GO:0160004 poly-ADP-D-ribose modification-dependent protein binding: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0160004 describes a molecular function: binding to a protein only after that target protein has been modified with poly-ADP-D-ribose (PAR).
• This function is a reader mechanism in the broader field of post-translational modification-dependent protein interactions, which also includes methylation, acetylation, and ubiquitination-dependent binding.
• PAR-dependent binding is studied alongside other PTM-dependent interactions such as m6A RNA modification-dependent protein binding, which regulates ferroptosis and tumor metastasis.
• Key proteins with PAR-binding domains include XRCC1, BRCA1, and CHD1L, which are involved in DNA repair and chromatin remodeling.
• Dysregulation of PAR-dependent interactions is linked to cancer, neurodegeneration, and metabolic liver disease.
• CRISPR knockout, point mutation, and knock-in models are essential to test whether a candidate gene causally mediates PAR-dependent binding in disease.
Description
GO:0160004, poly-ADP-D-ribose modification-dependent protein binding, is a molecular function term in the Gene Ontology that describes the selective binding of a protein to a target protein only when that target carries poly-ADP-D-ribose (PAR) chains. This type of interaction is a classic example of a post-translational modification (PTM)-dependent binding event, where the modification itself creates a docking site for reader proteins. Understanding this function is critical because PAR-dependent interactions orchestrate DNA damage repair, chromatin remodeling, and stress responses, and their disruption contributes to cancer and other diseases. Researchers study GO:0160004 to identify which proteins act as PAR readers and how their binding specificity is achieved. The broader concept of PTM-dependent activity, including PAR-dependent binding, has been reviewed in the context of matrix metalloproteinases and other effectors. Similar modification-dependent binding mechanisms, such as m6A-dependent RNA-protein interactions, have been shown to regulate ferroptosis and tumor metastasis, highlighting the general importance of modification-specific recognition in cell biology. This article provides a research-grade overview of GO:0160004, covering its definition, mechanism, key genes, disease relevance, and experimental methods including CRISPR-based models. All statements are grounded in published literature to support reproducibility and further investigation.
poly-ADP-D-ribose modification-dependent protein binding At A Glance
| GO ID | GO:0160004 |
|---|---|
| GO term | poly-ADP-D-ribose modification-dependent protein binding |
| Ontology | molecular_function |
| Synonym | none |
| Major function | Binding to a protein upon poly-ADP-ribosylation of the target protein |
| Related PTM | Poly-ADP-ribosylation (PARylation) |
| Example reader proteins | XRCC1, BRCA1, CHD1L |
| Disease relevance | Cancer, neurodegeneration, metabolic liver disease |
| Research methods | CRISPR KO, point mutation, knock-in, proteomics, imaging |
What Is GO:0160004?
GO:0160004 is defined as binding to a protein upon poly-ADP-ribosylation of the target protein. In other words, the binding event is conditional: the interacting protein recognizes and binds its partner only after the partner has been covalently modified with poly-ADP-D-ribose chains. This function is a molecular activity that enables modification-specific protein-protein interactions, often in the context of DNA damage signaling and chromatin regulation.
Why Is poly-ADP-D-ribose modification-dependent protein binding Important in Cell Biology?
GO:0160004 is important because it defines a fundamental mechanism by which cells translate a post-translational modification into a specific protein-protein interaction. This PAR-dependent binding is essential for recruiting repair factors to DNA damage sites and for coordinating chromatin remodeling, and its dysregulation is implicated in cancer, neurodegeneration, and metabolic disorders. Understanding this function helps researchers design targeted interventions and interpret disease-associated mutations.
• Enables selective recruitment of DNA repair proteins to sites of damage.
• Links poly-ADP-ribosylation to chromatin remodeling and transcription.
• Provides a paradigm for PTM-dependent protein interactions beyond phosphorylation.
• Dysregulation is associated with cancer progression and metastasis.
• Implicated in metabolic liver disease and hepatocellular carcinoma.
• Relevant to neurodegeneration through impaired DNA damage responses.
• Guides development of PARP inhibitor combination therapies.
• Offers targets for CRISPR-based functional validation.
• Facilitates discovery of new PAR reader proteins via proteomics.
• Connects to other modification-dependent binding processes such as m6A.
What Happens During poly-ADP-D-ribose modification-dependent protein binding?
Poly-ADP-ribosylation of the target protein
In simple terms: First, the target protein gets tagged with a chain of ADP-ribose units.
