Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis Thaliana

SUBMITTER: Yu Tang

PROVIDER: PXD056763 | iProX | Mon Oct 14 00:00:00 BST 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

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

FXR1 dominates mRNA export fate via riboregulation during hESC differentiation

Project description:mRNA export is required for its translation into functional protein, facilitated by the interaction between mRNA transporters and nuclear pore complex (NPC). However, only a few mRNA transporters associated with NPC were identified. Here, we comprehensively depicted NPC interactome in human embryonic stem cells (hESCs), from which we identified a series of novel mRNA transporters. Among them, FXR1 functioned as a cytoplasmic mRNA acceptor, promoted the release of G-quadruplex containing mRNA from its export receptor, simultaneously mediated the localization of nucleoporins mRNA on nuclear pore. FXR1 bound G-quadruplex or nucleoporin AGAA RNA via its RGG and KH domain respectively, which in turn weakened or enhanced its binding to nuclear pore, thus resulted in mRNA release or localization. More importantly, the decline of FXR1 and nuclear pore activity helped hESCs to achieve fate transition by impeding the nuclear export of transcribed RNAs, which was required for hESC differentiation.

2025-08-22 | GSE245777 | GEO

ChEC-seq2 profiling of Crm1 and Nup2 during degradation of Nup2 or inhibition/degradation of Crm1, respectively

Project description:Nuclear pore proteins (Nups) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC. In vitro, Crm1 binds both Gcn4 and Nup2 directly. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-GTP nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates docking of transcription factor-bound enhancers at the NPC.

2025-03-24 | GSE288549 | GEO

ChEC-seq2 profiling of Crm1, Nucleoporins (nups), and RNA Pol II from budding yeast grown in SDC

2025-03-24 | GSE288515 | GEO

thiol(SH)-linked alkylation for the metabolic sequencing (SLAM-seq) of RNA after Crm1 inhibition and Nup1/Nup2 degradation

2025-03-24 | GSE288633 | GEO

ChEC-seq2 profiling of yeast Gcn4 and Crm1-T539C localization after treatment with Leptomycin B.

2025-03-24 | GSE288550 | GEO

Nuclear transport surveillance of p53 by nuclear pores in glioblastoma

Project description:Nuclear pore complexes (NPCs) are the central apparatus of nucleocytoplasmic transport. Disease-specific alterations of NPCs contribute to the pathogenesis of many cancers; however, the roles of NPCs in glioblastoma (GBM) are unknown. In this study, we report genomic amplification of NUP107, a component of NPCs, in GBM and show that NUP107 is overexpressed simultaneously with MDM2, a critical E3 ligase that mediates p53 degradation. Depletion of NUP107 inhibits the growth of GBM cell lines through p53 protein stabilization. Mechanistically, NPCs establish a p53 degradation platform via an export pathway coupled with 26S proteasome tethering. NUP107 is the keystone for NPC assembly; the loss of NUP107 affects the integrity of the NPC structure, and thus the proportion of 26S proteasome in the vicinity of nuclear pores significantly decreases. Together, our findings establish roles of NPCs in transport surveillance and provide insights into p53 inactivation in GBM.

2023-08-19 | GSE216888 | GEO

Super-enhancer trapping by the nuclear pore via intrinsically disordered regions of proteins in squamous cell carcinoma cells

Project description:Master transcription factors such as TP63 establish super-enhancers (SEs) to drive core transcriptional networks in cancer cells, yet the spatiotemporal regulation of SEs within the nucleus remains unknown. The nuclear pore complex (NPC) may tether SEs to the nuclear pore where RNA export rates are maximal. Here, we report that NUP153, a component of the NPC, anchors SEs to the NPC and enhances TP63 expression by maximizing mRNA export. This anchoring is mediated through protein-protein interaction between the intrinsically disordered regions (IDRs) of NUP153 and the coactivator BRD4. Silencing of NUP153 excludes SEs from the nuclear periphery, decreases TP63 expression, impairs cellular growth, and induces epidermal differentiation of squamous cell carcinoma. Overall, this work reveals the critical roles of NUP153 IDRs in the regulation of SE localization, thus providing insights into a new layer of gene regulation at the epigenomic and spatial level.

2023-12-23 | GSE169295 | GEO

Homeostatic Regulation of Nucleoporins is the Primary Driver of Nuclear Pore Biogenesis

Project description:Nuclear pore complexes (NPCs) are the multiprotein channels that control the access to the genome. Because of their critical functions, the number of NPCs that cells assemble is tightly controlled and varies between different cell types, cellular states, and in diseases. However, the mechanisms that regulate NPC formation and numbers in mammalian cells remain largely unclear. Using a genome-wide siRNA screen for modulators of NPC assembly, we identified translation-related factors, proteasome components, and the CCR4-NOT mRNA deadenylase complex as the top regulators of NPC numbers. We found that stabilization of nucleoporin mRNAs by inhibition of the CCR4-NOT stoichiometrically increases nucleoporin protein levels and enhances NPC assembly in normal and cancer cells. Inhibiting protein translation in CCR4-NOT defective cells blocks the increase in NPC numbers, indicating that nucleoporin mRNA levels are rate-limiting for NPC biogenesis. We found that inhibiting proteasome activity also promotes NPC biogenesis, indicating that nucleoporins required for nuclear pore formation are normally produced in excess. Our findings show that nucleoporin mRNA and protein degradation restrict NPC assembly and indicate nucleoporin homeostasis is the main mechanism regulating NPC numbers in mammalian cells.

2025-03-18 | PXD052767 | Pride

Effect of nuclear pore complex (NPC) blockage by WGA treatment on zygotic genome activation (ZGA) during zebrafish early development

Project description:To investigate the function of nuclear pore complex (NPC) in the regulation of zygotic genome activation (ZGA), we microinjected medium dosage of WGA in zebrafish embryos at 1-cell stage to block NPC function. We then performed gene expression profiling analysis using data obtained from RNA-seq of control or WGA treated embryo at comparable developmental time point (4.3 hours post fertilization (hpf) ) or develomental stage (dome).

2023-02-22 | GSE212929 | 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