GO:0006265 DNA topological change: Mechanism, Genes, Functions and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0006265 DNA topological change is the biological process that alters the linking number of double-stranded DNA, changing its superhelical state.
• Topological changes are essential for DNA replication, transcription, recombination, and chromosome segregation, and are driven by topoisomerases and other DNA-remodeling machines.
• Type IA topoisomerases change linking number by a strand-passage mechanism that requires transient cleavage of one DNA strand.
• DNA superhelicity is a global property that influences promoter activity, DNA melting, and the formation of non-B DNA structures.
• Altered DNA topology is linked to cancer, where chemotherapeutic agents target topoisomerases and change DNA topological states.
• Topological boundaries such as CTCF sites organize chromatin loops and can regulate enhancer-oncogene interactions.
Description
DNA topological change (GO:0006265) is the process that induces a transformation in the topological structure of a double-stranded DNA helix, resulting in a change in linking number. This process is fundamental because DNA in cells is not a relaxed linear molecule; it is often underwound or overwound, and its topology affects nearly every DNA transaction, including replication, transcription, recombination, and chromosome segregation. The linking number, a topological invariant that describes the number of times one strand winds around the other, can only be changed by breaking and rejoining DNA strands, a reaction catalyzed by topoisomerases and related enzymes. Consequently, DNA topological change is a central node in genome biology and a target for therapeutic intervention. Researchers study this process to understand how cells manage DNA supercoiling, how topological boundaries are established, and how dysregulation contributes to disease. The QuickGO definition provides a precise framework: the process results in a change in linking number, distinguishing it from other DNA metabolic processes that do not alter topology.
DNA topological change At A Glance
| GO ID | GO:0006265 |
|---|---|
| GO term | DNA topological change |
| Ontology | biological_process |
| Synonym | DNA underwinding |
| Definition | The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number. |
| Major function | Alteration of DNA linking number to facilitate replication, transcription, recombination, and chromosome segregation. |
| Key enzymes | Type I and type II topoisomerases, gyrases, and other DNA-remodeling complexes. |
| Related processes | DNA supercoiling, DNA relaxation, DNA catenation/decatenation. |
What Is GO:0006265?
According to the Gene Ontology, DNA topological change (GO:0006265) is the process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number. This definition captures the essence of topological transformations: the number of times the two strands of the double helix are intertwined is altered. Such changes are essential for DNA metabolism and are mediated by enzymes that transiently break and rejoin DNA strands. The synonym DNA underwinding reflects a common outcome of this process, where negative supercoiling is introduced or removed.
Why Is DNA topological change Important in Cell Biology?
DNA topological change is important because it governs the physical state of the genome, influencing how DNA interacts with proteins and how genetic information is accessed and maintained. Without the ability to change DNA topology, cells cannot efficiently replicate their genomes, transcribe genes, or segregate chromosomes. Moreover, topological changes are implicated in human diseases, particularly cancer, where topoisomerase poisons are used as chemotherapeutic agents. Understanding this process also sheds light on how chromatin architecture is organized, including the formation of topologically associating domains and their boundaries.
• Enables DNA replication by relieving torsional stress ahead of replication forks.
• Facilitates transcription by allowing RNA polymerase to traverse supercoiled templates.
• Required for chromosome segregation and decatenation of intertwined DNA molecules.
• Influences DNA melting and the formation of non-B DNA structures such as premeltons.
• Targeted by anticancer and antibacterial drugs that inhibit topoisomerases.
• Contributes to the regulation of gene expression through topological boundaries.
• Plays a role in aging-related chromatin remodeling and transposon regulation.
• Provides a mechanism for DNA-based cell sorting in synthetic biology.
• Essential for plasmid maintenance and inheritance in bacteria.
• Dysregulation can lead to genomic instability and cancer.
What Happens During DNA topological change?
Strand Cleavage and Passage
In simple terms: The enzyme cuts one or both DNA strands, passes another strand through the break, and then reseals it.
