However, a four-fold reduction of Nup133, despite affecting basket assembly, is not sufficient to alter Nup210L and Lhx1 regulation. Finally, these two genes are misregulated in Seh1-deficient progenitors that only show a mild decrease in NPC density. Together these data reveal a shared function of Y-complex nucleoporins in gene regulation during neuroectodermal differentiation.

2023-05-26 | GSE218080 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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