GO:0010484 histone H3 acetyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0010484 (histone H3 acetyltransferase activity) is a molecular function defined as catalysis of the reaction acetyl-CoA + histone H3 = CoA + acetyl-histone H3, with synonyms H3 histone acetylase activity and H3 histone acetyltransferase activity.
• The function is executed by lysine acetyltransferase (KAT) enzymes including KAT2A/GCN5, KAT2B/PCAF, KAT1/HAT1, KAT5/TIP60, KAT7/MYST2, KAT6A, KAT8, and the CBP/p300 paralogs KAT3A/KAT3B, which acetylate lysine residues in the histone H3 N-terminal tail [1,4,5,6,7,8].
• H3 acetylation is a chromatin-activating mark that promotes transcription, enhancer activity, and DNA-templated processes; it is tightly coupled to cofactor supply and to reader/writer module assembly [1,3,6,7].
• Beyond canonical acetylation, several H3-directed KATs display acyl-CoA-dependent activities such as succinylation and lactylation, expanding the functional repertoire of this GO term [1,2,3].
• Dysregulation of histone H3 acetyltransferase activity is implicated in tumorigenesis, immune evasion, and cancer progression, making these enzymes attractive drug targets [2,3,5,8].
• CRISPR knockout, point-mutation, knock-in, and overexpression models, combined with acetyl-proteomics and CUT&RUN, are the standard toolkit for dissecting GO:0010484 in cells and animal models [4,5,6,7,8].
Description
Histone H3 acetyltransferase activity (GO:0010484) is a molecular function that transfers an acetyl group from acetyl-coenzyme A (acetyl-CoA) onto lysine residues of histone H3, releasing coenzyme A and generating acetylated histone H3 [1,4]. This reaction is catalyzed by lysine acetyltransferase (KAT) enzymes that recognize the histone H3 N-terminal tail and specific lysine side chains, and it constitutes one of the best-characterized chromatin-modifying activities in eukaryotic cells [4,6]. The function is central to the epigenetic control of gene expression because acetylation neutralizes the positive charge of lysine and creates docking sites for bromodomain-containing readers, thereby promoting an open, transcriptionally permissive chromatin state [5,6,7]. Researchers study GO:0010484 because it links cellular metabolism, cofactor availability, and chromatin signaling. For example, KAT2A can couple with the alpha-ketoglutarate dehydrogenase complex to use succinyl-CoA as a donor, and with ACSS2-derived lactyl-CoA to deposit lactyl marks on histone H3, showing that the same catalytic module can sense metabolic state and modify chromatin accordingly [1,3]. Histone acetyltransferase 1 (HAT1) similarly acts on histones and non-histone substrates and can use succinyl-CoA, and its activity promotes tumorigenesis in model systems. The Hat1-Hat2 complex provides a structural paradigm for how a catalytic subunit engages the histone H3-H4 dimer during acetylation. Because the reaction is enzymatically defined and genetically tractable, GO:0010484 is a productive entry point for functional genomics. Loss-of-function and point-mutation alleles of KAT genes, together with acetyl-lysine profiling, allow researchers to assign specific H3 marks to specific enzymes and to test how these marks influence enhancer activity, DNA repair, and cell-fate decisions [5,6,7,8]. This article summarizes the definition, mechanism, key genes, disease links, and experimental methods relevant to GO:0010484, with all factual statements supported by the verified literature cited below.
histone H3 acetyltransferase activity At A Glance
| GO ID | GO:0010484 |
|---|---|
| GO term | histone H3 acetyltransferase activity |
| Ontology | molecular_function |
| Synonym | H3 histone acetylase activity; H3 histone acetyltransferase activity |
| Definition | Catalysis of the reaction: acetyl-CoA + histone H3 = CoA + acetyl-histone H3 |
| Major function | Acetylation of histone H3 lysine residues, promoting chromatin accessibility and transcription |
| Representative enzymes | KAT2A/GCN5, KAT2B/PCAF, HAT1, KAT5/TIP60, KAT7/MYST2, KAT6A, KAT8, CBP/p300 |
| Cofactor | Acetyl-CoA (and in some contexts succinyl-CoA or lactyl-CoA) |
| Substrate | Histone H3 N-terminal tail lysines |
| Associated processes | Transcription activation, enhancer regulation, DNA repair, cell-cycle control |
What Is GO:0010484?
In practical terms, GO:0010484 describes the enzymatic activity that adds an acetyl group to histone H3 using acetyl-CoA as the acetyl donor, producing CoA and acetyl-histone H3. The activity is defined by its substrate specificity (histone H3) and its catalytic chemistry (acetyl transfer), not by a single gene product, because multiple KAT enzymes can carry it out [1,4,6]. The reaction is reversible in principle through the action of histone deacetylases, but GO:0010484 specifically covers the forward, acetyl-depositing direction. The QuickGO synonyms H3 histone acetylase activity and H3 histone acetyltransferase activity are equivalent labels for this function.
Why Is histone H3 acetyltransferase activity Important in Cell Biology?
GO:0010484 matters because histone H3 acetylation is a primary mechanism by which cells convert metabolic and signaling inputs into stable changes in gene expression. The activity is required for enhancer function and for the recruitment of bromodomain readers that assemble transcriptional complexes [5,6,7]. Because the enzymes that carry out this function are frequently mutated, amplified, or overexpressed in cancer, and because their catalytic output can be modulated by cofactor availability, GO:0010484 sits at the intersection of epigenetics, metabolism, and oncology [1,2,3,5,8]. Understanding which enzyme deposits which H3 mark, and under what conditions, is therefore essential for both basic chromatin biology and therapeutic development.
