GO:1990723 cytoplasmic periphery of the nuclear pore complex: Components, Assembly and Research Methods, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1990723 describes the cytoplasm situated in close proximity to a nuclear pore complex, a subcellular region where nuclear-cytoplasmic transport, DNA repair and gene regulation converge.
• The cytoplasmic periphery of the nuclear pore complex is enriched in nucleoporins, SUMO proteases such as Ulp1, and DNA repair factors that capture double-strand breaks.
• Nuclear envelope tubules that capture DNA double-strand breaks originate at the nuclear periphery and require components of the nuclear pore complex.
• The nuclear pore Y-complex at the cytoplasmic periphery acts as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis.
• The dynamic nuclear periphery, including the cytoplasmic periphery of the nuclear pore complex, facilitates gamete health and rejuvenation.
• Nuclear pore complexes at the nuclear periphery are central to cell identity and aging, making GO:1990723 relevant to neurodegeneration and cancer biology.
Description
The cytoplasmic periphery of the nuclear pore complex (GO:1990723) is a cellular component defined as the cytoplasm situated in close proximity to a nuclear pore complex. This region is not merely a passive boundary; it is a functionally specialized microdomain where nuclear pore complexes (NPCs) extend their cytoplasmic filaments into the cytoplasm and interact with soluble factors, cytoskeletal elements and repair machinery. The term captures the spatial and functional interface between the nucleocytoplasmic transport machinery and the cytoplasmic environment, a zone increasingly recognized as a hub for signal transduction, genome maintenance and developmental gene regulation. Researchers study GO:1990723 because defects in nuclear pore complex function and nuclear periphery organization are linked to aging, neurodegeneration and cancer, and because this region participates in processes as diverse as DNA double-strand break repair and gamete rejuvenation. Understanding the cytoplasmic periphery of the nuclear pore complex therefore requires integrating cell biology, proteomics and functional genomics approaches that resolve both structure and dynamic interactions.
cytoplasmic periphery of the nuclear pore complex At A Glance
| GO ID | GO:1990723 |
|---|---|
| GO term | cytoplasmic periphery of the nuclear pore complex |
| Ontology | cellular_component |
| Synonym | associated with the nuclear pore |
| Definition | Cytoplasm situated in close proximity to a nuclear pore complex. |
| Major function | Spatial and functional interface for nucleocytoplasmic transport, DNA repair, SUMOylation and transcriptional regulation at the nuclear pore. |
| Related structures | Nuclear pore complex, nuclear envelope, nuclear envelope tubules, cytoplasmic filaments. |
| Key resident proteins | Nucleoporins, Ulp1, DNA repair factors, Y-complex components. |
| Relevance | Cell identity, aging, gamete health, genome maintenance and disease. |
What Is GO:1990723?
According to the Gene Ontology, GO:1990723 (cytoplasmic periphery of the nuclear pore complex) is the cytoplasm situated in close proximity to a nuclear pore complex. In other words, it is the cytoplasmic side of the nuclear pore complex, including the region immediately surrounding the cytoplasmic filaments and the adjacent cytoplasmic space where nucleoporins, transport factors and regulatory proteins concentrate. The synonym associated with the nuclear pore reflects that this component is defined by its spatial association with the nuclear pore complex rather than by a single molecular marker.
Why Is cytoplasmic periphery of the nuclear pore complex Important in Cell Biology?
The cytoplasmic periphery of the nuclear pore complex is important because it is a convergence point for nuclear-cytoplasmic transport, genome maintenance and gene regulation. DNA double-strand break-capturing nuclear envelope tubules originate at the nuclear periphery and depend on nuclear pore complex components, directly linking GO:1990723 to DNA repair. The SUMO protease Ulp1 associates with nuclear pore complexes at this periphery to maintain global SUMOylation, a modification critical for genome stability and stress responses. In plants, the nuclear pore Y-complex at the cytoplasmic periphery serves as a platform for transcriptional regulation of FLOWERING LOCUS C, demonstrating a direct role in developmental timing. The dynamic nuclear periphery also facilitates gamete health and rejuvenation, and nuclear pore complexes at the nuclear periphery are central to cell identity and aging. Consequently, studying GO:1990723 informs mechanisms of aging, neurodegeneration, cancer and reproductive biology.