The core of DNA topological change is a strand-passage reaction. Type IA topoisomerases cleave a single DNA strand, forming a covalent enzyme-DNA intermediate, and then pass the intact strand through the break before religating the cleaved strand. This mechanism changes the linking number in steps of one. Type II topoisomerases cleave both strands of one DNA duplex, pass another duplex through the break, and reseal the break, changing the linking number in steps of two. These reactions are ATP-dependent for type II enzymes and are crucial for decatenation and relaxation.
Supercoiling and DNA Underwinding
In simple terms: The DNA becomes more or less twisted, which affects how easily it can be opened.
DNA superhelicity describes the coiling of the DNA helix axis and is a major determinant of DNA function. Negative supercoiling, or underwinding, facilitates strand separation and is required for processes such as replication and transcription. Positive supercoiling, which accumulates ahead of polymerases, must be removed to prevent stalling. The balance between these states is maintained by topoisomerases and other DNA-remodeling activities.
Formation of Non-B DNA Structures
In simple terms: Underwound DNA can adopt alternative shapes that affect protein binding.
Changes in DNA topology can promote the formation of non-B DNA structures, such as premeltons, which are regions of altered base stacking that may serve as nucleation sites for melting. These structures can influence DNA-protein interactions and are implicated in genomic instability. The interplay between superhelicity and non-B DNA formation is an active area of research.
Topological Boundaries and Chromatin Organization
In simple terms: DNA is organized into loops, and the boundaries of these loops are important for gene regulation.
In eukaryotic cells, DNA is organized into topologically associating domains (TADs) that are demarcated by boundary elements such as CTCF sites. These boundaries constrain the spread of topological changes and regulate enhancer-promoter interactions. Disruption of a CTCF boundary can lead to oncogene activation, highlighting the importance of topological organization in disease.
Plasmid Topology and Inheritance
In simple terms: In bacteria, the twisting of plasmid DNA affects how plasmids are copied and passed to daughter cells.
Plasmid DNA topology is dynamic and influences plasmid replication, segregation, and inheritance. Topological changes in plasmids are mediated by host topoisomerases and can affect plasmid stability. Understanding plasmid topology is important for biotechnology and antimicrobial research.
Key Genes Involved in GO:0006265 DNA topological change
The following genes and proteins are key players in DNA topological change, as supported by the cited literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| TOP1 | Type I topoisomerase; relieves supercoiling by single-strand passage | Target of camptothecin; involved in replication and transcription |
| TOP2A | Type II topoisomerase; decatenates and relaxes DNA | Target of etoposide; amplified in cancers |
| TOP2B | Type II topoisomerase; roles in transcription and development | Associated with neural development and drug response |
| GYRA | Bacterial DNA gyrase; introduces negative supercoils | Target of fluoroquinolones |
| GYRB | Bacterial DNA gyrase subunit; ATPase and strand passage | Antibacterial target |
| TOP3A | Type IA topoisomerase; resolves recombination intermediates | Maintains genome stability |
| TOP3B | Type IA topoisomerase; RNA and DNA processing | Linked to neurological disorders |
| CTCF | Topological boundary protein; organizes TADs | Boundary disruption can activate oncogenes |
| RAD51 | Homologous recombination; involved in topological stress response | Genome stability |
| PARP1 | Poly(ADP-ribose) polymerase; modulates chromatin topology | DNA repair and cancer therapy |
| HMO1 | High mobility group protein; affects DNA topology | Chromatin structure |
| Gyrase | Bacterial topoisomerase II; essential for supercoiling | Antibiotic target |
| Topo IV | Bacterial type II topoisomerase; decatenation | Essential for chromosome segregation |
| Premelton | Non-B DNA structure; affects melting | Topological intermediate |
| DNA framework | Synthetic DNA nanostructures; topological sorting | Cell sorting applications |
| Transposon | Mobile genetic elements; affected by topological changes | Aging and brain chromatin |
| Topoisomerase | General class of enzymes; change linking number | Broad therapeutic target |
How Is DNA topological change Regulated?
