CCDC101 Human

What is CCDC101 and what are its alternative names in scientific literature?

CCDC101 (coiled-coil domain containing 101) is a nuclear protein that functions as a subunit of two distinct histone acetyltransferase complexes. In the scientific literature, this protein is known by several alternative names including SGF29 (SAGA complex associated factor 29), STAF36, and TDRD29 . These alternative designations reflect its discovery in different contexts and its association with specific protein complexes. The protein is a member of the SGF29 family and plays a crucial role in transcriptional regulation through its interactions with chromatin-modifying complexes .

What is the genomic location of CCDC101 and what is known about its gene structure?

The CCDC101 gene maps to human chromosome 16p11.2 . This location is significant as chromosome 16 encodes over 900 genes and comprises nearly 3% of the human genome . The gene has been assigned the NCBI Gene ID 112869 . Understanding the chromosomal context of CCDC101 is important for researchers investigating potential genomic interactions, copy number variations, or chromosomal abnormalities that might affect CCDC101 function. The specific genomic architecture surrounding CCDC101 may provide insights into its regulation and potential involvement in chromosomal disorders associated with the 16p11.2 region.

What protein complexes is CCDC101 associated with and what is its basic function?

CCDC101 functions as a subunit of two distinct histone acetyltransferase complexes: the ADA2A (TADA2A)-containing (ATAC) complex and the SPT3 (SUPT3H)-TAF9-GCN5 (KAT2A)/PCAF (KAT2B) acetylase (STAGA) complex . Both of these complexes contain either GCN5 or PCAF, which are paralogous acetyltransferases . The protein plays a role in transcriptional regulation by contributing to histone acetylation, a process that modifies chromatin structure to facilitate gene expression . As a component of these complexes, CCDC101 likely assists in targeting the acetyltransferase activity to specific genomic locations, thereby influencing the epigenetic landscape and subsequent gene expression patterns.

What methodologies are most effective for studying CCDC101 expression patterns across human tissues?

For researchers investigating CCDC101 expression patterns, multiple complementary approaches should be considered:

• RNA-seq and Microarray Analysis: The Allen Brain Atlas datasets provide valuable resources for examining CCDC101 expression in brain tissues . Similar approaches can be extended to other tissue types, using publicly available datasets like GTEx or generating new data.

• Single-cell RNA-seq: For higher resolution analysis of expression in heterogeneous tissues, single-cell transcriptomics can reveal cell type-specific expression patterns of CCDC101.

• Quantitative PCR: For validation of expression in specific tissues or under various conditions, qPCR remains a reliable method to quantify CCDC101 transcript levels.

• Western Blotting and Immunohistochemistry: Protein-level expression can be assessed using antibodies specific to CCDC101, with careful controls to account for potential cross-reactivity with its homologs.

• Reporter Gene Assays: For studying the regulation of CCDC101 expression, reporter constructs containing the CCDC101 promoter can be valuable tools.

The Harmonizome database indicates that CCDC101 has 3,579 functional associations with biological entities spanning 8 categories extracted from 68 datasets, providing a rich resource for expression correlation analysis .

What experimental approaches are recommended for investigating CCDC101's role in histone acetylation?

To investigate CCDC101's specific contribution to histone acetylation mechanisms:

• CCDC101 Knockdown/Knockout Studies: siRNA-mediated knockdown (as available from commercial sources ) or CRISPR/Cas9-mediated knockout followed by ChIP-seq for histone acetylation marks can reveal genomic regions dependent on CCDC101 for proper acetylation.

• Protein Complex Immunoprecipitation: Co-IP experiments can define CCDC101's protein-protein interactions within the ATAC and STAGA complexes under various conditions.

• In Vitro Histone Acetyltransferase Assays: Reconstitution of HAT complexes with and without CCDC101 can determine its effect on enzymatic activity and substrate specificity.

• Domain Mutation Analysis: Generation of CCDC101 mutants lacking specific domains can help identify regions critical for complex association or acetyltransferase activity.

• ChIP-seq and CUT&RUN: These techniques can map CCDC101 binding sites genome-wide and correlate them with histone modification patterns and transcriptional activity.

When designing these experiments, researchers should consider that as a relatively new gene of interest, CCDC101 may have tissue-specific functions that could be masked in global analyses .

How can researchers differentiate between CCDC101's functions in the ATAC complex versus the STAGA complex?

Distinguishing the roles of CCDC101 in its two associated complexes requires sophisticated experimental approaches:

• Complex-Specific Protein Depletion: Selectively depleting components unique to either ATAC or STAGA complexes (e.g., ADA2A for ATAC or SPT3 for STAGA) while monitoring CCDC101-dependent functions.

• Proximity Labeling Techniques: BioID or APEX2 fusion proteins can identify proximity interactions specific to CCDC101 in each complex context.

• Complex-Specific ChIP-seq: Sequential ChIP (re-ChIP) using antibodies against CCDC101 followed by complex-specific components can identify genomic regions where CCDC101 functions within each specific complex.

• Mass Spectrometry of Isolated Complexes: Quantitative proteomics of purified ATAC versus STAGA complexes containing CCDC101 can reveal differential protein associations.

• Functional Genomics Screens: CRISPR screens designed to identify genetic interactions specific to CCDC101's role in each complex can provide functional insights.

These approaches should be complemented with careful bioinformatic analysis to identify complex-specific gene regulation patterns associated with CCDC101 activity.

What is known about evolutionary conservation of CCDC101 and how can comparative genomics inform human CCDC101 research?

