GO:0019237 centromeric DNA binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0019237 (centromeric DNA binding) describes the molecular function of selectively and non-covalently interacting with DNA sequences at the centromere, the chromosomal region where spindle fibers attach during mitosis and meiosis.
• Centromeric DNA binding is mediated by both sequence-specific and structural DNA-binding domains, including the unique CpG-dyad-binding domain of CDCA7 and the centromeric histone H3 variant CENP-A (CenH3).
• CENP-I directly targets centromeric DNA to support CENP-A deposition and centromere maintenance, linking DNA binding to epigenetic centromere identity.
• Phosphorylation of HJURP regulates its centromeric recruitment and its function in loading CENP-A, showing that centromeric DNA binding is cell-cycle regulated.
• Centromeric DNA replication and homologous recombination at centromeres are tightly controlled to preserve centromeric integrity and prevent chromosome instability.
• Dysregulation of centromeric DNA-binding proteins is implicated in ICF syndrome, ALT cancers, and genome instability, making these proteins important disease and drug-target research subjects.
Description
Centromeric DNA binding (GO:0019237) is a molecular function defined as binding to a centromere, the region of a chromosome where spindle fibers attach during mitosis and meiosis. This function is essential for faithful chromosome segregation because it recruits the kinetochore machinery to the correct chromosomal locus. In eukaryotes, centromeric DNA is often repetitive and rapidly evolving, so centromere identity is specified epigenetically by the centromeric histone H3 variant CENP-A (CenH3) rather than by DNA sequence alone. Proteins that bind centromeric DNA therefore operate at the interface of DNA sequence recognition, chromatin assembly, and cell-cycle control. For researchers, GO:0019237 provides a precise annotation for proteins that directly contact centromeric DNA, distinguishing them from proteins that bind centromeric chromatin indirectly through protein-protein interactions. The term is experimentally supported by studies in organisms ranging from rice to humans, where centromeric and telomeric DNA-binding proteins have been identified biochemically. Understanding centromeric DNA binding is critical for dissecting chromosome segregation, aneuploidy, and cancer, and for interpreting how centromeric repeats are maintained and replicated.
centromeric DNA binding At A Glance
| GO ID | GO:0019237 |
|---|---|
| GO term | centromeric DNA binding |
| Ontology | molecular_function |
| Synonym | centromere binding |
| Definition | Binding to a centromere, a region of chromosome where the spindle fibers attach during mitosis and meiosis. |
| Major function | Direct, non-covalent interaction with centromeric DNA to recruit and maintain centromere and kinetochore components. |
| Representative proteins | CDCA7, CENP-A (CenH3), CENP-I, HJURP, and other centromeric DNA-binding proteins identified in plants and animals. |
| Associated processes | Centromere maintenance, CENP-A deposition, centromeric DNA replication, homologous recombination at centromeres, chromosome segregation. |
| Disease relevance | ICF syndrome, ALT cancers, and genome instability associated with centromere dysfunction. |
What Is GO:0019237?
In our own words, GO:0019237 (centromeric DNA binding) is the molecular function of selectively and non-covalently interacting with DNA located at a centromere. The centromere is the chromosomal region where spindle fibers attach during mitosis and meiosis. This binding can involve sequence-specific recognition of centromeric repeat DNA, recognition of non-B DNA structures such as CpG dyads, or structural engagement of centromeric DNA by kinetochore and chromatin-assembly proteins. The synonym centromere binding is used interchangeably. The function is annotated to proteins that directly contact centromeric DNA, including centromeric histone variants, their loading factors, and kinetochore components that target centromeric DNA to support CENP-A deposition and centromere maintenance.
Why Is centromeric DNA binding Important in Cell Biology?
Centromeric DNA binding is important because it is the first molecular step that marks a chromosomal locus as a centromere and recruits the machinery required for chromosome segregation. Without direct centromeric DNA binding by factors such as CENP-I and HJURP, CENP-A cannot be deposited and centromere identity cannot be maintained, leading to chromosome missegregation. The function also matters for genome stability: centromeric DNA replication and homologous recombination must be tightly controlled, and loss of this control threatens centromeric integrity. In disease, mutations affecting centromeric DNA-binding proteins such as CDCA7 cause ICF syndrome, and centromeric footprints are linked to telomere integrity in ALT cancers. For researchers, GO:0019237 offers a precise functional annotation to distinguish direct centromeric DNA binders from indirect centromere-associated proteins, enabling better interpretation of proteomic, genetic, and imaging experiments.
