GO:0140816 NAD+-histone H2BS6 serine ADP-ribosyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0140816 describes the enzymatic transfer of ADP-ribose from NAD+ to serine-6 of histone H2B, a chromatin modification that influences DNA repair and transcription.
• This activity is carried out by PARP family enzymes, particularly PARP1 and PARP2, often in complex with accessory factors such as HPF1.
• Histone H2B serine ADP-ribosylation is a dynamic mark that recruits repair proteins and modulates chromatin structure during the DNA damage response.
• Dysregulation of this activity is linked to cancer, neurodegeneration, and metabolic disorders, making it a target for therapeutic intervention [1,5,7].
• CRISPR-based models (knockout, point mutation, knock-in, overexpression) are essential to dissect the causal roles of the enzymes and the modified histone residue [5,8].
• EDITGENE provides custom cell models and screening services to study GO:0140816 in relevant biological contexts.
Description
NAD+-histone H2BS6 serine ADP-ribosyltransferase activity (GO:0140816) is a molecular function that catalyzes the transfer of ADP-ribose groups from NAD+ to serine-6 of histone H2B. This modification, known as serine ADP-ribosylation, is a key chromatin mark that regulates the DNA damage response and transcription. The activity is primarily attributed to PARP family enzymes, especially PARP1 and PARP2, which are activated by DNA breaks and collaborate with accessory proteins like HPF1 to modify histone H2B at serine-6. Understanding this activity is crucial because it links NAD+ metabolism to chromatin regulation and genome stability. Research on GO:0140816 has gained momentum due to its implications in cancer therapy, where PARP inhibitors exploit defects in DNA repair pathways [5,7]. Moreover, the modification influences immune signaling and cell survival, as seen in melanoma and other malignancies. The precise mapping of this activity to specific enzymes and residues has been facilitated by advances in proteomics and CRISPR-based editing [2,8]. For researchers, GO:0140816 represents a focal point for studying how post-translational modifications of histones orchestrate cellular responses to stress. This article synthesizes current knowledge from authoritative databases and peer-reviewed literature to provide a comprehensive overview of the mechanisms, genes, and experimental approaches related to this activity.
NAD+-histone H2BS6 serine ADP-ribosyltransferase activity At A Glance
| GO ID | GO:0140816 |
|---|---|
| GO term | NAD+-histone H2BS6 serine ADP-ribosyltransferase activity |
| Ontology | molecular_function |
| Synonym | NAD+-histone H2B-S6 serine ADP-ribosyltransferase activity; NAD+-histone-serine ADP-ribosyltransferase activity (H2B-S6 specific) |
| Major function | Transfer of ADP-ribose from NAD+ to histone H2B serine-6, regulating chromatin structure and DNA repair |
| Cofactors | NAD+ as ADP-ribose donor; often requires HPF1 for serine specificity |
| Substrate | Histone H2B, specifically serine-6 residue |
| Associated enzymes | PARP1, PARP2, and other PARP family members [2,8] |
| Biological context | DNA damage response, transcription regulation, and cell survival [1,2] |
What Is GO:0140816?
GO:0140816 is defined as the catalysis of the transfer of ADP-ribose groups to the serine-6 or an equivalent residue of the N-terminal tail of histone H2B. This enzymatic activity uses NAD+ as a substrate and is specific for histone H2B at serine-6, distinguishing it from other ADP-ribosylation reactions.
Why Is NAD+-histone H2BS6 serine ADP-ribosyltransferase activity Important in Cell Biology?
GO:0140816 is important because it represents a critical link between NAD+ metabolism and chromatin regulation, influencing genome stability and gene expression. This activity is rapidly stimulated by DNA damage and is essential for recruiting repair factors to sites of damage. Dysregulation of this modification has been implicated in cancer progression, where it can promote cell survival and immune evasion. Furthermore, the enzymes that carry out this activity, such as PARP1, are targets of clinically approved inhibitors, underscoring its therapeutic relevance [5,7]. Understanding GO:0140816 therefore provides insights into basic chromatin biology and offers potential avenues for drug development.
• Regulates the DNA damage response by recruiting repair proteins to chromatin.
• Modulates chromatin structure and accessibility, affecting transcription.
• Linked to cancer cell survival and immune evasion, as shown in melanoma models.