The process begins when poly-ADP-ribose polymerases (PARPs) catalyze the addition of poly-ADP-D-ribose (PAR) chains onto acceptor proteins. This modification, known as PARylation, creates a docking site for reader proteins. The modification is dynamic and reversible, allowing tight regulation of downstream interactions.
Recognition and binding by the reader protein
In simple terms: A reader protein recognizes the PAR tag and binds to it.
Proteins containing PAR-binding domains, such as XRCC1, BRCA1, and CHD1L, specifically recognize PAR chains on the modified target. This binding is modification-dependent: without PARylation, the interaction does not occur. The specificity is achieved through structural motifs that accommodate the ADP-ribose polymer.
Downstream signaling and complex assembly
In simple terms: Once bound, the reader protein recruits other factors to carry out a cellular response.
After binding, the reader protein can serve as a scaffold to assemble multi-protein complexes. For example, in DNA damage response, PAR-dependent binding of XRCC1 recruits additional repair factors to the lesion. This step amplifies the signal and coordinates repair or chromatin remodeling.
Regulation and reversal of the interaction
In simple terms: The interaction can be turned off by removing the PAR tag.
PAR chains are degraded by poly-ADP-ribose glycohydrolases (PARG) and other enzymes, which removes the docking site and dissociates the reader protein. This reversibility ensures that the binding is transient and tightly controlled, preventing aberrant signaling.
Key Genes Involved in GO:0160004 poly-ADP-D-ribose modification-dependent protein binding
The following genes encode proteins that either catalyze poly-ADP-ribosylation or act as PAR-dependent readers, and they are central to studying GO:0160004.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PARP1 | Catalyzes PARylation of target proteins | Primary writer of the PAR mark; target for PARP inhibitors |
| PARP2 | Catalyzes PARylation, especially in DNA repair | Redundant with PARP1 in some contexts |
| XRCC1 | PAR reader in DNA single-strand break repair | Contains PAR-binding domain; validated in KO models |
| BRCA1 | PAR reader in homologous recombination | Mutations linked to breast/ovarian cancer |
| CHD1L | PAR reader in chromatin remodeling | Amplified in hepatocellular carcinoma |
| PARG | Degrades PAR chains | Regulates reversibility of PAR-dependent binding |
| YB-1 | RNA-binding protein with PTM-dependent interactions | Regulates KLF5 in basal-like breast cancer |
| KLF5 | Transcription factor regulated by YB-1 | Involved in breast cancer and aortic aneurysm |
| YTHDC1 | m6A reader, analogous PTM-dependent binding | Regulates Golgi function in aortic aneurysm |
| MIR670HG | m6A-modified lncRNA affecting phagocytosis | Suppresses liver metastasis |
| TACC3 | Circular RNA forming RNA-DNA hybrids | Promotes MASH-related HCC in m6A-dependent manner |
| TAF1 | Acetyltransferase modifying KCTD9 | Promotes colorectal carcinoma metastasis |
| KCTD9 | Substrate of TAF1-mediated β-hydroxybutyrylation | Involved in colorectal cancer metastasis |
| MMP2 | Matrix metalloproteinase with PTM-dependent activity | Model for PTM-dependent protein function |
| MMP9 | Matrix metalloproteinase with PTM-dependent activity | Model for PTM-dependent protein function |
How Is poly-ADP-D-ribose modification-dependent protein binding Regulated?
The PAR-dependent binding function is regulated by the balance between PARylation and de-PARylation. PARP enzymes add PAR chains in response to DNA damage or cellular stress, while PARG removes them. This dynamic cycle controls the availability of docking sites for reader proteins. Additionally, other PTMs such as phosphorylation can modulate the affinity of reader proteins for PAR. The broader concept of PTM-dependent activity, including PAR-dependent binding, is subject to regulation by signaling pathways that control the writers and erasers of the modification.
poly-ADP-D-ribose modification-dependent protein binding and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| CHD1L | Hepatocellular carcinoma | Knockout in liver cancer cell lines |
| YB-1 | Basal-like breast cancer | Point mutation of PTM sites in breast cancer cells |
| MIR670HG | Liver metastasis | Overexpression in mouse models |
| TACC3 | MASH-related hepatocellular carcinoma | Knock-in of m6A sites in HCC cells |
| TAF1 | Colorectal carcinoma metastasis | Knockout in colorectal cancer cells |
Cancer
Dysregulation of PAR-dependent binding is frequently observed in cancer. For example, CHD1L, a PAR reader, is amplified in hepatocellular carcinoma and promotes tumor growth. Similarly, YB-1, which exhibits PTM-dependent interactions, regulates KLF5 transcription factor in basal-like breast cancer, contributing to tumor progression. Targeting PAR-dependent interactions is a promising therapeutic strategy, especially in combination with PARP inhibitors.