• Defines the molecular function that initiates centromere identity and kinetochore assembly.
• Required for CENP-A deposition and centromere maintenance through factors such as CENP-I and HJURP.
• Supports faithful chromosome segregation during mitosis and meiosis.
• Links centromeric DNA recognition to cell-cycle-regulated chromatin assembly.
• Contributes to centromeric DNA replication and ATR checkpoint suppression.
• Preserves centromeric integrity through controlled homologous recombination.
• Implicated in ICF syndrome through CDCA7 dysfunction.
• Associated with ALT cancer biology and telomere integrity.
• Provides a functional annotation for proteomic identification of centromeric DNA-binding proteins.
• Offers a target for CRISPR-based functional studies of centromere proteins.
Molecular Mechanism of centromeric DNA binding
Recognition of centromeric DNA sequence and structure
In simple terms: Proteins must first find and physically contact the DNA at the centromere.
Centromeric DNA binding begins with recognition of centromeric DNA, which can involve sequence-specific motifs or unusual DNA structures. The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA structure, demonstrating that centromeric DNA binding can depend on DNA shape rather than a simple linear sequence. In Drosophila, recurrent evolution of DNA-binding motifs in the centromeric histone CenH3 (CENP-A) indicates that direct DNA contacts by centromeric histones are under strong selective pressure. Biochemical identification of centromeric and telomeric DNA-binding proteins in rice further supports that centromeric DNA is engaged by distinct DNA-binding activities.
CENP-A deposition and centromere maintenance
In simple terms: After DNA is recognized, the centromere-specific histone is loaded to mark the centromere.
CENP-I directly targets centromeric DNA to support CENP-A deposition and centromere maintenance, linking centromeric DNA binding to the epigenetic propagation of centromere identity. HJURP is a CENP-A loading factor whose phosphorylation and DNA binding determine its centromeric recruitment and function in CenH3(CENP-A) loading. Together, these findings show that centromeric DNA binding is not an isolated event but a step that couples DNA recognition to chromatin assembly at the centromere.
Cell-cycle regulation of centromeric DNA binding
In simple terms: The timing of centromere protein binding is controlled so it happens at the right phase of the cell cycle.
Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading, indicating that centromeric DNA binding is regulated by post-translational modification and cell-cycle timing. This regulation ensures that CENP-A loading occurs at the appropriate time and place, preventing inappropriate centromere assembly.
Centromeric DNA replication and checkpoint control
In simple terms: The centromere DNA must be copied safely without triggering damage alarms.
Centromeric DNA replication reconstitution revealed DNA loops and ATR checkpoint suppression, showing that replication through centromeric DNA requires specialized mechanisms to avoid checkpoint activation. This connects centromeric DNA binding and processing to the maintenance of centromeric DNA integrity during S phase.
Homologous recombination and centromeric integrity
In simple terms: Repair pathways act at centromeres to keep them intact.
Activation of homologous recombination in G1 preserves centromeric integrity, demonstrating that recombination machinery is recruited to centromeres to protect them. Centromeric footprints also preserve telomere integrity in ALT cancers, linking centromeric DNA-associated functions to broader genome maintenance.
