TBC1D13 Human

How does TBC1D13 gene structure compare in humans versus other species?

The gene structure of TBC1D13 appears to be conserved across mammalian species, though with some variations. In the western European hedgehog (Erinaceus europaeus), TBC1D13 has multiple isoforms, including three documented variants: isoform X1, X2, and X3 . The nucleotide sequence length of hedgehog TBC1D13 is 1203bp .

While the search results don't provide specific comparative data for humans, researchers should note that unlike TBC1D3 (which shows dramatic lineage-specific expansion in primates with copy number variations from 1-14 copies in humans ), TBC1D13 appears to have maintained a more consistent gene structure across evolutionary time.

Methodological approach for comparative genomics:

• Perform multiple sequence alignments across species using tools like MUSCLE or CLUSTALW

• Generate phylogenetic trees to visualize evolutionary relationships

• Analyze synteny to identify conserved gene neighborhoods

• Examine selection pressure using dN/dS ratios

What expression patterns does TBC1D13 exhibit across human tissues?

While the provided search results don't contain specific expression data for TBC1D13 in humans, researchers can utilize methodological approaches to characterize its expression:

• RNA-seq analysis across tissue panels

• Single-cell transcriptomics to identify cell-type specific expression

• Quantitative PCR validation of expression in tissues of interest

• Antibody-based approaches including Western blotting and immunohistochemistry

For context, the related gene TBC1D3 shows modest global expression with increased levels in testis and brain tissue according to GTEx data . Researchers investigating TBC1D13 should establish tissue-specific expression profiles as a foundation for functional studies.

How can researchers distinguish between TBC1D13 and other TBC domain family members in experimental settings?

The TBC domain family includes numerous members with similar structural features, creating challenges for specific detection and functional analysis. This is particularly relevant when studying TBC1D13 in relation to TBC1D3, which has undergone significant expansion in primates .

Methodological approach for specific detection:

• Target unique epitopes for antibody generation

  • Design peptides corresponding to regions with lowest sequence similarity

  • Validate antibody specificity against recombinant proteins of multiple TBC family members

• Design highly specific nucleic acid detection methods

  • Create primers targeting unique exon junctions

  • Employ droplet digital PCR for absolute quantification

  • Use RNA-FISH with highly specific probes for spatial localization

• CRISPR-based tagging systems

  • Insert epitope tags or fluorescent proteins at endogenous loci

  • Employ degron-based approaches for temporal control of protein levels

• Mass spectrometry identification

  • Identify unique peptide signatures that distinguish between family members

  • Use parallel reaction monitoring for targeted protein quantification

What are the optimal experimental systems for studying TBC1D13 function?

Based on what we know about TBC domain proteins and their roles in membrane trafficking, several experimental systems can be employed:

Methodological recommendations:

• Begin with well-characterized cell lines for basic localization and interaction studies

• Proceed to more specialized systems based on expression data

• Consider conditional knockout approaches to avoid developmental compensation effects

• Employ live-cell imaging with fluorescently tagged constructs to monitor dynamic processes

How might evolutionary analysis inform TBC1D13 functional studies?

Unlike TBC1D3, which has undergone significant lineage-specific expansions in primates with independent duplications in at least five primate lineages , TBC1D13 appears more evolutionarily conserved. This evolutionary context provides important insights for functional studies.

Methodological approach for evolutionary analysis:

• Perform detailed phylogenetic analysis across species

• Compare selection signatures between TBC1D13 and expanded families like TBC1D3

• Analyze syntenic regions to identify potential co-evolutionary patterns

• Examine conservation of protein domains and regulatory elements

The research on TBC1D3 shows that despite having multiple duplications, only specific paralogs (particularly TBC1D3-CDKL) show significant expression . Similar paralog-specific expression patterns could exist for TBC1D13 and should be investigated.

What are the technical challenges in analyzing potential TBC1D13 genetic variants in human populations?

Studying genetic variants in TBC1D13 presents several technical challenges that researchers should address:

• Primer design and sequencing challenges

  • Presence of pseudogenes or related family members can complicate specific amplification

  • High GC content regions may require specialized PCR conditions

• Copy number variation analysis

  • If TBC1D13 exhibits copy number variations like TBC1D3, specialized approaches are needed

  • Long-read sequencing technologies (PacBio, Oxford Nanopore) are recommended for resolving complex structural variants

• Variant interpretation

  • Distinguishing pathogenic from benign variants requires multiple lines of evidence

  • Functional validation in cellular models is essential for variant classification

• Population frequency assessment

  • Check representation in diverse population databases

  • Consider potential population-specific effects

Methodological recommendations include using a combination of short and long-read sequencing technologies, coupled with computational approaches that can account for sequence similarities within gene families.

