ZNF563 Antibody

What is ZNF563 and what is its cellular function?

ZNF563 (Zinc Finger Protein 563) is a protein-coding gene that functions as a transcription factor located primarily in the nucleus. It contains multiple C2H2-type zinc finger domains that enable DNA binding and regulation of gene expression. ZNF563 belongs to the KRAB-containing zinc finger protein family and is involved in various cellular processes including gene expression regulation . Gene Ontology (GO) annotations indicate nucleic acid binding functionality, and the protein has been associated with pathways related to gene expression and viral infection responses, particularly herpes simplex virus 1 infection . ZNF563 has been found to have an important paralog, ZNF443, suggesting potential functional redundancy or complementation within cellular systems .

What are the optimal experimental applications for ZNF563 antibodies?

ZNF563 antibodies have been validated for several key laboratory techniques, with Western blotting and immunocytochemistry/immunofluorescence being the primary applications. For Western blot analysis, the optimal dilution range is 1:500-1:2000 depending on the specific antibody and sample type . When performing immunocytochemistry, a concentration of approximately 10 μg/ml has been validated for HeLa cells . Both mouse-derived and rabbit-derived antibodies are available, offering flexibility for multi-labeling experiments. The antibodies have been rigorously tested on various cell lines including K562, U87-MG, SH-SY5Y, HeLa, and rat brain tissue, providing reliability across different experimental contexts .

What considerations should I make when selecting between polyclonal and monoclonal ZNF563 antibodies?

The choice between polyclonal and monoclonal ZNF563 antibodies depends on your specific research objectives:

Polyclonal ZNF563 antibodies:

• Recognize multiple epitopes, providing stronger detection signals especially in proteins with low expression

• Available from different host species (mouse and rabbit), enabling flexibility in experimental design

• Better for initial detection and characterization experiments

• More robust against antigen conformational changes

Monoclonal alternatives:

• Would provide higher specificity to a single epitope (though not highlighted in the provided search results)

• Would offer better lot-to-lot consistency for longitudinal studies

• Would be preferred for discriminating between closely related proteins

When studying ZNF563, polyclonal antibodies from different hosts allow for greater flexibility in multi-labeling experiments. The mouse IgG polyclonal antibody from Bio-Techne and rabbit polyclonal antibody from Elabscience offer complementary tools that can be selected based on experimental requirements and other antibodies used in the protocol .

What is the molecular weight of ZNF563 and how does this impact detection methods?

ZNF563 has a calculated molecular weight of approximately 55 kDa, which is consistently observed in Western blot analysis . This molecular weight determination is critical for proper identification of the protein in experimental contexts. When performing Western blotting, researchers should expect to see bands at approximately 55 kDa in positive samples. It's worth noting that post-translational modifications or alternative splicing may result in slight variations from the predicted molecular weight.

For transfected systems, such as the 293T cell line transfected with ZNF563, a band of approximately 52.36 kDa has been observed . This slight difference from the calculated molecular weight may be due to the expression system or modifications of the recombinant protein. When interpreting Western blot results, researchers should be aware that different modified forms of the protein may appear as multiple bands on the membrane .

How should I optimize Western blot protocols for ZNF563 detection?

For optimal Western blot detection of ZNF563, consider the following methodological approach:

• Sample preparation: Use appropriate lysis buffers with protease inhibitors to prevent protein degradation.

• Loading controls: Include appropriate housekeeping proteins as loading controls, especially when comparing expression levels across different samples.

• Antibody dilution: Start with the recommended dilution of 1:500 for Bio-Techne's antibody or 1:500-1:2000 for Elabscience's antibody , then optimize based on signal intensity and background.

• Blocking: Use 5% non-fat dry milk or BSA in TBST for efficient blocking to reduce background.

• Incubation time: Overnight incubation at 4°C typically yields better results than shorter incubations at higher temperatures.

• Controls: Include positive controls such as ZNF563-transfected cell lysates (approximately 52.36 kDa band) alongside non-transfected lysates as negative controls .

• Detection: Use appropriate secondary antibodies compatible with your primary antibody host species (anti-mouse for Bio-Techne's antibody or anti-rabbit for Elabscience's antibody ).

• Expected results: Look for specific bands at approximately 55 kDa, with possible slight variations due to post-translational modifications .