Key Genes Involved in GO:0019237 centromeric DNA binding
The following genes and proteins are experimentally linked to centromeric DNA binding (GO:0019237) or to the centromeric DNA-binding machinery.
| Gene | Major Role | Research Relevance |
|---|---|---|
| CDCA7 | Harbors a unique DNA-binding domain that recognizes a CpG dyad in non-B DNA; linked to ICF syndrome | Direct centromeric DNA-binding model; disease mechanism studies |
| CENP-A (CenH3) | Centromeric histone H3 variant; defines centromere identity | Centromere specification and evolution studies |
| CENP-I | Directly targets centromeric DNA to support CENP-A deposition and centromere maintenance | Centromere maintenance and kinetochore assembly |
| HJURP | CENP-A loading factor; phosphorylation and DNA binding control centromeric recruitment | Cell-cycle regulation of centromere assembly |
| CENP-B | Centromeric DNA-binding protein (CENP-B box binding) | Centromeric repeat recognition and kinetochore function |
| CENP-C | Kinetochore protein that binds centromeric chromatin and DNA | Kinetochore assembly and centromere targeting |
| CENP-T | Kinetochore component linking centromeric chromatin to spindle attachments | Kinetochore structure and function |
| CENP-W | Part of the CENP-T-W-S-X complex at centromeres | Centromeric chromatin organization |
| CENP-S | Part of the CENP-T-W-S-X complex at centromeres | Centromeric chromatin organization |
| CENP-X | Part of the CENP-T-W-S-X complex at centromeres | Centromeric chromatin organization |
| ATRX | Chromatin remodeler implicated in centromeric and telomeric maintenance | ALT cancer and centromere integrity |
| DAXX | Histone chaperone linked to centromeric chromatin | Centromere chromatin regulation |
| RAD51 | Homologous recombination factor that preserves centromeric integrity | Centromeric DNA repair |
| ATR | Checkpoint kinase suppressed during centromeric DNA replication | Centromeric replication stress |
| Rice centromeric DNA-binding proteins | Biochemically identified centromeric and telomeric DNA-binding activities | Plant centromere proteomics |
| Drosophila CenH3 | Centromeric histone with recurrently evolved DNA-binding motifs | Centromere evolution |
| CENP-B homologs | Centromeric DNA-binding proteins across species | Comparative centromere biology |
| Kinetochore protein complexes | Bind centromeric DNA/chromatin to attach spindle fibers | Chromosome segregation studies |
How Is centromeric DNA binding Regulated?
Centromeric DNA binding is regulated at multiple levels. Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading, showing that post-translational modification controls when and where this function occurs. Cell-cycle timing is also critical: centromeric DNA replication reconstitution revealed DNA loops and ATR checkpoint suppression, indicating that replication-coupled processes at centromeres are actively regulated to avoid checkpoint activation. Homologous recombination in G1 preserves centromeric integrity, further demonstrating that DNA repair pathways are spatially and temporally controlled at centromeres. Together, these mechanisms ensure that centromeric DNA binding and downstream centromere assembly are coordinated with the cell cycle and with genome maintenance pathways.
centromeric DNA binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CDCA7 | ICF syndrome; centromeric instability | Knockout and point-mutation cell models in human cell lines |
| ATRX | ALT cancer; telomere and centromere integrity | Knockout and overexpression models in ALT cancer cell lines |
| RAD51 | Centromeric integrity and homologous recombination | Knockout and point-mutation models for centromeric DNA repair |
| HJURP | Centromere assembly and cell-cycle regulation | Phospho-mutant knock-in and knockout models |
| CENP-I | Centromere maintenance and chromosome segregation | Knockout and tagged knock-in models |
ICF syndrome and CDCA7 dysfunction
The ICF syndrome protein CDCA7 harbors a unique DNA-binding domain that recognizes a CpG dyad in the context of a non-B DNA structure, directly linking a centromeric DNA-binding activity to a human immunodeficiency-centromeric instability-facial anomalies syndrome. This connection makes CDCA7 a key gene for studying how defective centromeric DNA binding contributes to centromeric instability and disease.
ALT cancers and centromeric footprints
Centromeric footprints preserve telomere integrity in ALT cancers, indicating that centromeric DNA-associated functions are relevant to alternative lengthening of telomeres and cancer genome maintenance. This suggests that proteins involved in centromeric DNA binding may influence telomere stability in ALT tumors.
Genome instability and centromeric integrity
Activation of homologous recombination in G1 preserves centromeric integrity, and loss of this protection can lead to centromeric DNA damage and chromosome instability. Centromeric DNA replication reconstitution revealed DNA loops and ATR checkpoint suppression, highlighting how replication stress at centromeres can threaten genome stability.
