NUP62CL Human

What is NUP62CL and what is its basic function in human cells?

NUP62CL encodes a protein containing domains found in nucleoporins, which are essential components of nuclear pore complexes (NPCs). These complexes regulate molecular transport between the nucleus and cytoplasm. According to the gene description, alternative splicing results in multiple transcript variants . As a nucleoporin family member, NUP62CL likely contributes to nucleocytoplasmic transport regulation, though its specific role may differ from canonical nucleoporins.

Methodologically, researchers investigating NUP62CL function should consider:

• Subcellular localization studies using fluorescent protein tagging or immunocytochemistry

• Protein-protein interaction analyses with other nuclear pore complex components

• Loss-of-function experiments via RNA interference or CRISPR-Cas9

• Rescue experiments with wild-type or mutant constructs to validate phenotypes

What expression patterns does NUP62CL exhibit across human tissues?

NUP62CL expression has been studied across multiple tissue types and developmental stages as evidenced by its inclusion in numerous expression databases:

Researchers can leverage these resources to identify tissues with high or low NUP62CL expression . Brain tissues appear to be of particular interest given the multiple brain-specific expression datasets containing NUP62CL data.

To validate expression patterns, researchers should employ:

• qRT-PCR across tissue panels

• Western blotting with validated antibodies

• Single-cell RNA sequencing for cellular resolution

• In situ hybridization for spatial context within tissues

How is NUP62CL regulated at the transcriptional level?

Transcriptional regulation of NUP62CL can be investigated through multiple approaches. Based on the Harmonizome database listings, NUP62CL appears in several transcription factor datasets:

• CHEA Transcription Factor Binding Site Profiles

• ENCODE Transcription Factor Binding Site Profiles

• ENCODE Histone Modification Site Profiles

These resources suggest that specific transcription factors may bind to the NUP62CL promoter region, and that histone modifications likely play a role in its expression regulation.

Recommended methodological approaches include:

• Chromatin immunoprecipitation (ChIP) to identify bound transcription factors

• Reporter gene assays with promoter constructs

• CRISPR-based epigenome editing to modulate specific regulatory elements

• DNase hypersensitivity assays to identify open chromatin regions

What are the most effective experimental approaches for studying NUP62CL's role in nuclear pore complex assembly?

As a protein containing nucleoporin domains, NUP62CL likely participates in nuclear pore complex (NPC) formation. Advanced experimental approaches should include:

• Proximity labeling techniques:

  • BioID or TurboID fusion proteins to identify proteins in close proximity to NUP62CL

  • APEX2 proximity labeling for temporal control of labeling reactions

  • Analysis of labeled proteins by mass spectrometry

• Live-cell imaging approaches:

  • Fluorescence Recovery After Photobleaching (FRAP) to study dynamics

  • Single-particle tracking to monitor movement within the NPC

  • Super-resolution microscopy (STORM, PALM) for detailed localization

• In vitro reconstitution:

  • Purification of recombinant NUP62CL and potential interacting partners

  • Electron microscopy of reconstituted subcomplexes

  • Biochemical assays to assess complex formation and stability

The cellular compartments containing NUP62CL protein can be revealed through analysis of the COMPARTMENTS Curated Protein Localization Evidence Scores dataset , providing guidance for experimental design.

How do disease-associated mutations impact NUP62CL function?

Disease associations for NUP62CL can be found in:

• CTD Gene-Disease Associations

• DisGeNET Gene-Disease Associations

To study the functional impact of disease-associated mutations:

• Structural analysis approaches:

  • Homology modeling of NUP62CL domains

  • Molecular dynamics simulations to predict mutation effects

  • In silico mutagenesis and stability predictions

• Functional characterization:

  • Site-directed mutagenesis to introduce disease-associated variants

  • Complementation assays in knockout/knockdown cells

  • Protein interaction studies comparing wild-type and mutant forms

  • Nucleocytoplasmic transport assays with reporter constructs

• Disease model development:

  • Patient-derived cell lines harboring mutations

  • CRISPR-engineered isogenic cell lines

  • Animal models with orthologous mutations

When analyzing disease associations, researchers should ensure careful validation of genotype-phenotype correlations and consider potential confounding factors.

