GO:0008186 ATP-dependent activity, acting on RNA: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0008186 describes ATP hydrolysis that requires RNA and drives a coupled reaction, commonly known as RNA-dependent ATPase activity.
• This activity is central to RNA helicases and chromatin remodelers that use ATP to unwind RNA, rearrange ribonucleoprotein complexes, or evict nucleosomes.
• Key proteins include DDX39, FRH, Dbp9p, and the BAF chromatin remodeler, all of which couple ATP binding and hydrolysis to RNA or RNA-associated remodeling.
• Dysregulation of ATP-dependent RNA activities is linked to cancer, circadian clock defects, and ribosome biogenesis disorders.
• CRISPR knockout, point mutation, knock-in, and overexpression models enable causal testing of these enzymes in human cells.
• EDITGENE provides end-to-end CRISPR cell model and library screening services to dissect GO:0008186-related mechanisms.
Description
GO:0008186, ATP-dependent activity, acting on RNA, is a molecular function defined as catalysis of ATP hydrolysis to ADP and phosphate in a reaction that requires RNA and drives a second reaction. This term captures the essential coupling of chemical energy to RNA-dependent mechanical or remodeling work, a hallmark of RNA helicases and certain chromatin-modifying machines. Researchers study this activity because it underlies fundamental processes such as spliceosomal U snRNA nuclear export, circadian clock regulation, and nucleosome eviction during transcription. The QuickGO definition emphasizes that RNA is not consumed but is required for the ATPase reaction to proceed, distinguishing this activity from generic ATPases. Real PubMed literature shows that proteins such as DDX39 and FRH directly exemplify this function, using ATP to load export factors onto RNA or to regulate kinase activity. Understanding GO:0008186 is therefore critical for interpreting how cells convert ATP into RNA-related regulatory events.
ATP-dependent activity, acting on RNA At A Glance
| GO ID | GO:0008186 |
|---|---|
| GO term | ATP-dependent activity, acting on RNA |
| Ontology | molecular_function |
| Synonym | RNA-dependent ATPase activity; ATPase, acting on RNA; RNA-dependent adenosinetriphosphatase activity |
| Major function | Couples ATP hydrolysis to RNA-dependent remodeling, unwinding, or complex assembly |
| Example proteins | DDX39, FRH, Dbp9p, BAF complex subunits |
| Cellular contexts | Nuclear export, circadian clock, ribosome biogenesis, chromatin remodeling |
| Coupled reaction | ATP + H2O = ADP + phosphate, requiring RNA and driving another reaction |
What Is GO:0008186?
In our own words, GO:0008186 describes an enzymatic activity in which ATP is hydrolyzed to ADP and phosphate, but this hydrolysis only occurs efficiently when RNA is present, and the energy released is used to drive another reaction, such as RNA unwinding, ribonucleoprotein remodeling, or nucleosome displacement. It is not simply an ATPase; it is an RNA-dependent ATPase that couples nucleotide turnover to a downstream RNA-associated process.
Why Is ATP-dependent activity, acting on RNA Important in Cell Biology?
GO:0008186 is important because it defines a mechanistic class of enzymes that translate ATP energy into RNA-dependent regulatory events, influencing gene expression, RNA processing, and chromatin architecture. Dysregulation of these enzymes has been implicated in cancer, circadian rhythm disorders, and ribosomopathies, making them attractive targets for therapeutic intervention and biomarkers.
• Enables RNA helicases to unwind RNA structures during spliceosomal U snRNA export.
• Drives chromatin remodeling by BAF, which evicts nucleosomes in a transcription-dependent manner.
• Regulates circadian clock by controlling CK1a activity through FRH.
• Required for 60S ribosomal subunit biogenesis via Dbp9p.
• Links ATP metabolism to RNA processing and nuclear export.
• Implicated in colorectal cancer through APC1-related pathways.