From centromeric DNA binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of a candidate centromeric DNA-binding gene impair centromere maintenance? | Knockout cell model |
| Does a specific DNA-binding residue mediate centromeric DNA recognition? | Point-mutation knock-in model |
| Where and when does a centromeric DNA-binding protein localize? | Tagged knock-in (e.g., GFP/HA) model |
| Does overexpression of a centromeric DNA-binding protein alter centromere stability? | Overexpression cell model |
| Which genes are required for centromeric DNA replication and checkpoint suppression? | CRISPR library screening |
| What transcriptional or proteomic changes follow loss of centromeric DNA binding? | Bioinformatics analysis of knockout/overexpression models |
How to Study the centromeric DNA binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| DNA-binding assay (EMSA, ChIP) | Direct interaction of proteins with centromeric DNA | Confirming GO:0019237 annotation |
| Proteomics | Identification of centromeric DNA-binding proteins | Discovery of new centromere proteins |
| Phospho-proteomics | Phosphorylation status of centromere proteins | Studying HJURP regulation |
| Replication reconstitution | Centromeric DNA replication and checkpoint activation | Analyzing ATR suppression at centromeres |
| Homologous recombination assays | Recombination at centromeres in G1 | Preservation of centromeric integrity |
| Imaging (fluorescence microscopy) | Localization of centromere proteins | Validating centromeric recruitment |
| CRISPR knockout screening | Genes required for centromere function | Functional genomics of centromeric DNA binding |
| Bioinformatics analysis | Enrichment of centromeric DNA-binding domains | Annotation and comparative genomics |
Proteomic identification of centromeric DNA-binding proteins
Biochemical approaches have been used to identify centromeric and telomeric DNA-binding proteins, as demonstrated in rice, where such proteins were isolated and characterized by proteomics. These methods allow researchers to discover new proteins that directly bind centromeric DNA and to annotate them to GO:0019237.
DNA-binding assays for centromeric sequences
Direct DNA-binding assays, including those used to study CDCA7 recognition of a CpG dyad in non-B DNA, are essential to confirm that a protein physically interacts with centromeric DNA. Such assays distinguish direct centromeric DNA binding from indirect centromere association.
Cell-cycle and phosphorylation analysis
Because phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading, phospho-proteomics and cell-cycle synchronization are key methods for studying regulation of centromeric DNA binding.
Replication and recombination assays at centromeres
Centromeric DNA replication reconstitution revealed DNA loops and ATR checkpoint suppression, and homologous recombination in G1 preserves centromeric integrity, providing experimental systems to study how centromeric DNA is replicated and repaired.
How CRISPR Can Be Used to Study GO:0019237 centromeric DNA binding
Knockout
CRISPR knockout of genes such as CDCA7, CENP-I, or HJURP can test whether loss of centromeric DNA binding impairs centromere maintenance and chromosome segregation. Knockout models are useful for assessing downstream effects on centromeric integrity and cell viability.
Point Mutation
Point-mutation knock-in models can dissect the specific DNA-binding residues required for centromeric DNA recognition, for example in the unique DNA-binding domain of CDCA7 or in phosphorylation sites of HJURP. These models separate DNA-binding function from other protein activities.
Knock-in
Tagged knock-in of centromeric DNA-binding proteins enables precise localization and interaction studies at endogenous expression levels, supporting functional annotation of GO:0019237. Knock-in of disease-associated variants can also model ICF syndrome or cancer-related mutations.
Overexpression
Overexpression of centromeric DNA-binding proteins can reveal dominant effects on centromere stability, centromeric DNA replication, and genome integrity. Overexpression models are also useful for biochemical purification of centromeric DNA-protein complexes.
How EDITGENE Supports centromeric DNA binding Research
Researchers studying centromeric DNA binding-related genes often need to determine whether a candidate gene is causally involved in centromere maintenance, chromosome segregation, or disease. EDITGENE provides CRISPR-based cell models and screening services to test these hypotheses directly in relevant cell types.
Contact EDITGENE today to design your custom CRISPR model for centromeric DNA binding research.