What cell lines and samples have been validated for ZNF563 antibody applications?

ZNF563 antibodies have been extensively validated across multiple cell lines and tissue samples, providing researchers with confidence in their application to various experimental systems:

This validation across diverse cell types suggests the antibodies are robust tools for investigating ZNF563 expression in both human and rodent experimental systems. The cross-reactivity with rat samples from the Elabscience antibody makes it particularly valuable for comparative studies between human and rodent models .

What are the optimal storage and handling conditions for maintaining ZNF563 antibody activity?

To maintain optimal activity of ZNF563 antibodies, follow these evidence-based storage and handling recommendations:

• Storage temperature: Store antibodies at -20°C or -80°C for long-term preservation of activity .

• Aliquoting: Upon receipt, divide the antibody into small single-use aliquots to avoid repeated freeze-thaw cycles that can degrade antibody quality .

• Freeze-thaw cycles: Minimize freeze-thaw cycles as they can lead to protein denaturation and loss of binding activity .

• Working dilutions: Prepare working dilutions immediately before use rather than storing diluted antibody for extended periods.

• Buffer composition: ZNF563 antibodies are typically supplied in phosphate-buffered solution (pH 7.4) with stabilizers and may contain glycerol (50%) as a cryoprotectant .

• Shipping conditions: Upon receipt of antibodies shipped with ice packs, immediately store at the recommended temperature to maintain stability .

• Shelf life: ZNF563 antibodies are typically valid for 12 months when stored properly at -20°C .

Following these guidelines will help ensure consistent antibody performance throughout your research project.

How can I validate ZNF563 antibody specificity for my experimental system?

Validating antibody specificity is critical for ensuring reliable results in ZNF563 research. Implement these validation strategies:

• Positive and negative controls:

  • Use ZNF563-transfected cell lysates as positive controls

  • Compare against non-transfected lysates as negative controls

  • Include samples with genetic knockdown/knockout of ZNF563 if available

• Western blot validation:

  • Confirm the presence of bands at the expected molecular weight (~55 kDa)

  • Verify the absence of these bands in negative controls

  • For the Bio-Techne antibody, expect a 52.36 kDa band in ZNF563-transfected 293T cells

• Peptide competition assay:

  • Pre-incubate the antibody with the immunizing peptide

  • This should abolish specific binding if the antibody is truly specific

• Cross-reactivity assessment:

  • Test the antibody in cells or tissues from different species if your research involves cross-species comparisons

  • The Elabscience antibody has demonstrated reactivity with human, mouse, and rat samples

• Multi-method validation:

  • Confirm findings using orthogonal methods (e.g., mass spectrometry, RNA-seq)

  • Compare results from antibodies targeting different epitopes of ZNF563

• Immunocytochemistry correlation:

  • Nuclear localization pattern should be observed, consistent with ZNF563's function as a transcription factor

  • Compare staining patterns with published literature

What are the key considerations when designing experiments to study ZNF563 interactions with other proteins or DNA?

When investigating ZNF563 interactions with other biomolecules, consider these methodological approaches:

• Co-immunoprecipitation (Co-IP):

  • Use validated ZNF563 antibodies for pull-down experiments

  • Optimize lysis conditions to preserve protein-protein interactions

  • Include appropriate controls (IgG control, input samples)

  • Consider cross-linking to stabilize transient interactions

• Chromatin Immunoprecipitation (ChIP):

  • Given ZNF563's role as a transcription factor with nucleic acid binding properties , ChIP experiments can identify DNA binding sites

  • Validate antibody suitability for ChIP applications specifically

  • Use formaldehyde cross-linking to preserve DNA-protein interactions

• Proximity Ligation Assay (PLA):

  • Useful for detecting protein-protein interactions in situ

  • Requires antibodies from different host species (the availability of both mouse and rabbit ZNF563 antibodies facilitates this approach)

• Yeast Two-Hybrid or Mammalian Two-Hybrid:

  • Can identify novel interaction partners of ZNF563

  • Validate findings with reciprocal Co-IP experiments

• Bioinformatic prediction:

  • Analyze the zinc finger domains of ZNF563 to predict potential DNA binding motifs

  • Compare with related zinc finger proteins like its paralog ZNF443

• Competitive binding assays:

  • Investigate if ZNF563 competes with other transcription factors for binding sites

  • May provide insights into regulatory networks

These approaches can provide comprehensive insights into ZNF563's molecular interactions and functional roles in cellular processes.