DNA topological change is regulated at multiple levels. Topoisomerase activity can be modulated by post-translational modifications, ATP availability, and interaction with accessory proteins. In bacteria, the ratio of gyrase to topoisomerase I activity determines the steady-state supercoiling level, which is responsive to environmental conditions. In eukaryotes, topoisomerases are regulated during the cell cycle, with TOP2A expression peaking in mitosis. Additionally, chromatin remodelers and boundary proteins such as CTCF can constrain topological changes to specific genomic regions. The interplay between transcription and topology also creates feedback loops, as RNA polymerase generates supercoiling that must be managed by topoisomerases.
DNA topological change and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TOP2A | Cancer; target of etoposide | KO and point-mutation cell lines; drug sensitivity assays |
| TOP1 | Cancer; target of camptothecin | Knockout and overexpression models; replication stress |
| TOP3B | Neurological disorders | Knock-in of patient mutations; neuronal differentiation |
| CTCF | Cancer; enhancer-oncogene regulation | Boundary deletion models; Hi-C and ChIP-seq |
| GYRA | Bacterial infection; fluoroquinolone resistance | Point mutations in bacterial strains; MIC assays |
Cancer and Topoisomerase Poisons
Altered DNA topology is a hallmark of cancer cells, which often have elevated topoisomerase activity to support rapid proliferation. Chemotherapeutic agents such as etoposide and doxorubicin target TOP2A and TOP2B, stabilizing the enzyme-DNA cleavage complex and causing DNA damage. Camptothecin derivatives target TOP1, leading to replication fork collapse. The efficacy of these drugs depends on the topological state of DNA and the expression levels of topoisomerases.
Neurological Disorders and TOP3B
Mutations in TOP3B, a type IA topoisomerase, have been associated with neurological disorders, including schizophrenia and autism spectrum disorders. TOP3B is involved in resolving RNA-DNA hybrids and maintaining genomic stability in neurons. Dysregulation of DNA topology in the brain may contribute to neurodegeneration and aging-related cognitive decline.
Aging and Chromatin Remodeling
Aging is associated with changes in chromatin topology, including transposon demethylation and TAD remodeling in the brain. These topological changes can lead to altered gene expression and genomic instability. Understanding how DNA topology is maintained during aging may reveal therapeutic targets for age-related diseases.
Bacterial Infections and Gyrase Inhibitors
Bacterial DNA gyrase and topoisomerase IV are essential for maintaining DNA topology and are targets of fluoroquinolone antibiotics. Resistance mutations often occur in the genes encoding these enzymes, altering their sensitivity to drugs. Studying plasmid topology in bacteria provides insights into resistance mechanisms.
From DNA topological change-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of TOP2A affect cell proliferation? | CRISPR knockout in cancer cell lines |
| How do point mutations in TOP1 confer drug resistance? | Knock-in of specific mutations; drug sensitivity |
| What is the role of TOP3B in neuronal development? | Knockout and knock-in in iPSC-derived neurons |
| How does CTCF boundary disruption affect oncogene expression? | CRISPR deletion of boundary elements; RNA-seq |
| Can overexpression of TOP1 induce replication stress? | Doxycycline-inducible overexpression |
| What is the effect of gyrase mutations on bacterial survival? | CRISPR-based point mutation in E. coli |
How to Study the DNA topological change Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Agarose gel electrophoresis | Supercoiling and catenation states | Topoisomerase activity assays |
| Two-dimensional gel electrophoresis | Topoisomer distribution | Drug studies |
| ChIP-seq | Topoisomerase and CTCF binding sites | Genome-wide mapping |
| Hi-C | Chromatin interactions and TADs | Boundary analysis |
| Fluorescence microscopy | DNA topology in live cells | Cell sorting and dynamics |
| In vitro cleavage assays | Enzyme-DNA covalent complexes | Mechanistic studies |
| ATPase assays | ATP hydrolysis by type II topoisomerases | Enzyme kinetics |
| CRISPR screening | Genes affecting drug sensitivity | Target discovery |
Topological Assays
DNA topology can be measured using agarose gel electrophoresis with chloroquine or ethidium bromide to resolve supercoiled, relaxed, and catenated species. Two-dimensional gel electrophoresis can detect specific topoisomers. These methods are used to assess the activity of topoisomerases and the effects of drugs.