• Influences sensitivity to PARP inhibitors in cancers with DNA repair defects [5,7].
• Plays a role in metabolic adaptation and stress responses in lymphoma.
• Involved in necroptosis and apoptosis regulation via mono-ADP-ribosylation.
• Potential biomarker for predicting response to DNA-damaging therapies.
• Target for therapeutic intervention in cancers and degenerative diseases [1,4].
• Connects NAD+ availability to epigenetic regulation.
• Provides a model for studying serine-specific ADP-ribosylation in chromatin.
What Happens During NAD+-histone H2BS6 serine ADP-ribosyltransferase activity?
Recognition of DNA Damage and Enzyme Activation
In simple terms: When DNA breaks, enzymes that add ADP-ribose to histones are turned on.
The activity of GO:0140816 is initiated by the detection of DNA strand breaks, which activates PARP family enzymes, particularly PARP1 and PARP2. These enzymes bind to damaged DNA and undergo conformational changes that stimulate their catalytic activity. This activation is a rapid response to genotoxic stress and is critical for recruiting downstream repair factors.
Formation of the PARP-HPF1 Complex
In simple terms: A helper protein called HPF1 joins the enzyme to ensure it modifies the correct amino acid.
For efficient and specific modification of histone H2B at serine-6, PARP1/2 often associates with HPF1 (histone PARylation factor 1). HPF1 alters the catalytic pocket of PARP enzymes, shifting their specificity from aspartate/glutamate to serine residues. This complex formation is essential for the serine ADP-ribosylation of histone H2B and for the subsequent cellular responses to DNA damage.
Transfer of ADP-Ribose to Histone H2B Serine-6
In simple terms: The enzyme takes ADP-ribose from NAD+ and attaches it to a specific spot on histone H2B.
The catalytic step involves the cleavage of NAD+ and the transfer of its ADP-ribose moiety to the hydroxyl group of serine-6 on histone H2B. This reaction can result in mono- or poly-ADP-ribosylation, depending on the enzyme and context. The modification is reversible and dynamic, allowing for tight regulation of the DNA damage response.
Recruitment of Repair Factors and Chromatin Remodeling
In simple terms: The ADP-ribose tag acts like a flag that attracts repair proteins and loosens chromatin.
Once histone H2B is ADP-ribosylated at serine-6, it serves as a docking site for proteins containing ADP-ribose-binding domains, such as XRCC1 and other repair factors. This recruitment facilitates the assembly of repair complexes at damage sites. Additionally, the modification can alter chromatin compaction, making DNA more accessible for repair.
Resolution and Removal of the Modification
In simple terms: After repair, the ADP-ribose tags are removed to restore normal chromatin.
The ADP-ribosylation mark is transient and is removed by enzymes such as PARG (poly(ADP-ribose) glycohydrolase) and possibly other hydrolases. This step is crucial for preventing persistent chromatin alterations and for allowing cells to recover from DNA damage. Dysregulation of this removal process can lead to genomic instability.
Key Genes Involved in GO:0140816 NAD+-histone H2BS6 serine ADP-ribosyltransferase activity
The following genes encode enzymes and accessory proteins directly involved in NAD+-histone H2BS6 serine ADP-ribosyltransferase activity or its regulation.