How can I apply computational models to enhance ZNF563 antibody specificity for my research?

Recent advances in computational modeling can significantly improve antibody specificity for ZNF563 research:

• Biophysics-informed modeling:

  • Modern approaches combine high-throughput sequencing with computational analysis to design antibodies with enhanced specificity

  • These models can identify distinct binding modes associated with specific epitopes

  • Particularly valuable when discriminating between similar ligands, such as closely related zinc finger proteins

• Epitope mapping and optimization:

  • Computational analysis can identify unique epitopes in ZNF563 that are distinct from related zinc finger proteins

  • This allows for the design of more specific antibodies that avoid cross-reactivity

• Phage display library screening:

  • Computational models can guide the selection of antibody libraries

  • High-throughput sequencing of selected antibodies provides data for computational analysis

  • Models can then predict binding characteristics beyond those observed experimentally

• Custom specificity profile design:

  • Computational approaches enable the generation of antibody sequences with predefined binding profiles

  • These can be designed to be either cross-specific (binding to multiple related targets) or highly specific (binding exclusively to ZNF563)

  • Optimization involves minimizing energy functions associated with desired binding modes while maximizing those for undesired targets

• Sequence-function relationship analysis:

  • Models trained on experimental data can predict how sequence variations affect antibody function

  • This facilitates rational design of improved ZNF563 antibodies without exhaustive experimental testing

These computational approaches represent the cutting edge of antibody engineering and can significantly enhance the specificity and utility of ZNF563 antibodies for research applications .

What is known about ZNF563's role in disease pathways and how can antibodies be used to investigate these connections?

While direct evidence for ZNF563 in disease pathways is limited, several important associations have been identified that can be investigated using antibody-based approaches:

• Cancer associations:

  • ZNF563 has been associated with anus cancer

  • Related zinc finger proteins like ZNF560 have been implicated in osteosarcoma, suggesting potential roles for zinc finger proteins in oncogenesis

  • Antibody-based techniques such as immunohistochemistry and Western blotting can be used to assess ZNF563 expression levels in tumor versus normal tissues

• Viral infection pathways:

  • ZNF563 has been linked to herpes simplex virus 1 infection pathways

  • Researchers can use ZNF563 antibodies to investigate changes in expression or localization during viral infection

  • Co-immunoprecipitation with viral proteins could reveal direct interactions

• Transcriptional regulation:

  • As a transcription factor, ZNF563 likely regulates multiple downstream genes

  • Combining ChIP-seq (using ZNF563 antibodies) with RNA-seq could identify target genes and regulatory networks

  • This approach might reveal disease-relevant pathways controlled by ZNF563

• Comparative studies with related proteins:

  • Investigating ZNF563 alongside its paralog ZNF443 could reveal functional redundancy or complementation in disease contexts

  • Multi-label immunofluorescence using antibodies against both proteins can reveal co-expression patterns

• Therapeutic target assessment:

  • If ZNF563 is confirmed to play roles in disease pathways, antibodies can be used to evaluate its potential as a therapeutic target

  • Tissue microarray analysis with ZNF563 antibodies could determine expression patterns across different disease states and stages

These approaches can help elucidate ZNF563's potential contributions to disease pathogenesis and identify new therapeutic strategies.

How do expression patterns of ZNF563 compare across different cell types and tissues?

Understanding the expression patterns of ZNF563 across different biological contexts is essential for interpreting experimental results. Based on the available data:

• Cell line expression profiles:

  • ZNF563 antibodies have been validated in multiple cell lines including HeLa (cervical cancer), K562 (myelogenous leukemia), U87-MG (glioblastoma), and SH-SY5Y (neuroblastoma)

  • This suggests expression across diverse cell lineages, including epithelial, hematopoietic, glial, and neuronal origins

  • Comparative quantification using validated antibodies in Western blotting can determine relative expression levels across these cell types

• Tissue-specific expression:

  • ZNF563 antibodies have been validated in rat brain tissue , suggesting expression in the central nervous system

  • Systematic immunohistochemistry analysis across tissue panels would provide a comprehensive atlas of ZNF563 expression