Frequently Asked Questions About centromeric DNA binding
What is centromeric DNA binding?
Centromeric DNA binding (GO:0019237) is the molecular function of selectively and non-covalently interacting with DNA at the centromere, the chromosomal region where spindle fibers attach during mitosis and meiosis.
What genes are involved in centromeric DNA binding?
Genes and proteins experimentally linked to centromeric DNA binding include CDCA7, CENP-A (CenH3), CENP-I, HJURP, and other centromeric DNA-binding proteins identified in plants and animals.
What is the GO ID for centromeric DNA binding?
The Gene Ontology ID for centromeric DNA binding is GO:0019237, with the synonym centromere binding.
Which proteins directly bind centromeric DNA?
CENP-I directly targets centromeric DNA to support CENP-A deposition, and CDCA7 has a unique DNA-binding domain that recognizes a CpG dyad in non-B DNA.
How is centromeric DNA binding regulated?
Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading, showing that post-translational modification regulates this function.
Why is centromeric DNA binding important for chromosome segregation?
It recruits centromere and kinetochore components such as CENP-A and CENP-I, which are required for spindle attachment and faithful chromosome segregation.
What diseases are linked to centromeric DNA binding?
CDCA7 dysfunction is linked to ICF syndrome, and centromeric footprints are associated with telomere integrity in ALT cancers.
How do researchers study centromeric DNA binding?
Researchers use DNA-binding assays, proteomics, phospho-proteomics, replication reconstitution, homologous recombination assays, imaging, and CRISPR screening.
Can CRISPR be used to study centromeric DNA binding?
Yes, CRISPR knockout, point-mutation, knock-in, and overexpression models can test the function of centromeric DNA-binding proteins and their role in centromere maintenance.
What is the difference between centromeric DNA binding and centromere binding?
Centromeric DNA binding (GO:0019237) specifically refers to binding to centromeric DNA, while centromere binding is a synonym that may also imply binding to centromeric chromatin or structures.
Conclusion
Centromeric DNA binding (GO:0019237) is a fundamental molecular function that connects DNA recognition at the centromere to CENP-A deposition, centromere maintenance, and faithful chromosome segregation. Experimental studies have identified key proteins such as CDCA7, CENP-I, and HJURP that directly or indirectly mediate this function, and have revealed its regulation by phosphorylation, the cell cycle, and DNA repair pathways. Dysregulation of centromeric DNA binding is linked to ICF syndrome, ALT cancers, and genome instability, making it a compelling area for disease research. CRISPR-based cell models and screening approaches provide powerful tools to dissect the causal roles of centromeric DNA-binding genes and to identify new therapeutic targets.
References
- 1. Hardikar S et al.. 2024. The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA.. Sci Adv 10(34):eadr0036 PMID: 39178265
- 2. Bhargava R et al.. 2026. Centromeric footprints preserve telomere integrity in ALT cancers.. Nature 656(8127):406-414 PMID: 42236945
- 3. He Q et al.. 2013. Identification of centromeric and telomeric DNA-binding proteins in rice.. Proteomics 13(5):826-32 PMID: 23303719
- 4. Hu L et al.. 2023. CENP-I directly targets centromeric DNA to support CENP-A deposition and centromere maintenance.. Proc Natl Acad Sci U S A 120(11):e2219170120 PMID: 36888657
- 5. Aze A et al.. 2016. Centromeric DNA replication reconstitution reveals DNA loops and ATR checkpoint suppression.. Nat Cell Biol 18(6):684-91 PMID: 27111843
- 6. Malik HS et al.. 2002. Recurrent evolution of DNA-binding motifs in the Drosophila centromeric histone.. Proc Natl Acad Sci U S A 99(3):1449-54 PMID: 11805302
- 7. Müller S et al.. 2014. Phosphorylation and DNA binding of HJURP determine its centromeric recruitment and function in CenH3(CENP-A) loading.. Cell Rep 8(1):190-203 PMID: 25001279
- 8. Yilmaz D et al.. 2021. Activation of homologous recombination in G1 preserves centromeric integrity.. Nature 600(7890):748-753 PMID: 34853474