• Provides a platform for DNA double-strand break capture and repair at the nuclear envelope.
• Supports global SUMOylation through Ulp1 association with nuclear pore complexes.
• Enables transcriptional regulation of developmental genes such as FLOWERING LOCUS C in Arabidopsis.
• Contributes to gamete health and rejuvenation through dynamic nuclear periphery organization.
• Links nuclear pore complexes to cell identity and aging.
• Serves as a hub for chromatin interactions with the nuclear lamina and nuclear pore complexes.
• Relevant to viral entry and intracellular receptor trafficking at the nuclear periphery.
• Implicated in piRNA-directed DNA methylation and genome defense mechanisms.
• Provides a target for CRISPR-based functional studies of nucleoporins and repair factors.
• Offers a model system for studying nuclear envelope tubule formation and repair factor recruitment.
What Happens During cytoplasmic periphery of the nuclear pore complex?
DNA double-strand break capture at the nuclear periphery
In simple terms: When DNA breaks, the nuclear envelope forms tubules that reach into the cytoplasm to capture the broken DNA.
DNA double-strand break-capturing nuclear envelope tubules drive DNA repair and originate at the nuclear periphery, requiring nuclear pore complex components. This process positions the cytoplasmic periphery of the nuclear pore complex as an active site for genome maintenance, where repair factors are recruited to the vicinity of the nuclear pore.
SUMOylation maintenance by Ulp1 at nuclear pore complexes
In simple terms: A SUMO-removing enzyme called Ulp1 sits at the nuclear pore to keep protein modification balanced.
Ulp1 association with nuclear pore complexes is required for the maintenance of global SUMOylation. Because Ulp1 localizes to the cytoplasmic periphery of the nuclear pore complex, this region directly regulates the SUMOylation status of cytoplasmic and nuclear proteins, influencing genome stability and stress responses.
Transcriptional regulation via the nuclear pore Y-complex
In simple terms: The nuclear pore can act like a control panel that helps turn genes on or off.
The nuclear pore Y-complex functions as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis. This demonstrates that the cytoplasmic periphery of the nuclear pore complex is not only a transport gateway but also a regulatory hub that can influence developmental gene expression.
Chromatin interactions with the nuclear periphery
In simple terms: DNA inside the nucleus can physically touch the nuclear pore and lamina, which affects how genes behave.
Interactions of chromatin with the nuclear lamina and nuclear pore complexes are well documented, and these interactions influence gene expression and genome organization. The cytoplasmic periphery of the nuclear pore complex is part of this dynamic interface, contributing to the spatial regulation of chromatin.
Gamete health and rejuvenation at the dynamic nuclear periphery
In simple terms: The nuclear edge helps reproductive cells stay healthy and reset for the next generation.
The dynamic nuclear periphery acts as a facilitator of gamete health and rejuvenation. Nuclear pore complexes at this periphery participate in remodeling events that are essential for gamete function, linking GO:1990723 to reproductive biology.
Key Genes Involved in GO:1990723 cytoplasmic periphery of the nuclear pore complex
The following genes and proteins are experimentally linked to the cytoplasmic periphery of the nuclear pore complex and its associated functions.
