GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:2000373 describes any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity, a type II topoisomerase function essential for DNA topology control.
• Type II topoisomerases are ATP-dependent enzymes that relax positive supercoils and decatenate DNA, and their positive regulation shapes 3D chromatin folding.
• Positive regulation of topoisomerase genes maintains topological homeostasis in bacteria such as Streptomyces coelicolor and Streptococcus pneumoniae.
• In eukaryotes, physiological regulation of topoisomerase II is coordinated with the cell cycle and chromatin state.
• ARIP4 helicase resolves R-loops to promote androgen-mediated transcription induction, indirectly influencing topoisomerase activity.
• EWS::FLI1-DHX9 interaction alters R-loop metabolism and sensitizes Ewing sarcoma to topoisomerase 1 poisons.
Description
GO:2000373, positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity, is a biological process that increases the activity of ATP-dependent DNA topoisomerases, also known as type II topoisomerases. These enzymes are critical for resolving topological stress generated during DNA replication, transcription, and chromatin remodeling. The term encompasses both direct activation of the enzyme and indirect mechanisms that elevate its catalytic rate or frequency. Understanding this process is essential because topoisomerase activity must be tightly regulated to maintain genome stability and proper chromatin architecture. Dysregulation of topoisomerase activity is linked to cancer, developmental disorders, and sensitivity to chemotherapeutic agents. Researchers study GO:2000373 to identify regulatory factors, understand chromatin dynamics, and develop targeted therapies.
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity At A Glance
| GO ID | GO:2000373 |
|---|---|
| GO term | positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity |
| Ontology | biological_process |
| Synonym | positive regulation of DNA topoisomerase II; positive regulation of type II DNA topoisomerase activity; positive regulation of topoisomerase II |
| Major function | Increases the activity of ATP-dependent DNA topoisomerases, which relax positive supercoils and decatenate DNA |
| Related enzymes | Type II topoisomerases (e.g., TOP2A, TOP2B, gyrase, topoisomerase IV) |
| Biological context | DNA replication, transcription, chromatin folding, and topological homeostasis |
| Regulatory inputs | Cell cycle signals, chromatin state, and accessory proteins such as ARIP4 and DHX9 |
What Is GO:2000373?
GO:2000373 is defined as any process that activates or increases the frequency, rate or extent of DNA topoisomerase (ATP-hydrolyzing) activity. This includes positive regulation of type II DNA topoisomerase, DNA topoisomerase II, DNA topoisomerase IV, and related ATP-dependent topoisomerase activities. The term is a biological process and is distinct from the enzymatic activity itself; it describes the regulatory events that enhance the enzyme's function.
Why Is positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity Important in Cell Biology?
Positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity is vital because type II topoisomerases manage DNA topology during essential processes like replication and transcription. Without proper regulation, cells face DNA damage, genome instability, and impaired chromatin organization. This process also influences the efficacy of topoisomerase-targeting drugs, making it a focal point for cancer research and antibiotic development.
• Maintains topological homeostasis during DNA replication and transcription.
• Shapes 3D chromatin folding by relaxing positive supercoils.
• Regulates gene expression through R-loop metabolism and transcription induction.
• Modulates sensitivity to topoisomerase poisons used in chemotherapy.
• Contributes to bacterial chromosome segregation and antibiotic susceptibility.
• Involved in androgen receptor-mediated transcription in prostate cancer models.
• Affects Ewing sarcoma pathogenesis via EWS::FLI1-DHX9 interactions.
• Provides targets for understanding drug resistance in bacteria and cancer.
• Links chromatin architecture to enzymatic activity of topoisomerases.
• Offers experimental entry points for CRISPR screens and functional genomics.
What Happens During positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity?
Recognition of topological stress
In simple terms: The cell senses when DNA is too twisted or tangled.
Positive supercoils and catenanes accumulate during replication and transcription, creating topological stress that is detected by chromatin-associated factors. This stress can be modulated by R-loop formation, which influences the recruitment of topoisomerases.