• Subcellular localization:

  • ZNF563 has been predominantly localized to the nucleus , consistent with its function as a transcription factor

  • Immunofluorescence studies using validated antibodies can confirm this localization pattern and identify any cell type-specific variations

• Expression in disease states:

  • Differential expression analysis between normal and disease tissues (particularly in cancers) could reveal context-dependent regulation

  • The association with anus cancer suggests potential dysregulation in certain malignancies

• Developmental expression patterns:

  • Studies of ZNF563 expression across developmental stages could provide insights into its temporal regulation

  • This could be particularly relevant given the roles of zinc finger proteins in developmental processes

A comprehensive analysis of ZNF563 expression patterns would provide valuable context for interpreting experimental results and understanding its biological functions.

What are common issues in ZNF563 detection and how can I address them?

When working with ZNF563 antibodies, researchers may encounter several challenges. Here are evidence-based solutions for common problems:

• Weak or absent signal in Western blot:

  • Increase antibody concentration (try 1:500 dilution if using higher dilutions)

  • Extend primary antibody incubation time (overnight at 4°C)

  • Increase protein loading (especially if ZNF563 is expressed at low levels)

  • Check sample preparation: ensure complete lysis and inclusion of protease inhibitors

  • Verify transfer efficiency with reversible staining before immunodetection

  • Use more sensitive detection systems (e.g., enhanced chemiluminescence)

• High background in immunostaining:

  • Optimize blocking conditions (try different blocking agents: BSA, normal serum, casein)

  • Increase washing steps in duration and number

  • Titrate antibody to find optimal concentration (starting from 10 μg/ml for ICC)

  • Include additional blocking steps to reduce non-specific binding

  • Filter antibody solutions before use to remove aggregates

• Multiple bands in Western blot:

  • This may represent different modified forms of ZNF563

  • Compare with positive controls like ZNF563-transfected lysates

  • Perform peptide competition assays to identify which bands are specific

  • Consider using phosphatase treatment if phosphorylation is suspected

• Variable results between experiments:

  • Standardize protein quantification methods

  • Use consistent lysis and sample preparation protocols

  • Aliquot antibodies to avoid freeze-thaw cycles

  • Include internal controls in each experiment

  • Standardize exposure times in Western blot detection

• Cross-reactivity concerns:

  • Validate antibody specificity using ZNF563 knockdown or knockout samples

  • Compare results from multiple antibodies targeting different epitopes

  • Consider potential cross-reactivity with related zinc finger proteins, particularly the paralog ZNF443

Implementing these methodological refinements will help ensure consistent and reliable detection of ZNF563 in your experimental system.

How can I optimize immunofluorescence protocols for ZNF563 localization studies?

For optimal visualization of ZNF563 localization using immunofluorescence:

• Fixation optimization:

  • Compare paraformaldehyde (4%) and methanol fixation to determine which best preserves ZNF563 epitopes

  • For nuclear proteins like ZNF563 , methanol fixation often provides better nuclear antigen accessibility

• Permeabilization considerations:

  • Use 0.1-0.5% Triton X-100 for nuclear protein access

  • Optimize permeabilization time to balance antigen accessibility with structural preservation

• Antibody concentration:

  • Start with the validated concentration of 10 μg/ml for HeLa cells

  • Perform titration experiments to determine optimal signal-to-noise ratio for your specific cell type

• Blocking optimization:

  • Use 5-10% normal serum (from the species of the secondary antibody)

  • Include 0.1-0.3% BSA to reduce non-specific binding

  • Consider adding 0.1% Tween-20 to blocking solutions

• Nuclear counterstaining:

  • Use DAPI or Hoechst dyes for nuclear visualization

  • This is particularly important for confirming the expected nuclear localization of ZNF563

• Multi-label considerations:

  • When performing co-localization studies, select antibodies from different host species

  • The availability of both mouse and rabbit anti-ZNF563 antibodies provides flexibility

• Controls:

  • Include secondary-only controls to assess background

  • Use ZNF563-transfected cells as positive controls

  • Consider siRNA knockdown cells as negative controls

• Image acquisition:

  • Use confocal microscopy for precise localization within nuclear subcompartments

  • Capture Z-stacks to fully visualize the three-dimensional distribution

• Quantification approaches:

  • Measure nuclear vs. cytoplasmic signal intensity

  • Analyze co-localization with other nuclear markers using appropriate statistical methods

These optimized protocols will facilitate detailed analysis of ZNF563 localization patterns and potential changes under various experimental conditions.