• Provides mechanistic insight into prokaryotic stress responses via RNA helicases.
• Offers targets for small-molecule inhibitors of RNA-dependent ATPases.
• Essential for understanding ribosomopathies and translation defects.
• Facilitates CRISPR-based functional genomics of RNA remodeling.
Molecular Mechanism of ATP-dependent activity, acting on RNA
RNA-dependent ATP binding and hydrolysis
In simple terms: The enzyme first grabs ATP, but only when RNA is around does it cut ATP into ADP and phosphate.
Proteins with GO:0008186 activity, such as DDX39, bind ATP and RNA in a coordinated manner; RNA binding stimulates ATP hydrolysis, which is required for subsequent remodeling steps. The QuickGO definition specifies that RNA is required for the ATPase reaction and that the energy released drives another reaction.
Coupling to RNA unwinding or remodeling
In simple terms: The energy from ATP is used to change the shape of RNA or its protein partners.
In FRH, ATP hydrolysis is coupled to regulation of CK1a in the circadian clock, demonstrating that the activity can drive conformational changes in target proteins rather than RNA unwinding alone. Similarly, DDX39 uses ATP to load PHAX onto U snRNA for nuclear export, a remodeling event essential for spliceosome function.
Chromatin remodeling and nucleosome eviction
In simple terms: Some ATP-dependent RNA-acting machines also move nucleosomes to control gene expression.
The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes, an ATP-dependent process that can be RNA-associated. ChAHP remodeling activity restricts transcription factor access to chromatin, further linking ATP-dependent remodeling to RNA-related regulation.
Ribosome biogenesis and RNA processing
In simple terms: ATP-powered RNA enzymes help build ribosomes and process RNA.
Dbp9p is a putative ATP-dependent RNA helicase involved in 60S ribosomal subunit biogenesis and functionally interacts with Dbp6p, illustrating the role of GO:0008186 in ribosome assembly. Prokaryotic RNA helicases also use ATP to respond to abiotic stress, showing evolutionary conservation.
Key Genes Involved in GO:0008186 ATP-dependent activity, acting on RNA
The following genes and proteins represent real examples of ATP-dependent activities acting on RNA, as supported by the verified literature.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DDX39 | RNA helicase that loads PHAX onto U snRNA for nuclear export | Spliceosome function and RNA export studies |
| FRH | ATP-dependent regulator of CK1a in circadian clock | Circadian rhythm and kinase regulation |
| Dbp9p | ATP-dependent RNA helicase in 60S ribosomal subunit biogenesis | Ribosome assembly and ribosomopathies |
| BAF complex subunits | ATP-dependent chromatin remodeling and nucleosome eviction | Transcription and chromatin dynamics |
| ChAHP complex | Remodeling activity restricting transcription factor access | Chromatin accessibility and gene regulation |
| APC1 | Potential biological roles in colorectal cancer | Cancer biomarker and therapeutic target |
| Prokaryotic RNA helicases | Diverse roles in abiotic stress response | Stress adaptation and RNA metabolism |
| RNA polymerase II | Synergizes with BAF for nucleosome eviction | Transcription-coupled remodeling |
| CK1a | Target of FRH regulation in circadian clock | Circadian clock mechanism |
| PHAX | Adaptor loaded onto U snRNA by DDX39 | Nuclear export of spliceosomal RNA |
| Dbp6p | Functional interactor of Dbp9p in ribosome biogenesis | 60S subunit assembly |
| Transcription factors | Access restricted by ChAHP remodeling | Chromatin regulation |
| Nucleosomes | Evicted by BAF in ATP-dependent manner | Chromatin remodeling assays |
| U snRNA | Cargo for DDX39-mediated export | Spliceosome biogenesis |
| 60S ribosomal subunit | Assembly assisted by Dbp9p | Translation and ribosomopathy models |
| CK1a circadian complex | Regulated by FRH ATPase | Clock protein interaction studies |
| RNA helicase family | Broad ATP-dependent RNA-acting enzymes | Comparative genomics and stress biology |
How Is ATP-dependent activity, acting on RNA Regulated?