Recruitment and activation of type II topoisomerases
In simple terms: The cell calls in enzymes that can cut and untangle DNA.
ATP-dependent topoisomerases such as TOP2A and TOP2B are recruited to sites of supercoiling, where their activity is enhanced by regulatory proteins and post-translational modifications. In bacteria, positive regulators like StaR increase topoisomerase I activity to maintain supercoiling homeostasis.
ATP-dependent DNA strand passage
In simple terms: The enzyme uses energy to pass one DNA strand through another, relieving twists.
Type II topoisomerases hydrolyze ATP to drive conformational changes that allow double-strand passage, relaxing positive supercoils and decatenating intertwined DNA. This catalytic cycle is the target of positive regulation.
Chromatin remodeling and 3D folding
In simple terms: Untangling DNA helps organize the genome in three dimensions.
Topoisomerase II-mediated relaxation of positive supercoils shapes multi-scale 3D chromatin folding, influencing gene regulation and nuclear organization.
Feedback and homeostasis
In simple terms: The cell adjusts enzyme levels to keep DNA topology balanced.
Coordinated positive regulation of topoisomerase genes maintains topological homeostasis, as shown in Streptomyces coelicolor where multiple topoisomerase genes are upregulated in response to stress. In eukaryotes, physiological regulation of topoisomerase II is cell-cycle dependent.
Key Genes Involved in GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
The following genes and proteins are experimentally implicated in the positive regulation of ATP-dependent DNA topoisomerase activity or in related regulatory pathways.
| Gene | Major Role | Research Relevance |
|---|---|---|
| TOP2A | ATP-dependent type II topoisomerase; relaxes positive supercoils | Target of positive regulation; cancer drug target |
| TOP2B | Type II topoisomerase; chromatin folding | Regulated in neuronal development and cancer |
| ARIP4 | Helicase that resolves R-loops | Promotes androgen-mediated transcription, indirectly affecting topoisomerase activity |
| DHX9 | RNA helicase involved in R-loop metabolism | Interacts with EWS::FLI1 in Ewing sarcoma, influencing topoisomerase 1 sensitivity |
| EWS::FLI1 | Fusion oncoprotein | Alters R-loop metabolism and topoisomerase poison sensitivity |
| StaR | Positive regulator of topoisomerase I in Streptococcus pneumoniae | Maintains supercoiling homeostasis |
| GyrA | Bacterial type II topoisomerase subunit | Target of positive regulation in Streptomyces |
| GyrB | Bacterial type II topoisomerase subunit | ATP-binding subunit; regulated with GyrA |
| ParC | Topoisomerase IV subunit | Involved in decatenation; regulated in bacteria |
| ParE | Topoisomerase IV subunit | ATP-dependent activity; positive regulation in Streptomyces |
| TopA | Bacterial topoisomerase I | Regulated by StaR in S. pneumoniae |
| SP_TOP1 | Topoisomerase I in S. pneumoniae | Activity enhanced by StaR |
| Hsp90 | Chaperone | May influence topoisomerase stability and activity |
| CK2 | Protein kinase | Phosphorylates topoisomerase II, modulating activity |
| PARP1 | Poly(ADP-ribose) polymerase | Affects chromatin and topoisomerase recruitment |
| CTCF | Chromatin organizer | Interacts with topoisomerase II at boundaries |
| Cohesin | Sister chromatid cohesion | Functional interplay with topoisomerase II |
| RNA Pol II | Transcription machinery | Generates supercoils that recruit topoisomerases |
How Is positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity Regulated?
Positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity is controlled at multiple levels. In eukaryotes, topoisomerase II activity fluctuates with the cell cycle and is influenced by phosphorylation by kinases such as CK2. Chromatin state and histone modifications regulate access to DNA and torsional energy, thereby modulating topoisomerase II-mediated relaxation. In bacteria, coordinated positive regulation of topoisomerase genes maintains topological homeostasis in response to environmental stress. Additionally, R-loop metabolism and helicases like ARIP4 and DHX9 can indirectly enhance or redirect topoisomerase activity during transcription.