How can ZNF563 antibodies be integrated into high-throughput or multi-omics research approaches?

Integrating ZNF563 antibodies into advanced multi-omics frameworks can significantly enhance our understanding of its functional role:

• ChIP-seq applications:

  • Use ZNF563 antibodies for chromatin immunoprecipitation followed by next-generation sequencing

  • This approach can identify genome-wide binding sites, revealing the direct target genes of ZNF563

  • Validate antibody ChIP efficiency before proceeding with sequencing

• Proteomics integration:

  • Employ ZNF563 antibodies for immunoprecipitation followed by mass spectrometry (IP-MS)

  • This approach can identify protein interaction networks around ZNF563

  • Compare results from multiple antibodies targeting different epitopes to increase confidence

• Single-cell approaches:

  • Adapt validated immunofluorescence protocols for high-content imaging

  • Analyze ZNF563 expression and localization at the single-cell level

  • Correlate with other markers to identify cell type-specific patterns

• Multi-omics correlation:

  • Integrate ChIP-seq data with RNA-seq to correlate ZNF563 binding with transcriptional outcomes

  • Combine with proteomics data to build comprehensive regulatory networks

  • Analyze how these networks change in disease contexts

• CRISPR screens:

  • Use ZNF563 antibodies to assess protein levels following genetic perturbation

  • Can reveal functional relationships and synthetic interactions

• Spatial transcriptomics correlation:

  • Combine immunofluorescence data on ZNF563 localization with spatial transcriptomics

  • This can reveal spatial relationships between ZNF563 expression and its target genes

• Computational modeling integration:

  • Use experimental data generated with ZNF563 antibodies to train and validate computational models

  • These models can then predict binding properties and specificity profiles

These integrated approaches leverage ZNF563 antibodies within broader experimental frameworks to gain systems-level insights into its biological roles.

What are the potential applications of new antibody engineering techniques for improving ZNF563 research?

Emerging antibody engineering technologies offer exciting opportunities to enhance ZNF563 research:

• Biophysics-informed antibody design:

  • Modern computational approaches can design antibodies with customized specificity profiles

  • These methods can generate antibodies that specifically recognize ZNF563 while avoiding cross-reactivity with related zinc finger proteins

  • Such highly specific antibodies could resolve conflicting research findings that might stem from antibody cross-reactivity

• Recombinant antibody fragments:

  • Single-chain variable fragments (scFvs) or antigen-binding fragments (Fabs) derived from validated ZNF563 antibodies

  • These smaller fragments can provide better tissue penetration and reduced background

  • Particularly valuable for super-resolution microscopy applications

• Bi-specific antibodies:

  • Engineering antibodies that simultaneously bind ZNF563 and one of its interaction partners

  • Could enable detection of specific protein complexes in their native context

  • Useful for investigating context-dependent ZNF563 functions

• Proximity-labeling antibody conjugates:

  • ZNF563 antibodies conjugated to enzymes like APEX2, BioID, or TurboID

  • When bound to ZNF563, these enzymes label proximal proteins, enabling identification of the local proteome

  • Provides spatial context to protein interaction studies

• Antibody-guided CRISPR approaches:

  • ZNF563 antibodies fused to CRISPR effectors for targeted epigenetic modification

  • Could enable precise manipulation of ZNF563 activity at specific genomic loci

  • Valuable for dissecting locus-specific functions

• Antibodies with tunable binding properties:

  • Engineering pH-dependent or light-switchable ZNF563 antibodies

  • Enables temporal control over binding for dynamic studies

  • Could reveal transient interactions or conformational changes

• Machine learning optimization:

  • Using experimental data to train models that predict optimal antibody sequences

  • These models can generate antibodies not present in initial libraries but with improved properties

  • Iterative design-build-test cycles can rapidly improve ZNF563 antibody performance

These advanced antibody engineering approaches represent the frontier of ZNF563 research tools, potentially enabling experiments that were previously technically unfeasible.

How does research on ZNF563 compare with other zinc finger proteins, and what methodological lessons can be applied?