| Gene | Major Role | Research Relevance |
|---|---|---|
| PARP1 | Primary enzyme catalyzing ADP-ribosylation of histone H2B at serine-6 | Target of PARP inhibitors; knockout models show defective DNA repair [2,5] |
| PARP2 | Enzyme with overlapping function in histone ADP-ribosylation | Compensates for PARP1 loss; double knockout is lethal |
| HPF1 | Accessory factor that directs PARP1/2 to serine residues | Knockout abolishes serine ADP-ribosylation; used to study specificity |
| H2B | Histone substrate; serine-6 is the modification site | Point mutations at S6 prevent ADP-ribosylation; knock-in models |
| PARG | Removes ADP-ribose polymers from histones | Regulates dynamics; knockout leads to accumulation of ADP-ribose |
| XRCC1 | Scaffold protein recruited by ADP-ribosylation | Required for single-strand break repair; mutations cause disease |
| SIRT7 | NAD+-dependent deacetylase; may influence NAD+ availability | Linked to melanoma progression and UPR activation |
| SIRT2 | Deacetylase with roles in cardiac hypertrophy | Potential crosstalk with ADP-ribosylation pathways |
| SIRT3 | Mitochondrial deacetylase; regulates oxidative stress | Implicated in osteoarthritis and ferroptosis |
| GSK3B | Kinase that influences DNA repair choice | Modulates response to PARP1 inhibition |
| MRPL21 | Mitochondrial ribosomal protein; interacts with PARP1 | Promotes cisplatin resistance in head and neck cancer |
| PARP12 | Mono-ADP-ribosyltransferase | Regulates necroptosis and apoptosis |
| AMPK | Energy sensor kinase | Activated by SIRT3 to suppress ferroptosis |
| BRCA1 | Homologous recombination repair protein | Defects sensitize to PARP inhibitors |
| PI3K/AKT/mTOR | Signaling pathway | Modulated by MRPL21-PARP1 axis in cisplatin resistance |
| L-asparaginase | Metabolic enzyme | Induces vulnerability to PARP1/2 inhibitors in lymphoma |
How Is NAD+-histone H2BS6 serine ADP-ribosyltransferase activity Regulated?
The activity of GO:0140816 is tightly regulated at multiple levels. Enzyme activation is triggered by DNA damage through PARP1/2 binding to broken DNA ends. HPF1 binding further modulates substrate specificity, favoring serine residues on histone H2B. NAD+ availability, influenced by metabolic pathways and enzymes like SIRT7, can affect the overall rate of ADP-ribosylation. Additionally, the removal of ADP-ribose by PARG ensures the transient nature of the mark. Signaling pathways such as AMPK and PI3K/AKT/mTOR can indirectly influence this activity by altering cellular metabolism and stress responses [4,6].
NAD+-histone H2BS6 serine ADP-ribosyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| PARP1 | Cancer (breast, ovarian, melanoma) | Knockout and point-mutation cell lines; xenograft models |
| SIRT7 | Melanoma progression and immune evasion | Overexpression and knockout melanoma cells |
| MRPL21 | Cisplatin resistance in head and neck cancer | Knockdown and overexpression in HNSCC lines |
| PARP12 | Necroptosis and apoptosis regulation | Knockout cells treated with death ligands |
| SIRT3 | Osteoarthritis and ferroptosis | Chondrocyte knockout and overexpression models |
Cancer
Dysregulation of NAD+-histone H2BS6 serine ADP-ribosyltransferase activity is implicated in various cancers. In melanoma, SIRT7 promotes cell survival and immune evasion via the unfolded protein response, potentially involving NAD+ metabolism. PARP1-mediated ADP-ribosylation is a key target in cancers with homologous recombination defects, such as BRCA1-mutated tumors, where PARP inhibitors show efficacy. In head and neck squamous cell carcinoma, the MRPL21-PARP1 axis contributes to cisplatin resistance by inhibiting autophagy through PI3K/AKT/mTOR signaling. Furthermore, L-asparaginase treatment in B-cell lymphomas induces metabolic adaptation that creates vulnerability to PARP1/2 inhibitors.
Cardiovascular and Metabolic Diseases
SIRT2, a deacetylase that consumes NAD+, acts as a cardioprotective factor in pathological cardiac hypertrophy. Although direct links to histone H2B serine ADP-ribosylation are not fully established, the shared NAD+ dependence suggests crosstalk between sirtuins and PARPs in cardiac stress responses. In osteoarthritis, SIRT3 mitigates disease by suppressing ferroptosis through AMPK activation, highlighting the role of NAD+ metabolism in degenerative joint disease.
Cell Death and Inflammation
PARP12-mediated mono-ADP-ribosylation acts as a checkpoint for necroptosis and apoptosis, influencing cell fate decisions. This suggests that ADP-ribosylation of histones and other targets can modulate inflammatory and cell death pathways, with implications for autoimmune and neurodegenerative conditions.