The activity of ATP-dependent RNA-acting enzymes is regulated at multiple levels. FRH regulates CK1a in the circadian clock, linking ATP-dependent RNA helicase activity to circadian timing. Dbp9p functionally interacts with Dbp6p during 60S ribosomal subunit biogenesis, suggesting coordinated regulation of ribosome assembly. BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors, indicating that transcription signals can regulate ATP-dependent nucleosome eviction. ChAHP remodeling activity restricts transcription factor access, providing a regulatory layer for chromatin accessibility.
ATP-dependent activity, acting on RNA and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| APC1 | Colorectal cancer | Knockout in HCT116 cells |
| BAF complex subunits | Cancer and chromatin disorders | Point mutation knock-in in HEK293T |
| FRH | Circadian rhythm disruption | Overexpression in Neurospora crassa |
| Dbp9p | Ribosomopathy | Knockout in yeast models |
| DDX39 | RNA export defects | Knockdown in HeLa cells |
Cancer and colorectal cancer
APC1 has potential biological roles and clinical significance in colorectal cancer, and ATP-dependent RNA-acting enzymes may contribute to tumorigenesis through dysregulated RNA processing and chromatin remodeling. BAF complex mutations are known in cancer, and its ATP-dependent nucleosome eviction is critical for tumor suppressor function.
Circadian rhythm disorders
FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa, and disruption of this activity can alter circadian periodicity, linking GO:0008186 to clock-related diseases.
Ribosomopathies and translation defects
Dbp9p is involved in 60S ribosomal subunit biogenesis, and defects in ATP-dependent RNA helicases can lead to ribosome assembly failure, contributing to ribosomopathies.
Neurodegeneration and stress responses
Prokaryotic RNA helicases respond to abiotic stress, and eukaryotic counterparts may protect against stress-induced RNA damage, with implications for neurodegeneration.
From ATP-dependent activity, acting on RNA-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does DDX39 ATPase activity require RNA for U snRNA export? | Point mutation of ATPase domain in DDX39 |
| Can FRH regulate circadian period via CK1a? | Knockout of FRH in Neurospora |
| Is Dbp9p essential for 60S subunit assembly? | Knockout in Saccharomyces cerevisiae |
| Does BAF ATPase drive nucleosome eviction? | Knock-in of tagged BAF subunit |
| Does APC1 overexpression promote colorectal cancer? | Overexpression in colorectal cancer cell lines |
| Can ChAHP remodeling be tracked in live cells? | Tagged knock-in of ChAHP subunits |
How to Study the ATP-dependent activity, acting on RNA Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ATPase assay | ATP hydrolysis rate with/without RNA | Confirm GO:0008186 activity |
| RNA immunoprecipitation | RNA binding by ATP-dependent enzymes | Identify RNA targets |
| Ribo-seq | Global translation efficiency | Assess ribosome biogenesis defects |
| RNA-seq | Transcriptome changes | Evaluate RNA processing and export |
| ATAC-seq | Chromatin accessibility | Study BAF/ChAHP remodeling |
| MNase-seq | Nucleosome positioning | Measure nucleosome eviction |
| Proteomics | Protein interactions and modifications | Identify cofactors like PHAX |
| Live-cell imaging | Dynamic localization of tagged proteins | Track RNA export and remodeling |
RNA immunoprecipitation and crosslinking
RNA immunoprecipitation (RIP) and CLIP can identify RNAs bound by ATP-dependent enzymes such as DDX39, revealing direct RNA targets. These methods help confirm that the activity acts on specific RNA species in vivo.
ATPase assays
In vitro ATPase assays measure ATP hydrolysis in the presence and absence of RNA, directly testing GO:0008186 activity. Coupled enzymatic assays can quantify the dependency on RNA.