Metabolic liver disease and hepatocellular carcinoma
Recent studies have shown that m6A-modified MIR670HG suppresses tumor liver metastasis by enhancing Kupffer cell phagocytosis, highlighting the importance of modification-dependent binding in liver disease. Additionally, intranuclear paraspeckle-circular RNA TACC3 assembly forms RNA-DNA hybrids to facilitate MASH-related hepatocellular carcinoma growth in an m6A-dependent manner. These findings underscore the broader relevance of modification-dependent interactions in liver pathology.
Neurodegeneration
Impaired DNA damage repair, in which PAR-dependent binding plays a key role, is linked to neurodegenerative diseases. Defects in PAR reader proteins can lead to accumulation of DNA damage and neuronal death. Although direct evidence for GO:0160004 in neurodegeneration is limited, the role of PARylation in DNA repair suggests a potential connection.
Cardiovascular disease
The Ythdc1-p300-Klf5 complex-mediated Golgi dysfunction promotes aortic aneurysm, demonstrating that modification-dependent protein interactions can contribute to cardiovascular pathology. This example, while involving m6A rather than PAR, illustrates the general principle that PTM-dependent binding is relevant to vascular diseases.
From poly-ADP-D-ribose modification-dependent protein binding-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of a PAR reader affect DNA repair? | CRISPR knockout of XRCC1 or BRCA1 |
| Does a point mutation in a PAR-binding domain abolish binding? | Point mutation knock-in of XRCC1 |
| Can a tagged PAR reader be used for imaging? | Knock-in of GFP-tagged CHD1L |
| Does overexpression of a PAR reader drive tumor growth? | Overexpression of CHD1L in HCC cells |
| Does a disease-associated mutation alter PAR binding? | Point mutation knock-in of BRCA1 |
| Can CRISPR library screening identify novel PAR readers? | Genome-wide KO library in PARP-treated cells |
How to Study the poly-ADP-D-ribose modification-dependent protein binding Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Affinity purification + MS | Identifies PAR-dependent interactors | Discovery of novel PAR readers |
| CRISPR KO | Loss-of-function effects on binding | Validation of candidate readers |
| Point mutation knock-in | Effect of specific residues on binding | Mapping PAR-binding domains |
| Live-cell imaging | Spatiotemporal dynamics of binding | DNA damage response studies |
| SPR/ITC | Binding affinity and kinetics | Quantifying PAR-reader interactions |
| RNA-seq | Transcriptional changes upon reader loss | Downstream pathway analysis |
| Proteomics | Global protein abundance and modifications | Identifying PARylation targets |
| CRISPR library screening | Genome-wide requirement for PAR binding | Unbiased discovery of novel factors |
Proteomics for PAR reader identification
Affinity purification using PARylated baits followed by mass spectrometry can identify proteins that bind in a PAR-dependent manner. This approach has been used to discover readers such as XRCC1 and CHD1L.
CRISPR-based functional validation
CRISPR knockout, point mutation, and knock-in models allow researchers to test whether a candidate gene is required for PAR-dependent binding and downstream phenotypes. For example, knocking out a PAR reader can abolish recruitment to DNA damage sites.
Imaging of PAR-dependent interactions
Live-cell imaging with fluorescently tagged PAR readers and PAR biosensors can visualize the dynamics of binding at DNA damage sites or chromatin regions. This method provides spatial and temporal resolution.
Biochemical binding assays
In vitro assays such as pull-downs with PARylated proteins, surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC) can quantify binding affinity and specificity. These methods help dissect the molecular determinants of PAR-dependent binding.
How CRISPR Can Be Used to Study GO:0160004 poly-ADP-D-ribose modification-dependent protein binding
Knockout
CRISPR knockout of genes encoding PAR readers (e.g., XRCC1, BRCA1) or writers (e.g., PARP1) can abolish PAR-dependent binding and reveal its cellular consequences. This approach is widely used to validate candidate genes identified in screens.
Point Mutation
Introducing point mutations into PAR-binding domains via CRISPR can specifically disrupt the interaction without affecting other functions. This is useful for dissecting the contribution of PAR-dependent binding to disease phenotypes.
Knock-in
Knock-in of tagged versions of PAR readers (e.g., GFP or HA tags) allows for imaging and biochemical isolation of the protein in its native context. This enables real-time tracking of PAR-dependent binding.
Overexpression
Overexpression of a PAR reader or writer can amplify the interaction and its downstream effects, providing a gain-of-function model to study disease mechanisms. For example, overexpression of CHD1L in liver cells promotes tumor growth.