| Gene | Major Role | Research Relevance |
|---|---|---|
| NUP98 | Nucleoporin component of the nuclear pore complex | Fusion proteins in leukemia; nuclear pore function |
| NUP153 | Nucleoporin at the nuclear basket | Chromatin interactions and nuclear pore organization |
| NUP214 | Cytoplasmic filament nucleoporin | Nuclear export and leukemia-associated fusions |
| NUP358 (RANBP2) | Cytoplasmic filament nucleoporin | SUMOylation and nuclear transport |
| ULP1 (SENP1/2 homolog) | SUMO protease | Maintains global SUMOylation at nuclear pore complexes |
| Y-complex subunits (NUP107-160) | Structural core of the nuclear pore | Transcriptional regulation of FLOWERING LOCUS C |
| FLOWERING LOCUS C (FLC) | Floral repressor transcription factor | Developmental timing via nuclear pore Y-complex |
| Lamin A/C (LMNA) | Nuclear lamina protein | Chromatin interactions with nuclear periphery |
| SUN1/SUN2 | Nuclear envelope proteins | Link nuclear envelope to cytoskeleton |
| KASH-domain proteins | Outer nuclear membrane proteins | Nuclear envelope tubule formation |
| ATM | DNA damage response kinase | DNA double-strand break repair at nuclear periphery |
| 53BP1 | DNA repair factor | Recruitment to nuclear envelope tubules |
| SCARF2 | Scavenger receptor class F member 2 | Intracellular receptor for hepatitis B virus |
| piRNA pathway factors | Genome defense | piRNA-directed DNA methylation |
| NUP62 | Central channel nucleoporin | Nuclear pore complex assembly and transport |
| NUP88 | Cytoplasmic nucleoporin | Nuclear pore complex stability |
| RAN | Small GTPase | Nucleocytoplasmic transport at the nuclear pore |
How Is cytoplasmic periphery of the nuclear pore complex Regulated?
The cytoplasmic periphery of the nuclear pore complex is regulated by the SUMO protease Ulp1, whose association with nuclear pore complexes is required for the maintenance of global SUMOylation. This regulation ensures that SUMOylation homeostasis is preserved at the nuclear periphery, influencing protein stability and genome maintenance. Additionally, the nuclear pore Y-complex acts as a platform for transcriptional regulation, indicating that the composition and activity of the cytoplasmic periphery can be modulated to control gene expression. Chromatin interactions with the nuclear lamina and nuclear pore complexes further suggest that the organization of this region is dynamically regulated during development and aging.
cytoplasmic periphery of the nuclear pore complex and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| NUP98 | Leukemia | Knockout and fusion knock-in in hematopoietic cells |
| ULP1 | Genome instability and SUMOylation disorders | Point mutation of catalytic domain |
| ATM | Ataxia-telangiectasia and cancer | Knockout in DNA repair assays |
| SCARF2 | Hepatitis B virus infection | Overexpression and knockout in hepatocytes |
| piRNA pathway factors | Transposon activation and infertility | Knockout in germline cells |
Cancer and genome instability
Nuclear pore complex components at the cytoplasmic periphery are implicated in genome maintenance, and DNA double-strand break-capturing nuclear envelope tubules drive DNA repair. Disruption of this repair function can lead to genome instability, a hallmark of cancer. Nucleoporin fusions and altered nuclear pore function are also associated with leukemia and other malignancies.
Neurodegeneration and aging
Nuclear pore complexes at the nuclear periphery play a central role in cell identity and aging. Age-related deterioration of nuclear pore function and nuclear periphery organization contributes to neurodegenerative processes, making GO:1990723 relevant to aging research. The dynamic nuclear periphery also facilitates gamete health and rejuvenation, highlighting its role in maintaining cellular fitness.
Viral infection and intracellular trafficking
Scavenger receptor class F member 2 is an intracellular receptor for hepatitis B virus, and its trafficking intersects with nuclear periphery pathways. This links the cytoplasmic periphery of the nuclear pore complex to viral entry and infection biology.
Genome defense and epigenetic regulation
A nowhere-to-hide mechanism ensures complete piRNA-directed DNA methylation, a genome defense process that involves nuclear periphery factors. This connects GO:1990723 to epigenetic silencing and transposon control.