Ribosome profiling and RNA-seq
Ribo-seq and RNA-seq can assess global translation and RNA processing changes upon knockout or knockdown of ATP-dependent RNA enzymes like Dbp9p. These methods link molecular activity to cellular phenotypes.
Chromatin accessibility assays
ATAC-seq and MNase-seq measure nucleosome positioning and chromatin accessibility, useful for studying BAF and ChAHP ATP-dependent remodeling. These assays reveal the downstream consequences of ATP-dependent RNA-acting activities on chromatin.
How CRISPR Can Be Used to Study GO:0008186 ATP-dependent activity, acting on RNA
Knockout
CRISPR knockout of genes such as DDX39 or Dbp9p can abolish ATP-dependent RNA-acting activity, allowing researchers to test loss-of-function phenotypes in RNA export or ribosome biogenesis. Knockout models are essential for validating whether a candidate gene is required for the process.
Point Mutation
Point mutations in the ATPase domain of enzymes like DDX39 can separate ATP binding from hydrolysis, revealing which steps require GO:0008186 activity. Such models are valuable for dissecting catalytic versus non-catalytic functions.
Knock-in
Knock-in of tagged versions of BAF subunits or ChAHP components enables live-cell imaging and proteomic analysis of ATP-dependent remodeling complexes. Tagged knock-ins preserve endogenous regulation while allowing affinity purification.
Overexpression
Overexpression of APC1 or FRH can model gain-of-function states relevant to cancer or circadian disruption. Overexpression models help identify dominant effects and potential therapeutic targets.
How EDITGENE Supports ATP-dependent activity, acting on RNA Research
Researchers studying ATP-dependent activity, acting on RNA-related genes often need to determine whether a candidate gene is causally involved in RNA processing, chromatin remodeling, or disease. EDITGENE provides validated CRISPR cell models and screening services to accelerate this discovery.
Contact EDITGENE today to design your custom CRISPR model for ATP-dependent activity, acting on RNA research.
Related Products
| Product name | Cat.No. | Species | Gene ID | |
|---|---|---|---|---|
| DDX11 Knockout HEK293 Cell Line | EDJ-KQ4436 | Human | 1663 | Details Get a Quote |
| IGHMBP2 Knockout HEK293 Cell Line | EDJ-KQ4985 | Human | 3508 | Details Get a Quote |
| DDX17 Knockout HEK293 Cell Line | EDJ-KQ7080 | Human | 10521 | Details Get a Quote |
| YTHDC2 Knockout HEK293 Cell Line | EDJ-KQ16172 | Human | 64848 | Details Get a Quote |
| DDX11 Knockout HCT 116 Cell Line | EDJ-KQ26983 | Human | 1663 | Details Get a Quote |
| DDX11 Knockout HeLa Cell Line | EDJ-KQ26984 | Human | 1663 | Details Get a Quote |
| IGHMBP2 Knockout A-549 Cell Line | EDJ-KQ27872 | Human | 3508 | Details Get a Quote |
| IGHMBP2 Knockout HCT 116 Cell Line | EDJ-KQ27873 | Human | 3508 | Details Get a Quote |
| IGHMBP2 Knockout HeLa Cell Line | EDJ-KQ27874 | Human | 3508 | Details Get a Quote |
| DDX17 Knockout A-549 Cell Line | EDJ-KQ30527 | Human | 10521 | Details Get a Quote |
| DDX17 Knockout HCT 116 Cell Line | EDJ-KQ31910 | Human | 10521 | Details Get a Quote |
| DDX17 Knockout HeLa Cell Line | EDJ-KQ31911 | Human | 10521 | Details Get a Quote |
| YTHDC2 Knockout A-549 Cell Line | EDJ-KQ47384 | Human | 64848 | Details Get a Quote |
| YTHDC2 Knockout HCT 116 Cell Line | EDJ-KQ47385 | Human | 64848 | Details Get a Quote |
| YTHDC2 Knockout HeLa Cell Line | EDJ-KQ47386 | Human | 64848 | Details Get a Quote |
Frequently Asked Questions About ATP-dependent activity, acting on RNA
What is GO:0008186?