Understanding the evolutionary context of CCDC101 provides valuable insights into its core functions:

• Phylogenetic Analysis Approach: Researchers should conduct comparative sequence analysis across primates and other mammals to determine the conservation level of CCDC101. This can be particularly informative given findings about primate-specific genes often being implicated in brain function and male reproduction .

• Domain Conservation Assessment: Identifying highly conserved domains within CCDC101 can pinpoint functionally critical regions. Techniques include calculating the dN/dS ratio across species to detect signatures of selection.

• Cross-Species Functional Complementation: Experimental replacement of human CCDC101 with orthologs from model organisms can test functional conservation in various cellular contexts.

• Paralog Analysis: Investigating whether CCDC101 belongs to a gene family that has undergone recent expansion in humans, which is common for new genes, might reveal redundant or specialized functions .

When considering the evolutionary profile, researchers should be aware that annotation of newer genes can be problematic and unstable across different database versions, requiring careful verification of gene models .

What are the challenges in studying CCDC101 protein-protein interactions and how can they be addressed?

Investigating CCDC101's protein interaction network presents several technical challenges:

• Complex Stability Issues: The histone acetyltransferase complexes containing CCDC101 may have dynamic compositions depending on cellular context. Researchers should employ stabilization methods such as crosslinking prior to immunoprecipitation to capture transient interactions.

• Specificity of Antibodies: Validation of antibody specificity is crucial, especially given the presence of homologous domains in related proteins. Multiple antibodies targeting different epitopes should be used for confirmation.

• Nuclear Protein Extraction Optimization: As a nuclear protein involved in chromatin-associated complexes , efficient extraction protocols that maintain complex integrity are essential. Stepwise extraction methods that separate nucleoplasmic and chromatin-bound fractions can provide better resolution.

• Quantitative Interaction Mapping: Beyond identifying binary interactions, techniques such as SILAC combined with AP-MS can quantify the stoichiometry and dynamics of CCDC101 within its complexes under different cellular conditions.

These methodological considerations are especially important given that CCDC101 functions at the intersection of multiple regulatory pathways affecting gene expression.

What experimental considerations are important when using CCDC101 knockdown models?

When designing RNA interference experiments targeting CCDC101:

• siRNA Design and Validation: Commercial siRNAs targeting CCDC101 (such as sc-142044 ) should be validated for knockdown efficiency and specificity. Researchers should verify target reduction at both mRNA (qPCR) and protein (Western blot) levels.

• Off-target Effect Mitigation: Multiple independent siRNA sequences should be tested, and rescue experiments with siRNA-resistant CCDC101 constructs should be performed to confirm phenotype specificity.

• Temporal Considerations: Acute versus sustained knockdown may reveal different aspects of CCDC101 function, particularly in processes like transcriptional memory or epigenetic inheritance.

• Cell Type Selection: Given that histone modification patterns vary across cell types, knockdown effects should be assessed in multiple relevant cell types, including those where CCDC101 shows highest expression based on tissue expression databases .

• Compensatory Mechanism Assessment: Long-term knockdown studies should monitor potential upregulation of functionally related proteins that might compensate for CCDC101 loss.

These considerations help ensure that observed phenotypes accurately reflect CCDC101's biological functions rather than technical artifacts.

How might CCDC101 research contribute to understanding human disease mechanisms?

CCDC101's involvement in epigenetic regulation positions it as potentially relevant to multiple disease contexts:

• Cancer Biology: As a component of acetyltransferase complexes that regulate gene expression, CCDC101 may have parallels with other new genes that have been found to either promote or suppress tumorigenesis . Researchers should investigate CCDC101 expression patterns in cancer datasets and potential correlations with patient outcomes.

• Neurodevelopmental Disorders: Given that CCDC101 is located on chromosome 16p11.2 , a region associated with neurodevelopmental conditions, and that new genes are often recruited into brain expression , researchers should examine its potential role in brain-related disorders.

• Chromatin-Related Syndromes: Mutations affecting chromatin modifiers cause various developmental disorders. CCDC101 variant analysis in patient cohorts with unexplained developmental disorders might reveal previously unrecognized disease associations.

• Pleiotropic Effects Framework: The selection, pleiotropy and compensation hypothesis (SPC) for adaptive evolution provides a theoretical framework for investigating how CCDC101 might simultaneously confer advantages while potentially contributing to disease susceptibility.

Understanding CCDC101's role in normal cellular functions will provide the foundation for exploring its potential contributions to pathological processes.

What are the emerging technologies that could advance CCDC101 research?

Several cutting-edge technologies hold promise for deepening our understanding of CCDC101 biology:

• CUT&Tag and CUT&RUN: These techniques offer higher resolution mapping of chromatin-associated factors than traditional ChIP-seq, allowing more precise identification of CCDC101 genomic binding sites and associated histone modifications.

• Single-cell Multi-omics: Integrating single-cell transcriptomics with chromatin accessibility and histone modification profiling can reveal cell type-specific functions of CCDC101 in heterogeneous tissues.

• Cryo-EM Structure Analysis: Structural determination of CCDC101 within its native complexes can provide mechanistic insights into how it contributes to acetyltransferase activity and complex assembly.

• CRISPR Base Editing: Precise modification of endogenous CCDC101 can create allelic series to test the functional importance of specific amino acids without complete protein disruption.

• Spatial Transcriptomics: Examining CCDC101 expression patterns in the spatial context of tissues may reveal localized functions not apparent in bulk tissue analyses.

These technologies will help address the challenge of studying new genes like CCDC101, which often have complex, context-dependent functions that traditional approaches might miss .