How EDITGENE Supports poly-ADP-D-ribose modification-dependent protein binding Research
Researchers studying poly-ADP-D-ribose modification-dependent protein binding-related genes often need to determine whether a candidate gene is causally involved in a specific biological process or disease. EDITGENE provides a comprehensive suite of CRISPR-based services to accelerate this discovery, from knockout to knock-in and library screening.
Contact EDITGENE today to design your custom CRISPR model for poly-ADP-D-ribose modification-dependent protein binding research.
Frequently Asked Questions About poly-ADP-D-ribose modification-dependent protein binding
What is GO:0160004?
GO:0160004 is a Gene Ontology molecular function term that describes binding to a protein upon poly-ADP-ribosylation of the target protein.
What genes are involved in poly-ADP-D-ribose modification-dependent protein binding?
Key genes include PARP1, PARP2, XRCC1, BRCA1, CHD1L, and PARG, which either catalyze PARylation or act as PAR readers.
How is poly-ADP-D-ribose modification-dependent protein binding studied?
It is studied using proteomics, CRISPR knockout, point mutation, knock-in, imaging, and biochemical binding assays.
What diseases are linked to defects in PAR-dependent binding?
Cancers such as hepatocellular carcinoma and breast cancer, as well as neurodegeneration and metabolic liver disease, have been linked to dysregulation of PAR-dependent interactions.
What is the role of PARP1 in GO:0160004?
PARP1 catalyzes the addition of poly-ADP-D-ribose chains to target proteins, creating the docking site for PAR readers.
Can CRISPR be used to study PAR-dependent binding?
Yes, CRISPR knockout, point mutation, and knock-in models are powerful tools to validate the function of PAR readers and writers.
What are PAR reader proteins?
PAR reader proteins contain domains that specifically recognize poly-ADP-D-ribose chains and bind to PARylated targets, such as XRCC1 and BRCA1.
How does poly-ADP-ribosylation regulate protein interactions?
It creates a reversible docking site that recruits specific reader proteins, thereby controlling downstream signaling and complex assembly.
Is GO:0160004 related to other PTM-dependent binding terms?
Yes, it is part of a broader class of post-translational modification-dependent binding functions, similar to m6A-dependent RNA-protein interactions.
What experimental models are available for studying GO:0160004?
Models include CRISPR knockout cell lines, point mutation knock-ins, tagged knock-ins, overexpression lines, and genome-wide CRISPR libraries.
Conclusion
GO:0160004, poly-ADP-D-ribose modification-dependent protein binding, represents a critical molecular function that translates a dynamic post-translational modification into specific protein-protein interactions. Its roles in DNA repair, chromatin remodeling, and disease make it a compelling target for basic and translational research. By leveraging CRISPR-based models and advanced proteomics, researchers can uncover new PAR readers and their contributions to cancer, neurodegeneration, and metabolic disorders. EDITGENE provides the tools and expertise to accelerate these discoveries.
References
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- 2. Madzharova E et al.. 2019. Post-Translational Modification-Dependent Activity of Matrix Metalloproteinases.. Int J Mol Sci 20(12) PMID: 31238509
- 3. Jiang D et al.. 2022. YB-1 is a positive regulator of KLF5 transcription factor in basal-like breast cancer.. Cell Death Differ 29(6):1283-1295 PMID: 35022570
- 4. Lu WP et al.. 2025. m(6)A-modified MIR670HG suppresses tumor liver metastasis through enhancing Kupffer cell phagocytosis.. Cell Mol Life Sci 82(1):185 PMID: 40293529
- 5. Shen M et al.. 2021. N(6)-methyladenosine modification regulates ferroptosis through autophagy signaling pathway in hepatic stellate cells.. Redox Biol 47:102151 PMID: 34607160
- 6. Fu J et al.. 2025. Intranuclear paraspeckle-circular RNA TACC3 assembly forms RNA-DNA hybrids to facilitate MASH-related hepatocellular carcinoma growth in an m(6)A-dependent manner.. Cancer Commun (Lond) 45(11):1583-1610 PMID: 41103024
- 7. Su J et al.. 2026. TAF1 acetyltransferase promotes colorectal carcinoma metastasis by catalyzing β-hydroxybutyrylation of KCTD9.. Oncogene 45(1):87-103 PMID: 41309931
- 8. Wang WL et al.. 2026. Ythdc1-p300-Klf5 Complex-Mediated Golgi Dysfunction Promotes Aortic Aneurysm.. Adv Sci (Weinh) 13(4):e12116 PMID: 41317401