What is the relationship between NUP62CL expression and cell cycle progression?

Nucleoporins often play critical roles in cell division and cell cycle regulation. To investigate NUP62CL's potential role:

• Cell synchronization experiments:

  • Serum starvation/release protocols

  • Double thymidine block for S-phase synchronization

  • Nocodazole treatment for mitotic arrest

  • Analysis of NUP62CL expression and localization across cell cycle phases

• Live-cell imaging approaches:

  • Time-lapse microscopy with fluorescently tagged NUP62CL

  • Correlation with cell cycle markers

  • Quantitative image analysis of nuclear envelope dynamics

• Perturbation studies:

  • Cell cycle analysis after NUP62CL depletion or overexpression

  • Rescue experiments with cell cycle-regulated variants

  • Combined perturbation with cell cycle regulators

The CMAP and GEO Signatures datasets may contain information about how chemical perturbations affecting cell cycle also impact NUP62CL expression .

How do post-translational modifications regulate NUP62CL function?

Post-translational modifications (PTMs) often regulate nucleoporin function:

• PTM identification strategies:

  • Mass spectrometry analysis of immunoprecipitated NUP62CL

  • Phospho-specific antibodies for common modifications

  • PTM-specific enrichment techniques (e.g., TiO₂ for phosphopeptides)

• Functional analysis of PTMs:

  • Site-directed mutagenesis of modified residues

  • Phosphomimetic mutations (e.g., Ser→Asp) or phospho-null mutations (e.g., Ser→Ala)

  • Cell cycle-dependent analysis of modifications

  • Kinase/phosphatase inhibitor treatments

• Enzymes responsible for modifications:

  • Kinase prediction algorithms

  • In vitro kinase assays

  • Targeted knockdown of candidate modifying enzymes

Building a comprehensive PTM map will help understand how NUP62CL is dynamically regulated in different cellular contexts.

What are the key considerations when generating antibodies against NUP62CL?

Developing specific antibodies for NUP62CL research requires careful planning:

• Epitope selection considerations:

  • Analyze sequence similarity with other nucleoporins, especially NUP62

  • Target unique regions to avoid cross-reactivity

  • Consider accessibility in the native protein conformation

  • Evaluate potential post-translational modification sites

• Validation strategies:

  • Western blotting with overexpression and knockout controls

  • Immunoprecipitation followed by mass spectrometry

  • Immunofluorescence with siRNA knockdown controls

  • Peptide competition assays

• Application-specific optimization:

  • Fixation conditions for immunohistochemistry

  • Detergent selection for nuclear envelope proteins

  • Blocking conditions to reduce background

When commercial antibodies are unavailable or unsatisfactory, epitope tagging approaches (FLAG, HA, etc.) offer alternatives for detection in experimental systems.

How can researchers analyze NUP62CL dependence in cancer cell lines?

The DepMap CRISPR Gene Dependency dataset contains information about how cancer cell lines respond to NUP62CL knockout :

• Bioinformatic analysis approaches:

  • Mining DepMap and other dependency databases for NUP62CL patterns

  • Correlation with genomic features (mutations, CNVs, expression)

  • Cell line clustering based on dependency profiles

• Experimental validation methods:

  • CRISPR knockout in selective cell line panels

  • shRNA knockdown with multiple constructs

  • Growth, survival, and phenotypic assays

  • Complementation with wild-type or mutant constructs

• Data interpretation framework:

  • Distinguishing context-dependent from general dependencies

  • Correlation with NUP62CL expression levels (CCLE data)

  • Integration with copy number variation data (COSMIC, CCLE)

  • Analysis of potential synthetic lethal interactions

The COSMIC Cell Line Gene CNV Profiles and CCLE Cell Line Gene CNV Profiles datasets provide additional information about NUP62CL copy number variations across cancer cell lines.

What splice variants of NUP62CL exist and how should researchers account for them?