From NAD+-histone H2BS6 serine ADP-ribosyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does PARP1 catalytic activity require HPF1 for H2B S6 ADP-ribosylation? | HPF1 knockout cells with PARP1 overexpression |
| What is the role of H2B S6 ADP-ribosylation in DNA repair? | H2B S6A point-mutation knock-in cells |
| Can PARP1 inhibition sensitize lymphoma to L-asparaginase? | PARP1 knockout lymphoma cells treated with L-asparaginase |
| Does SIRT7 modulate NAD+ levels and affect ADP-ribosylation? | SIRT7 overexpression and knockout melanoma cells |
| How does MRPL21-PARP1 axis affect cisplatin resistance? | MRPL21 knockdown in head and neck cancer cells |
| Is PARP12-mediated mono-ADP-ribosylation critical for necroptosis? | PARP12 knockout cells with necroptosis inducers |
How to Study the NAD+-histone H2BS6 serine ADP-ribosyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Western blot with anti-ADP-ribose antibody | Levels of ADP-ribosylated proteins | Detecting global changes after DNA damage |
| Mass spectrometry | Precise site and stoichiometry of modification | Mapping H2B S6 ADP-ribosylation |
| CRISPR knockout | Loss-of-function phenotypes | Studying PARP1, HPF1, or H2B mutants [2,5] |
| Comet assay | DNA strand breaks | Assessing repair capacity in edited cells |
| RNA-seq | Transcriptional changes | Identifying pathways affected by ADP-ribosylation |
| Immunofluorescence | Localization of repair factors | Recruitment to damage sites |
| PARP inhibitor sensitivity assay | Cell survival | Testing therapeutic relevance [5,7] |
| Proximity ligation assay | Protein-protein interactions | Detecting PARP1-HPF1 complex formation |
Detection of ADP-Ribosylation
ADP-ribosylation of histone H2B at serine-6 can be detected using specific antibodies or mass spectrometry. Antibodies against ADP-ribose or site-specific modifications enable Western blotting and immunofluorescence. Mass spectrometry-based proteomics allows precise mapping of the modified residue and quantification of modification levels.
Genetic Manipulation with CRISPR
CRISPR-Cas9 genome editing is used to create knockout, point-mutation, and knock-in cell lines to study the function of PARP1, PARP2, HPF1, and histone H2B [2,5]. These models help determine causality between the modification and cellular phenotypes. Overexpression of wild-type or mutant enzymes can reveal dominant effects.
Functional Assays for DNA Repair
DNA repair capacity can be assessed using comet assays, gamma-H2AX foci formation, and survival assays after DNA-damaging agents [2,5]. These assays measure the impact of ADP-ribosylation on repair efficiency. PARP inhibitors are often used to probe pathway dependence.
Transcriptomics and Proteomics
RNA sequencing (RNA-seq) and proteomics can reveal global changes in gene expression and protein recruitment upon modulation of ADP-ribosylation [1,6]. These approaches identify downstream effectors and pathways. Bioinformatics analysis of public datasets can further link the modification to disease signatures.
How CRISPR Can Be Used to Study GO:0140816 NAD+-histone H2BS6 serine ADP-ribosyltransferase activity
Knockout
CRISPR knockout of PARP1, PARP2, or HPF1 abolishes or reduces NAD+-histone H2BS6 serine ADP-ribosyltransferase activity, leading to defective DNA repair and increased sensitivity to genotoxic agents [2,5]. These models are essential for establishing the requirement of specific enzymes for the modification.
Point Mutation
Introducing point mutations such as H2B S6A (serine to alanine) via CRISPR knock-in prevents ADP-ribosylation at this site, allowing researchers to study the specific contribution of this modification to chromatin dynamics and repair. Similarly, catalytic-dead mutants of PARP1 can distinguish enzymatic activity from scaffolding functions.
Knock-in
Knock-in of tagged histone H2B or PARP1 (e.g., GFP or HA tags) enables visualization and immunoprecipitation of the modified proteins. This approach helps track the modification in live cells and identify interaction partners.
Overexpression
Overexpression of wild-type or mutant PARP1, HPF1, or SIRT7 can amplify or disrupt the pathway, revealing gain-of-function phenotypes and dominant-negative effects [1,2]. Overexpression models are useful for studying the impact of elevated ADP-ribosylation on cancer cell survival and immune evasion.
How EDITGENE Supports NAD+-histone H2BS6 serine ADP-ribosyltransferase activity Research
Researchers studying NAD+-histone H2BS6 serine ADP-ribosyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in the modification, DNA repair, or disease phenotypes. EDITGENE provides a comprehensive suite of CRISPR-based services to generate precisely engineered cell models, enabling rigorous functional studies.