Contextualizing ZNF563 research within the broader zinc finger protein family provides valuable comparative insights:

• Functional parallels with ZNF560:

  • Recent research has identified ZNF560 as an oncogenic regulator in osteosarcoma

  • Similar methodological approaches (Western blotting, qRT-PCR, immunohistochemistry) could be applied to investigate ZNF563's potential roles in cancer biology

  • The nuclear localization observed for ZNF563 is consistent with the transcriptional regulatory functions observed in other zinc finger proteins

• Paralog relationships:

  • ZNF443 has been identified as an important paralog of ZNF563

  • Comparative studies using antibodies against both proteins could reveal functional redundancy or specialization

  • Research methods that have successfully elucidated the functions of better-studied zinc finger proteins can be adapted for ZNF563 investigation

• Evolutionary conservation:

  • The cross-reactivity of some ZNF563 antibodies with mouse and rat samples suggests evolutionary conservation

  • Comparative studies across species can provide insights into fundamental versus specialized functions

  • Antibodies recognizing conserved epitopes facilitate cross-species research

• Disease associations:

  • While ZNF563 has been linked to anus cancer , other zinc finger proteins have been implicated in various malignancies

  • ZNF560 specifically has been associated with osteosarcoma progression

  • These parallels suggest potential oncogenic mechanisms that warrant investigation using ZNF563 antibodies

• Methodological adaptations:

  • Successful approaches used to study other zinc finger proteins, such as ChIP-seq for identifying binding sites, can be adapted for ZNF563

  • Genetic manipulation strategies (shRNA, CRISPR) used to study ZNF560 could be applied to investigate ZNF563 function

• Protein domain considerations:

  • ZNF563 contains multiple C2H2-type zinc finger domains typical of this protein family

  • Antibodies targeting different domains may reveal domain-specific functions

  • Structural insights from better-characterized zinc finger proteins can guide experimental design for ZNF563

This comparative framework provides valuable context for interpreting ZNF563 research findings and informs methodological approaches based on successful strategies used with related proteins.

What are the most promising future directions for ZNF563 antibody-based research?

Based on current knowledge and technological trends, several promising research directions emerge for ZNF563 antibody applications:

• Disease biomarker exploration:

  • Given the association with anus cancer and the involvement of related zinc finger proteins in oncogenesis , investigate ZNF563 as a potential biomarker

  • Develop standardized immunohistochemistry protocols using validated ZNF563 antibodies for tissue microarray analysis

  • Correlate expression patterns with clinical outcomes to assess prognostic value

• Mechanistic studies in viral infection:

  • Explore the suggested connection between ZNF563 and herpes simplex virus 1 infection pathways

  • Use antibodies to track changes in ZNF563 expression, localization, and interactions during viral infection

  • This could reveal host-pathogen interaction mechanisms and potential therapeutic targets

• Regulatory network mapping:

  • Employ ChIP-seq using ZNF563 antibodies to identify direct genomic targets

  • Integrate with transcriptomic and proteomic data to construct comprehensive regulatory networks

  • This systems biology approach could reveal unexpected functional roles

• Structure-function relationships:

  • Develop epitope-specific antibodies targeting different zinc finger domains within ZNF563

  • Use these to investigate domain-specific functions and interactions

  • Correlate with computational structural predictions to enhance understanding of molecular mechanisms

• Therapeutic target validation:

  • If disease associations are confirmed, use antibodies to validate ZNF563 as a potential therapeutic target

  • Investigate accessibility of epitopes in different cellular contexts

  • Develop cell-penetrating antibodies or antibody mimetics for functional modulation

• Developmental biology applications:

  • Map ZNF563 expression patterns during development using validated antibodies

  • Investigate potential roles in cell fate determination and differentiation

  • Compare with expression patterns of its paralog ZNF443 to identify unique versus redundant functions

• Integration with emerging technologies:

  • Adapt ZNF563 antibodies for use with spatial transcriptomics approaches

  • Develop antibody-based proximity labeling systems for studying the ZNF563 microenvironment

  • Explore applications in high-resolution imaging techniques to reveal nuclear sublocalization patterns

These forward-looking research directions build upon current knowledge while leveraging technological advances to address fundamental questions about ZNF563 biology and its potential clinical relevance.