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| TOP2A | Cancer, drug resistance | CRISPR knockout in cancer cell lines; overexpression |
| EWS::FLI1 | Ewing sarcoma | Knock-in of fusion gene; point mutations |
| ARIP4 | Prostate cancer | Knockout and overexpression in prostate cancer cells |
| StaR | Pneumococcal infection | Bacterial knockout and complementation |
| GyrA/ParC | Bacterial infections | Point mutations in quinolone resistance |
Cancer and topoisomerase poisons
Dysregulation of topoisomerase activity is central to cancer biology. EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism. Positive regulation of topoisomerase II affects chemotherapy response, as drugs like etoposide target the enzyme.
Prostate cancer and androgen signaling
ARIP4 helicase resolves R-loops to promote androgen-mediated transcription induction, which can influence topoisomerase activity and prostate cancer progression.
Bacterial infections and antibiotic resistance
In Streptococcus pneumoniae, StaR positively regulates topoisomerase I activity, contributing to supercoiling maintenance and potentially affecting antibiotic susceptibility. In Streptomyces coelicolor, coordinated regulation of topoisomerase genes supports topological homeostasis.
Chromatin architecture and developmental disorders
Type II topoisomerases shape 3D chromatin folding; their dysregulation may contribute to developmental disorders linked to chromatin organization.
From positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does gene X regulate topoisomerase II activity? | CRISPR knockout of gene X in HeLa or HEK293T cells |
| How does a point mutation in TOP2A affect drug sensitivity? | Point mutation knock-in via CRISPR |
| Can overexpression of ARIP4 enhance topoisomerase activity? | Overexpression of ARIP4 in prostate cancer cells |
| What is the role of StaR in supercoiling? | Bacterial knockout and overexpression in S. pneumoniae |
| How does EWS::FLI1 affect R-loop metabolism? | Knock-in of EWS::FLI1 in mesenchymal stem cells |
| Does chromatin state regulate topoisomerase II? | CRISPR interference or histone modification screens |
How to Study the positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Decatenation assay | Topoisomerase II catalytic activity | Drug screening and enzyme kinetics |
| Hi-C | 3D chromatin folding | Effects of topoisomerase on genome organization |
| DRIP-seq | R-loop levels | Transcription-associated topoisomerase regulation |
| CRISPR knockout screen | Gene essentiality and drug response | Identify positive regulators |
| ChIP-seq | Topoisomerase binding sites | Genome-wide mapping |
| ATPase assay | ATP hydrolysis rate | Measure ATP-dependent topoisomerase activity |
| Supercoiling assay | DNA supercoil density | Bacterial topoisomerase regulation |
| Proteomics | Protein interactions | Identify regulatory complexes |
Topoisomerase activity assays
In vitro decatenation and relaxation assays using plasmid DNA measure the catalytic activity of type II topoisomerases. These assays can be coupled with ATP to specifically assess ATP-hydrolyzing topoisomerase activity.
Chromatin conformation capture
Hi-C and related techniques assess 3D chromatin folding changes upon modulation of topoisomerase activity, revealing multi-scale effects.
R-loop detection
DRIP-seq and R-loop immunoprecipitation quantify R-loop levels, which are linked to topoisomerase regulation and transcription.
CRISPR screens
Genome-wide CRISPR knockout or activation screens identify positive regulators of topoisomerase activity by selecting for drug sensitivity or resistance.
How CRISPR Can Be Used to Study GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
Knockout
CRISPR knockout of candidate positive regulators (e.g., ARIP4, DHX9) can determine whether they are required for topoisomerase activity. Knockout of TOP2A itself is lethal in most cells, so conditional or inducible systems are used.
Point Mutation
Point mutations in TOP2A or bacterial gyrase can mimic drug-resistant alleles or alter ATP hydrolysis, allowing structure-function studies of positive regulation.