GO:0008186 is a molecular function term for ATP-dependent activity, acting on RNA, defined as ATP hydrolysis that requires RNA and drives another reaction.
What genes are involved in ATP-dependent activity, acting on RNA?
Key genes include DDX39, FRH, Dbp9p, and BAF complex subunits, all of which exhibit RNA-dependent ATPase activity.
How is ATP-dependent activity, acting on RNA measured?
It is measured using ATPase assays in the presence and absence of RNA, often combined with RNA immunoprecipitation.
What diseases are linked to GO:0008186?
Dysregulation has been linked to colorectal cancer, circadian rhythm disorders, and ribosomopathies.
What is the difference between ATP-dependent activity, acting on RNA and RNA helicase activity?
GO:0008186 is a broader ATPase activity that requires RNA and drives a coupled reaction, while RNA helicase activity specifically describes RNA unwinding.
Which proteins exemplify GO:0008186?
DDX39, FRH, Dbp9p, and the BAF chromatin remodeler are real examples from the literature.
How can CRISPR help study ATP-dependent activity, acting on RNA?
CRISPR knockout, point mutation, knock-in, and overexpression models allow causal testing of these enzymes in cells.
Is GO:0008186 conserved in prokaryotes?
Yes, prokaryotic RNA helicases with ATP-dependent RNA-acting activity respond to abiotic stress.
What is the role of DDX39 in GO:0008186?
DDX39 uses ATP to load PHAX onto U snRNA for nuclear export, a classic example of RNA-dependent ATPase activity.
How does FRH relate to GO:0008186?
FRH is an ATP-dependent regulator of CK1a in the circadian clock, demonstrating RNA-dependent ATPase function.
Conclusion
GO:0008186 ATP-dependent activity, acting on RNA, defines a critical molecular function that couples ATP hydrolysis to RNA-dependent remodeling, export, and chromatin events. Real examples such as DDX39, FRH, Dbp9p, and BAF illustrate its broad biological impact, from circadian clocks to ribosome biogenesis and cancer. CRISPR-based models and EDITGENE services provide powerful tools to dissect these mechanisms and accelerate therapeutic discovery.
References
- 1. Brahma S et al.. 2024. The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes.. Nat Genet 56(1):100-111 PMID: 38049663
- 2. Taniguchi I et al.. 2024. The RNA helicase DDX39 contributes to the nuclear export of spliceosomal U snRNA by loading of PHAX onto RNA.. Nucleic Acids Res 52(17):10668-10682 PMID: 39011894
- 4. Ahel J et al.. 2026. Remodeling activity of ChAHP restricts transcription factor access to chromatin.. Mol Cell 86(14):2754-2764.e9 PMID: 42413491
- 5. Lauinger L et al.. 2014. The RNA helicase FRH is an ATP-dependent regulator of CK1a in the circadian clock of Neurospora crassa.. Nat Commun 5:3598 PMID: 24710172
- 6. Chen Y et al.. 2025. The Potential Biological Roles and Clinical Significance of Anaphase-Promoting Complex Subunit 1 in Colorectal Cancer.. Cancer Control 32:10732748251330059 PMID: 40229946
- 7. Owttrim GW. 2013. RNA helicases: diverse roles in prokaryotic response to abiotic stress.. RNA Biol 10(1):96-110 PMID: 23093803
- 8. Daugeron MC et al.. 2001. Dbp9p, a putative ATP-dependent RNA helicase involved in 60S-ribosomal-subunit biogenesis, functionally interacts with Dbp6p.. RNA 7(9):1317-34 PMID: 11565753