What protein interaction studies best characterize TBC1D13's functional network?

Understanding TBC1D13's protein interaction network is crucial for elucidating its function. Several complementary approaches should be employed:

• Proximity-dependent biotin labeling (BioID or TurboID)

  • Tags TBC1D13 with a biotin ligase to label proximal proteins

  • Identifies both stable and transient interactions in living cells

  • Can be targeted to specific subcellular compartments

• Affinity purification mass spectrometry (AP-MS)

  • More suitable for stable interactions

  • Can identify protein complexes

  • Use both N- and C-terminal tags to avoid interference with function

• Yeast two-hybrid screening

  • Tests for direct binary interactions

  • Can identify novel binding partners

  • Requires validation in mammalian systems

• Co-immunoprecipitation with specific Rab GTPases

  • Tests specific hypotheses about TBC1D13's GAP activity

  • Measures interaction under different nucleotide-binding states

  • Can be coupled with activity assays

For data analysis, compare interactomes to other TBC domain proteins to identify both shared and unique interaction partners. This approach has proven valuable in characterizing other TBC family members and would likely yield insights into TBC1D13's specific cellular roles.

How can researchers effectively study the role of TBC1D13 in cellular trafficking pathways?

As a putative Rab GAP protein, TBC1D13 likely regulates specific steps in membrane trafficking. To characterize these functions:

• Fluorescent cargo trafficking assays

  • Track movement of fluorescently labeled cargo proteins

  • Measure kinetics of internalization, recycling, or degradation

  • Quantify colocalization with compartment markers

• Live-cell imaging approaches

  • Use fluorescently tagged TBC1D13 to monitor dynamic localization

  • Employ photoactivatable or photoconvertible tags for pulse-chase analysis

  • Implement super-resolution microscopy for detailed localization

• In vitro GAP activity assays

  • Test GAP activity against panel of purified Rab proteins

  • Measure GTP hydrolysis rates using fluorescent or radioactive nucleotides

  • Identify key catalytic residues through structure-guided mutagenesis

• Computational prediction and validation

  • Use structural modeling to predict Rab specificity

  • Validate predictions experimentally

  • Model how variants might affect GAP activity

These approaches should be implemented in both gain- and loss-of-function experimental designs to comprehensively characterize TBC1D13's role in trafficking pathways.

How might single-cell approaches advance our understanding of TBC1D13 function?

Single-cell technologies offer unprecedented resolution for studying gene function and can address several questions about TBC1D13:

• Single-cell RNA sequencing applications:

  • Identify cell populations with highest TBC1D13 expression

  • Detect co-expression patterns to infer functional relationships

  • Track expression changes during development or disease progression

• Spatial transcriptomics approaches:

  • Map TBC1D13 expression within tissue architecture

  • Correlate with cell type markers and functional zones

  • Identify potential region-specific functions

• Single-cell proteomics:

  • Quantify TBC1D13 protein levels at single-cell resolution

  • Correlate with pathway activation markers

  • Detect post-translational modifications

• Integrative analysis:

  • Combine transcriptomic and proteomic data

  • Develop predictive models of TBC1D13 function

  • Identify cell state-specific roles

These approaches provide critical context for interpreting functional studies and may reveal unexpected cell type-specific functions that would be missed in bulk analysis.

What comparative insights might be gained by studying TBC1D13 versus the expanded TBC1D3 gene family?

Comparing TBC1D13 with the expanded TBC1D3 gene family offers unique evolutionary and functional insights:

• Evolutionary comparison points:

  • TBC1D3 shows lineage-specific expansion in primates with independent duplications in at least five primate lineages

  • TBC1D3 varies from 1-14 copies in humans with high structural variability

  • TBC1D3 duplications are enriched at chromosomal rearrangement sites

• Expression pattern differences:

  • Despite multiple duplications, TBC1D3 expression is primarily from a single paralog group (TBC1D3-CDKL)

  • This selective expression may represent a mechanism for maintaining critical functions despite high copy number variation

• Methodological approaches for comparison:

  • Generate evolutionary models of domain conservation

  • Perform comparative functional assays in cellular models

  • Analyze promoter and regulatory element differences

  • Study differences in post-translational regulation

• Implications for genetic studies:

  • Understanding how gene families maintain function despite structural variation

  • Insights into how new functions emerge from duplicated genes

  • Guidelines for interpreting copy number variations in clinical contexts

This comparative approach may reveal fundamental principles about the evolution of gene function and regulation that extend beyond these specific gene families.