Genome-Wide Mapping of Topoisomerase Binding
ChIP-seq and related techniques can map the binding sites of topoisomerases and boundary proteins such as CTCF across the genome. These approaches reveal how topological changes are localized and how they correlate with gene expression.
Chromosome Conformation Capture
Hi-C and its variants measure the three-dimensional organization of chromatin, including TADs and loops. These methods are essential for studying how topological boundaries are established and maintained.
Live-Cell Imaging of DNA Topology
Fluorescent reporters and DNA framework-based sensors can visualize topological changes in living cells. These tools enable real-time monitoring of DNA supercoiling and cell sorting based on topological states.
How CRISPR Can Be Used to Study GO:0006265 DNA topological change
Knockout
CRISPR knockout of topoisomerase genes such as TOP1, TOP2A, or TOP3B can reveal their essential roles in DNA topology and cell viability. Knockout cell lines are valuable for studying drug resistance and synthetic lethality.
Point Mutation
Point mutations in topoisomerase genes can mimic clinical resistance mutations or alter catalytic activity. CRISPR-mediated knock-in of specific mutations allows precise structure-function studies.
Knock-in
Knock-in of tagged topoisomerases (e.g., GFP or HaloTag) enables live-cell imaging and proteomic analysis of topological complexes. Knock-in of patient-derived mutations can model neurological disorders.
Overexpression
Overexpression of topoisomerases can induce topological stress and replication fork stalling, providing a model for cancer-associated genome instability. Inducible systems allow temporal control of expression.
How EDITGENE Supports DNA topological change Research
Researchers studying DNA topological change-related genes often need to determine whether a candidate gene is causally involved in a specific topological or disease phenotype. This requires precise genetic models that can knockout, mutate, tag, or overexpress the gene of interest in relevant cell types. EDITGENE provides a comprehensive suite of CRISPR services to accelerate such studies.
Contact EDITGENE today to design your custom CRISPR model for DNA topological change research.
Frequently Asked Questions About DNA topological change
What is DNA topological change?
DNA topological change (GO:0006265) is the process that alters the linking number of double-stranded DNA, changing its superhelical state.
What genes are involved in DNA topological change?
Key genes include TOP1, TOP2A, TOP2B, TOP3A, TOP3B, GYRA, GYRB, and CTCF, among others.
How do topoisomerases change DNA topology?
Type I topoisomerases cleave one strand and pass the other through, while type II topoisomerases cleave both strands and pass a duplex through, changing linking number.
Why is DNA supercoiling important?
Supercoiling affects DNA melting, protein binding, and processes like replication and transcription.
What diseases are linked to DNA topological change?
Cancer, neurological disorders, and bacterial infections are linked to altered DNA topology.
How can I study DNA topological change in the lab?
Common methods include gel electrophoresis, ChIP-seq, Hi-C, and live-cell imaging.
What are topoisomerase poisons?
Drugs like etoposide and camptothecin that stabilize the enzyme-DNA cleavage complex and cause DNA damage.
What is the role of CTCF in DNA topology?
CTCF acts as a topological boundary that organizes chromatin loops and regulates enhancer-promoter interactions.
Can CRISPR be used to study DNA topology?
Yes, CRISPR knockout, knock-in, and overexpression models are widely used to dissect gene function in DNA topology.
What is DNA underwinding?
DNA underwinding is a synonym for DNA topological change, referring to the introduction of negative supercoils.
Conclusion
DNA topological change (GO:0006265) is a fundamental biological process that controls the physical state of the genome and is essential for replication, transcription, and chromosome segregation. Dysregulation of this process is implicated in cancer, neurological disorders, and bacterial infections, making it a prime target for therapeutic intervention. Advances in CRISPR-based models and topological assays continue to unravel the complex regulation and function of DNA topology. EDITGENE provides the tools and services to accelerate research in this dynamic field.
References
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- 5. Sobell HM. 2016. Premeltons in DNA.. J Struct Funct Genomics 17(1):17-31 PMID: 26984848
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- 8. Dasgupta T et al.. 2020. Mechanism of Type IA Topoisomerases.. Molecules 25(20) PMID: 33080770