The gene description indicates that alternative splicing results in multiple transcript variants of NUP62CL . Researchers should address this complexity through:

• Transcript identification strategies:

  • RNA-Seq analysis with junction-spanning reads

  • PCR with primers flanking alternative exons

  • 5' and 3' RACE to capture all transcript ends

  • Long-read sequencing (PacBio, Nanopore) for full-length isoforms

• Isoform-specific experimental design:

  • PCR primers targeting unique exon junctions

  • siRNAs targeting specific variants

  • Expression constructs for individual isoforms

  • Antibodies recognizing shared or unique epitopes

• Functional comparison methods:

  • Rescue experiments with different isoforms

  • Localization studies of individual variants

  • Interaction partner analysis for each isoform

  • Temporal and spatial expression pattern analysis

A comprehensive isoform catalog should be established before undertaking detailed functional studies to ensure biological relevance.

How should researchers integrate multi-omics data to understand NUP62CL function?

The Harmonizome database indicates that NUP62CL appears in numerous datasets spanning different biological data types . Effective integration requires:

• Data integration strategies:

  • Network-based approaches linking transcriptomic, proteomic, and genetic data

  • Pathway enrichment analysis across multiple data types

  • Correlation analysis between expression and functional readouts

  • Machine learning approaches to identify patterns across datasets

• Recommended computational resources:

  • Cytoscape for network visualization and analysis

  • R packages for multi-omics integration (mixOmics, MultiAssayExperiment)

  • Galaxy workflows for reproducible analysis pipelines

  • Database query tools for mining existing datasets

• Validation and interpretation frameworks:

  • Hypothesis generation from integrated data

  • Targeted experimental validation of computational predictions

  • Iterative refinement of models based on new data

  • Context-specific interpretation considering cell type and condition

The comprehensive list of datasets containing NUP62CL information provides a valuable starting point for multi-omics integration efforts .

How can researchers resolve contradictory findings about NUP62CL function?

Scientific literature often contains seemingly contradictory results, which may stem from:

• Sources of contradiction:

  • Different experimental systems (cell lines, tissues, organisms)

  • Varied technical approaches and sensitivity

  • Context-dependent functions of NUP62CL

  • Isoform-specific effects not accounted for

  • Antibody cross-reactivity issues

• Resolution strategies:

  • Systematic comparison of experimental conditions

  • Direct replication studies with controlled variables

  • Meta-analysis of published findings

  • Development of unified models accounting for context-dependency

• Experimental design recommendations:

  • Include multiple complementary approaches

  • Test findings across different cell types or tissues

  • Control for expression of specific isoforms

  • Use genetic rescue experiments to confirm specificity

  • Report detailed methodological information to facilitate replication

When evaluating chemical interaction effects, researchers should consult the CTD Gene-Chemical Interactions dataset to understand how different compounds may influence NUP62CL expression or function.

What is the potential role of NUP62CL in viral infections?

The GEO Signatures of Differentially Expressed Genes for Viral Infections dataset contains information about how viral infections affect NUP62CL expression :

• Investigation approaches:

  • Analysis of NUP62CL expression changes during infection

  • Localization studies in infected versus uninfected cells

  • Protein-protein interaction studies with viral components

  • Loss-of-function studies to assess viral replication effects

• Mechanistic considerations:

  • Role in viral nuclear import/export

  • Potential viral targeting of nuclear pore complex

  • Involvement in antiviral signaling pathways

  • Subversion mechanisms employed by viruses

• Therapeutic implications:

  • Potential as antiviral target

  • Biomarker for specific viral infections

  • Role in determining cell type tropism

Understanding NUP62CL's role in viral infections could provide insights into both basic virology and potential therapeutic approaches.

How does NUP62CL function differ from other nucleoporins?

Despite sharing domains with other nucleoporins, NUP62CL likely has unique functions:

• Comparative analysis approaches:

  • Sequence and structural comparisons with other nucleoporins

  • Phylogenetic analysis across species

  • Expression pattern comparisons

  • Interaction partner analysis

• Functional differentiation methods:

  • Rescue experiments in cells depleted of different nucleoporins

  • Cargo specificity determination

  • Localization within the nuclear pore complex architecture

  • Response to cellular stresses or signaling events

• Evolutionary considerations:

  • Analysis of selective pressures on different domains

  • Comparison of domain architecture across species

  • Investigation of lineage-specific functions

The "CL" (C-terminal like) designation suggests structural similarities with the C-terminal region of NUP62, but likely with functional divergence that merits detailed investigation.