Post-translational modification of MYC localizes MYC to the nuclear pore basket to regulate local histone acetylation and gene expression
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ABSTRACT:
PROVIDER: PRJNA430935 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7995430.fastq.gz | Fastqsanger.gz | |||
| SRR7995440_1.fastq.gz | Fastqsanger.gz | |||
| SRR7995440_2.fastq.gz | Fastqsanger.gz | |||
| SRR7995431_1.fastq.gz | Fastqsanger.gz | |||
| SRR7995431_2.fastq.gz | Fastqsanger.gz |
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Project description:This SuperSeries is composed of the SubSeries listed below.
2018-11-20 | GSE109459 | GEO
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
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
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
Project description:Using phosphoproteomics and time-lapse fluorescence microscopy, we report that NPCs nuclear pore complexes (NPCs) undergo two distinct modularity events for the nucleoporins Nup60 and Nup2 during budding yeast meiosis: partial and full nuclear basket detachment.
2022-12-08 | PXD033245 | Pride
Project description:While nuclear pore proteins mediate nucleo-cytoplasmic transport, they can have important roles in other activities such as transcription, chromatin organization, and cell cycle regulation. The fission yeast nuclear pore protein nup211 localizes to the nuclear basket and is essential for cell viability. Nup211 is important for RNA quality control and the nuclear export of polyadenylated RNAs. Interestingly, several nup211 orthologs have also been shown to regulate transcription at the chromatin level. Although nup211 preferentially associates with heterochromatin, it is unclear whether it modulates transcription. To further investigate the functions of nup211, we constructed a strain in which nup211 expression can be reduced through the addition of thiamine to the growth medium (nup211-so) and examined how cells were affected when nup211 protein was reduced. Down-regulation of nup211 led to severe defects in cell cycle regulation, including septation and cytokinesis. Using RNA-Seq and RT-qPCR, we revealed that loss of nup211 significantly altered global gene expression. Our findings suggest a new role for nup211 in regulating the transcriptome.
2024-10-04 | GSE216106 | GEO
Project description:Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with its Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing at the Mediator level. In sum, we provide insight into how NPC-associated adaptor complexes can access the core transcription machinery. RNAseq was performed from WT, sac3∆, cdk8∆ and Sac3 R288D mutant cells. For each strain triplicates were analyzed. WT strain was sac3∆ transformed with pRS315 SAC3 WT
2015-08-27 | E-GEOD-67431 | biostudies-arrayexpress
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
Project description:Nuclear pore complexes (NPCs) influence gene expression besides their established function in nuclear transport. The TREX-2 complex localizes to the NPC basket and affects gene-NPC interactions, transcription and mRNA export. How TREX-2 regulates the gene expression machinery is unknown. Here, we show that TREX-2 interacts with the Mediator complex, an essential regulator of RNA Polymerase (Pol) II. Structural and biochemical studies identify a conserved region on TREX-2, which directly binds the Mediator Med31/Med7N submodule. TREX-2 regulates assembly of Mediator with its Cdk8 kinase and is required for recruitment and site-specific phosphorylation of Pol II. Transcriptome and phenotypic profiling confirm that TREX-2 and Med31 are functionally interdependent. TREX-2 additionally uses its Mediator-interacting surface to regulate mRNA export suggesting a mechanism for coupling transcription initiation and early steps of mRNA processing at the Mediator level. In sum, we provide insight into how NPC-associated adaptor complexes can access the core transcription machinery.
2015-08-27 | GSE67431 | GEO
Project description:Previous BioID experiments targeting the nucleoporin (NUP) NUP158 and the nuclear transport factor MEX67 indicated (PMID: 36410438; PXD031245) that proximity labelling delivers highly specific interactome data in the confined localisation of the nuclear pore, with a labelling radius well below the size of the nuclear pore. Here we extended this approach to target NUPs NUP110, NUP76 and NUP96 with a TurboID-HA tandem tag fused to both, the N and C-terminus of each respective target protein. While the central NUP96 biotinylated most nuclear pore proteins with the marked exception of the nuclear basket, NUP158, NUP110 and NUP76 caused biotinylation of specific sub-complexes of the pore and Mex67 labelled NUPs lining the pore channel.
2023-12-04 | PXD047268 | Pride