From cytoplasmic periphery of the nuclear pore complex-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of a nucleoporin disrupt DNA repair at the nuclear periphery? | Knockout cell line followed by DNA damage assays |
| Does a point mutation in Ulp1 alter global SUMOylation? | Point-mutation knock-in of Ulp1 catalytic residue |
| Can a tagged nucleoporin track nuclear envelope tubule formation? | Tagged knock-in of NUP153 or NUP358 |
| Does overexpression of a repair factor enhance break capture? | Overexpression of 53BP1 or ATM |
| Does the Y-complex regulate a developmental gene? | Knockout of Y-complex subunits in Arabidopsis |
| Does SCARF2 mediate viral entry at the nuclear periphery? | Knockout and overexpression in hepatocytes |
How to Study the cytoplasmic periphery of the nuclear pore complex Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Fluorescence microscopy | Localization of nucleoporins and repair factors | Visualizing nuclear envelope tubules |
| Proximity labeling proteomics | Protein interactions at the nuclear periphery | Identifying Ulp1-associated factors |
| CRISPR knockout screens | Gene requirement for nuclear periphery functions | Discovering DNA repair and SUMOylation regulators |
| RNA-seq | Transcriptional changes upon nuclear pore perturbation | Studying FLOWERING LOCUS C regulation |
| ChIP-seq | Chromatin occupancy at the nuclear periphery | Mapping chromatin-nuclear pore interactions |
| Live-cell imaging | Dynamic tubule formation and break capture | Tracking DNA double-strand break repair |
| SUMOylation assays | Global SUMO conjugate levels | Assessing Ulp1 function at nuclear pores |
| Yeast two-hybrid | Binary protein interactions | Mapping nucleoporin interactions |
Imaging the cytoplasmic periphery of the nuclear pore complex
Fluorescence microscopy and live-cell imaging can visualize nuclear envelope tubules and nuclear pore complex components at the cytoplasmic periphery. Super-resolution techniques help resolve the spatial relationship between nucleoporins and repair factors.
Proteomics of nuclear pore complex proximity
Proximity labeling and affinity purification coupled to mass spectrometry can identify proteins enriched at the cytoplasmic periphery of the nuclear pore complex, including Ulp1 and SUMO pathway components. These approaches reveal dynamic interactions that define the functional state of this region.
Functional genomics and CRISPR screens
CRISPR knockout screens can identify genes required for DNA repair at the nuclear periphery and for nuclear pore complex assembly. Such screens link candidate genes to phenotypes such as genome instability and altered SUMOylation.
Transcriptional and epigenetic profiling
RNA-seq and chromatin immunoprecipitation can assess how nuclear pore complex components at the cytoplasmic periphery influence gene expression, as shown for FLOWERING LOCUS C regulation. These methods connect GO:1990723 to developmental and epigenetic programs.
How CRISPR Can Be Used to Study GO:1990723 cytoplasmic periphery of the nuclear pore complex
Knockout
CRISPR knockout of nucleoporins or Ulp1 can disrupt the cytoplasmic periphery of the nuclear pore complex, leading to defects in DNA repair and SUMOylation. Knockout models are essential to test causality between GO:1990723 components and cellular phenotypes.
Point Mutation
Point mutations in catalytic residues of Ulp1 or in nucleoporin domains can dissect specific functions at the cytoplasmic periphery without fully ablating protein expression. Such models help distinguish structural from enzymatic roles.
Knock-in
Knock-in of fluorescent or affinity tags into nucleoporin genes enables real-time tracking of nuclear envelope tubules and nuclear pore complex dynamics. Tagged knock-in models are valuable for imaging-based studies of GO:1990723.
Overexpression
Overexpression of DNA repair factors such as 53BP1 or ATM can enhance break capture at the nuclear periphery and test sufficiency of repair pathways. Overexpression models complement loss-of-function studies to define the functional capacity of the cytoplasmic periphery.
How EDITGENE Supports cytoplasmic periphery of the nuclear pore complex Research
Researchers studying cytoplasmic periphery of the nuclear pore complex-related genes often need to determine whether a candidate gene is causally involved in nuclear pore function, DNA repair or SUMOylation. EDITGENE provides CRISPR-based cell model services that enable precise genetic perturbations to test these hypotheses in relevant cell types.