Contact EDITGENE today to design your custom CRISPR model for NAD+-histone H2BS6 serine ADP-ribosyltransferase activity research.
Frequently Asked Questions About NAD+-histone H2BS6 serine ADP-ribosyltransferase activity
What is NAD+-histone H2BS6 serine ADP-ribosyltransferase activity?
It is an enzymatic activity (GO:0140816) that transfers ADP-ribose from NAD+ to serine-6 of histone H2B, regulating chromatin and DNA repair.
What genes are involved in NAD+-histone H2BS6 serine ADP-ribosyltransferase activity?
Key genes include PARP1, PARP2, HPF1, and histone H2B, along with regulatory proteins like SIRT7 and PARG [1,2].
Which enzymes catalyze histone H2B serine ADP-ribosylation?
PARP1 and PARP2, often in complex with HPF1, are the primary enzymes responsible for this modification.
How is histone H2B serine ADP-ribosylation detected?
It can be detected by mass spectrometry, specific antibodies, and Western blotting, often combined with DNA damage induction.
What diseases are associated with dysregulated H2B serine ADP-ribosylation?
Cancers such as melanoma, breast, and ovarian cancer, as well as metabolic and cardiovascular disorders, have been linked to this pathway [1,5,7].
Can CRISPR be used to study NAD+-histone H2BS6 serine ADP-ribosyltransferase activity?
Yes, CRISPR knockout, point mutation, and knock-in models are widely used to dissect the function of enzymes and the modified histone residue [2,5].
What is the role of HPF1 in this activity?
HPF1 is an accessory factor that directs PARP1/2 to modify serine residues, including H2B serine-6, instead of acidic residues.
How does NAD+ metabolism affect histone ADP-ribosylation?
NAD+ availability, influenced by enzymes like SIRT7, can limit or enhance the rate of ADP-ribosylation.
Is H2B serine ADP-ribosylation reversible?
Yes, it is removed by PARG and other hydrolases, making it a dynamic and transient mark.
What experimental models are best for studying this activity?
Knockout and point-mutation cell lines, along with overexpression models, are ideal for functional studies [2,5].
Conclusion
NAD+-histone H2BS6 serine ADP-ribosyltransferase activity (GO:0140816) is a critical chromatin modification that links NAD+ metabolism to DNA repair and transcription. Its dysregulation contributes to cancer and other diseases, making it a promising therapeutic target. Continued research using CRISPR-based models and advanced omics will further elucidate its mechanisms and clinical potential.
References
- 1. Yi X et al.. 2023. SIRT7 orchestrates melanoma progression by simultaneously promoting cell survival and immune evasion via UPR activation.. Signal Transduct Target Ther 8(1):107 PMID: 36918544
- 2. Hrychova K et al.. 2024. Dispensability of HPF1 for cellular removal of DNA single-strand breaks.. Nucleic Acids Res 52(18):10986-10998 PMID: 39162207
- 3. Tang X et al.. 2017. SIRT2 Acts as a Cardioprotective Deacetylase in Pathological Cardiac Hypertrophy.. Circulation 136(21):2051-2067 PMID: 28947430
- 4. Tian W et al.. 2025. SIRT3 mitigates osteoarthritis by suppressing ferroptosis through activating AMPK signaling pathway.. Cell Signal 135:112063 PMID: 40818538
- 5. Allam HS et al.. 2025. GSK3B directs DNA repair choice and determines tumor response to PARP1 inhibition independent of BRCA1.. J Clin Invest 135(22) PMID: 41243969
- 6. Guan R et al.. 2025. MRPL21-PARP1 axis promotes cisplatin resistance in head and neck squamous cell carcinoma by inhibiting autophagy through the PI3K/AKT/mTOR signaling pathway.. J Exp Clin Cancer Res 44(1):221 PMID: 40713706
- 7. Aussel A et al.. 2026. Tumor metabolic adaptation induced by L-asparaginase reveals a vulnerability to PARP1/2 inhibitor in B-cell lymphomas.. Nat Commun 17(1) PMID: 41760625
- 8. Huang X et al.. 2025. PARP12-mediated mono-ADP-ribosylation as a checkpoint for necroptosis and apoptosis.. Proc Natl Acad Sci U S A 122(24):e2426660122 PMID: 40489618