Knock-in
Knock-in of fusion genes such as EWS::FLI1 or tagged versions of topoisomerases enables tracking of regulatory interactions and R-loop metabolism.
Overexpression
Overexpression of positive regulators like StaR or ARIP4 can enhance topoisomerase activity and test sufficiency in maintaining topological homeostasis.
How EDITGENE Supports positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity Research
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Frequently Asked Questions About positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
What is GO:2000373?
GO:2000373 is the Gene Ontology term for positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity, describing processes that increase the activity of ATP-dependent type II topoisomerases.
What genes are involved in positive regulation of DNA topoisomerase activity?
Key genes include TOP2A, TOP2B, ARIP4, DHX9, and bacterial regulators like StaR and gyrase subunits.
How does positive regulation of topoisomerase II affect chromatin?
It shapes 3D chromatin folding by relaxing positive supercoils, influencing gene expression and genome organization.
What diseases are linked to topoisomerase regulation?
Cancer, bacterial infections, and developmental disorders are associated with dysregulated topoisomerase activity.
What methods study topoisomerase activity?
Decatenation assays, Hi-C, DRIP-seq, and CRISPR screens are commonly used.
Can CRISPR knockout be used to study topoisomerase regulators?
Yes, knockout of candidate regulators like ARIP4 or DHX9 can reveal their role in topoisomerase activity.
What is the role of ATP in type II topoisomerase activity?
ATP hydrolysis drives conformational changes needed for DNA strand passage and supercoil relaxation.
How is topoisomerase activity regulated in bacteria?
Coordinated positive regulation of topoisomerase genes maintains topological homeostasis, as shown in Streptomyces and Streptococcus.
What are topoisomerase poisons?
Drugs like etoposide target type II topoisomerases; positive regulation can affect sensitivity.
How does ARIP4 influence topoisomerase activity?
ARIP4 resolves R-loops to promote androgen-mediated transcription, indirectly affecting topoisomerase recruitment and activity.
Conclusion
GO:2000373, positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity, is a critical biological process that ensures proper DNA topology during replication, transcription, and chromatin organization. Its dysregulation is implicated in cancer, bacterial infections, and developmental disorders, making it a valuable target for therapeutic intervention. Continued research using CRISPR models and advanced screening will uncover new regulatory mechanisms and drug targets.
References
- 1. Ng RR et al.. 2024. R-loop resolution by ARIP4 helicase promotes androgen-mediated transcription induction.. Sci Adv 10(29):eadm9577 PMID: 39028815
- 2. Isaacs RJ et al.. 1998. Physiological regulation of eukaryotic topoisomerase II.. Biochim Biophys Acta 1400(1-3):121-37 PMID: 9748535
- 3. Longo GMC et al.. 2024. Type II topoisomerases shape multi-scale 3D chromatin folding in regions of positive supercoils.. Mol Cell 84(22):4267-4281.e8 PMID: 39486417
- 4. Szafran MJ et al.. 2016. The Coordinated Positive Regulation of Topoisomerase Genes Maintains Topological Homeostasis in Streptomyces coelicolor.. J Bacteriol 198(21):3016-3028 PMID: 27551021
- 5. de Vasconcelos Junior AA et al.. 2023. StaR Is a Positive Regulator of Topoisomerase I Activity Involved in Supercoiling Maintenance in Streptococcus pneumoniae.. Int J Mol Sci 24(6) PMID: 36983048
- 7. Olmedo-Pelayo J et al.. 2025. EWS::FLI1-DHX9 interaction promotes Ewing sarcoma sensitivity to DNA topoisomerase 1 poisons by altering R-loop metabolism.. Oncogene 44(38):3537-3552 PMID: 40721661
- 8. Fernández X et al.. 2014. Chromatin regulates DNA torsional energy via topoisomerase II-mediated relaxation of positive supercoils.. EMBO J 33(13):1492-501 PMID: 24859967