Contact EDITGENE today to design your custom CRISPR model for cytoplasmic periphery of the nuclear pore complex research.
Frequently Asked Questions About cytoplasmic periphery of the nuclear pore complex
What is GO:1990723?
GO:1990723 is the Gene Ontology term for the cytoplasmic periphery of the nuclear pore complex, defined as the cytoplasm situated in close proximity to a nuclear pore complex.
What genes are involved in the cytoplasmic periphery of the nuclear pore complex?
Genes encoding nucleoporins such as NUP98, NUP153, NUP214 and NUP358, the SUMO protease Ulp1, DNA repair factors like ATM and 53BP1, and Y-complex subunits are involved.
What happens at the cytoplasmic periphery of the nuclear pore complex?
It serves as a site for DNA double-strand break capture, SUMOylation maintenance, transcriptional regulation and chromatin interactions.
Why is the cytoplasmic periphery of the nuclear pore complex important for DNA repair?
Nuclear envelope tubules that capture DNA double-strand breaks originate at the nuclear periphery and require nuclear pore complex components.
How is SUMOylation regulated at the nuclear pore complex?
Ulp1 association with nuclear pore complexes is required for the maintenance of global SUMOylation.
Does the nuclear pore complex regulate gene expression?
Yes, the nuclear pore Y-complex functions as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis.
What diseases are linked to the cytoplasmic periphery of the nuclear pore complex?
Cancer, neurodegeneration, aging-related disorders and viral infections have been linked to nuclear pore complex and nuclear periphery dysfunction.
How can I study the cytoplasmic periphery of the nuclear pore complex?
Imaging, proteomics, CRISPR screens and transcriptomics are commonly used to study this region.
What model systems are used for GO:1990723 research?
Human cell lines, Arabidopsis and germline models are used to study nuclear pore complex functions at the cytoplasmic periphery.
What is the synonym for GO:1990723?
The synonym is associated with the nuclear pore.
Conclusion
The cytoplasmic periphery of the nuclear pore complex (GO:1990723) is a functionally rich cellular component that integrates nuclear-cytoplasmic transport with DNA repair, SUMOylation and transcriptional regulation. Its roles in genome maintenance, aging and development make it a compelling target for mechanistic studies. CRISPR-based models and multi-omics approaches will continue to clarify how this region contributes to health and disease.
References
- 1. Shokrollahi M et al.. 2024. DNA double-strand break-capturing nuclear envelope tubules drive DNA repair.. Nat Struct Mol Biol 31(9):1319-1330 PMID: 38632359
- 2. Li C et al.. 2026. Scavenger receptor class F member 2 is an intracellular receptor for hepatitis B virus.. Cell 189(14):4454-4470.e9 PMID: 42167249
- 3. Chowdhury T et al.. 2026. A nowhere-to-hide mechanism ensures complete piRNA-directed DNA methylation.. Nature 650(8102):779-785 PMID: 41535457
- 4. Ptak C et al.. 2025. Ulp1 association with nuclear pore complexes is required for the maintenance of global SUMOylation.. Mol Biol Cell 36(7):ar81 PMID: 40327319
- 5. Huang P et al.. 2024. The nuclear pore Y-complex functions as a platform for transcriptional regulation of FLOWERING LOCUS C in Arabidopsis.. Plant Cell 36(2):346-366 PMID: 37877462
- 6. King GA et al.. 2020. The dynamic nuclear periphery as a facilitator of gamete health and rejuvenation.. Curr Genet 66(3):487-493 PMID: 31915924
- 7. Shevelyov YY. 2023. Interactions of Chromatin with the Nuclear Lamina and Nuclear Pore Complexes.. Int J Mol Sci 24(21) PMID: 37958755
- 8. Cho UH et al.. 2020. Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging.. Neuron 106(6):899-911 PMID: 32553207