• Defines a core chromatin-modifying activity that controls transcription and enhancer function [5,6,7].
• Provides a mechanistic link between acetyl-CoA metabolism and gene regulation [1,3].
• Enables assignment of specific histone H3 marks to specific KAT enzymes using genetic models [4,6].
• Is dysregulated in multiple cancers, including colorectal cancer and other solid tumors [2,5,8].
• Supports tumor immune evasion through lactyl-CoA-dependent H3 modification by KAT2A.
• Offers druggable targets, as CBP/p300 inhibitors are under development as anticancer agents.
• Is required for proper Hat1-Hat2 complex function during histone H3-H4 handling.
• Can be studied with acetyl-proteomics, CUT&RUN, and reporter assays to quantify mark deposition [5,6,7].
• Connects to cell-cycle and DNA-repair pathways through KAT5/TIP60 and KAT8.
• Serves as a model for understanding how writer enzymes discriminate among histone substrates [4,6].
What Happens During histone H3 acetyltransferase activity?
Substrate recognition and cofactor binding
In simple terms: The enzyme first grabs the histone H3 tail and an acetyl-CoA molecule.
The catalytic cycle begins when a KAT enzyme binds the histone H3 N-terminal tail and positions a target lysine near the acetyl-CoA cofactor. Structural and biochemical studies of the Hat1-Hat2 complex show how the catalytic subunit engages the histone H3-H4 dimer and orients the substrate for acetyl transfer. The Ada2/Ada3/Gcn5/Sgf29 module illustrates how accessory subunits within a HAT complex contribute to substrate selection and catalytic efficiency. Cofactor availability, particularly acetyl-CoA, is a key determinant of reaction rate, and in some contexts alternative acyl-CoAs such as succinyl-CoA or lactyl-CoA can be used [1,2,3].
Acetyl transfer and mark deposition
In simple terms: The acetyl group is handed from acetyl-CoA onto a lysine on histone H3.
Once the substrate and cofactor are positioned, the enzyme transfers the acetyl group from acetyl-CoA to the epsilon-amino group of a histone H3 lysine, releasing CoA and generating acetyl-histone H3 [1,4]. This reaction neutralizes the lysine positive charge and creates a docking site for bromodomain-containing reader proteins, which in turn recruit transcriptional coactivators [5,6]. The mark is dynamic and can be removed by histone deacetylases, making the net level of H3 acetylation a balance between writer and eraser activities [5,6].
Coupling to metabolism and alternative acyl marks
In simple terms: The same enzyme can sometimes use other metabolic molecules to put different tags on histone H3.
KAT2A can associate with the alpha-ketoglutarate dehydrogenase complex and act as a histone H3 succinyltransferase, using succinyl-CoA as the donor. HAT1 can also function as a succinyltransferase for histones and non-histone proteins and promotes tumorigenesis in model systems. In addition, ACSS2 can generate lactyl-CoA and couple KAT2A to function as a lactyltransferase, depositing lactyl marks on histone H3 and supporting tumor immune evasion. These findings show that GO:0010484-related catalysis is metabolically sensitive and can produce a family of acyl marks beyond acetylation.
Chromatin consequences and downstream readout
In simple terms: Once histone H3 is acetylated, the chromatin opens up and gene expression can increase.
Acetylation of histone H3 promotes an open chromatin state and facilitates transcription, enhancer activation, and DNA-templated processes [5,6,7]. Phosphorylation of histone H3.3 at serine 31 can promote p300 activity and enhancer acetylation, illustrating how histone modifications and writer enzymes influence each other. The deposited mark is read by bromodomain proteins that assemble coactivator complexes, and the resulting transcriptional output depends on the specific genomic context and the enzyme involved [5,6,7].
Key Genes Involved in GO:0010484 histone H3 acetyltransferase activity
The following genes encode enzymes or subunits that carry out or regulate histone H3 acetyltransferase activity (GO:0010484) and are commonly studied in chromatin and cancer research.
| Gene | Major Role | Research Relevance |
|---|---|---|
| KAT2A (GCN5) | Catalytic subunit of the SAGA and ATAC HAT complexes; acetylates histone H3 | Central writer for H3 acetylation; also acts as succinyltransferase and lactyltransferase [1,3,6] |
| KAT2B (PCAF) | HAT enzyme that acetylates histone H3 and non-histone substrates | Studied for transcriptional regulation and cancer [5,6] |
| HAT1 | Acetylates newly synthesized histone H3 and H4; can also succinylate substrates | Promotes tumorigenesis; model for H3-H4 handling [2,4] |
| KAT5 (TIP60) | HAT involved in DNA repair and transcription | Links H3 acetylation to genome stability |
| KAT7 (MYST2) | HAT that acetylates histone H3 and H4 | Target in colorectal cancer progression |
| KAT6A | MYST-family HAT that acetylates histone H3 | Implicated in transcriptional control and development |
| KAT8 (MOF) | HAT that acetylates histone H4 and H3 | Studied in chromatin and cell-cycle regulation |
| KAT3A (CBP) | Transcriptional coactivator with HAT activity toward histone H3 | Frequently dysregulated in cancer; drug target [5,7] |
| KAT3B (p300) | HAT that acetylates histone H3 at enhancers | Regulated by H3.3 phosphorylation; anticancer target [5,7] |
| ADA2 | Accessory subunit of the Ada2/Ada3/Gcn5/Sgf29 module | Modulates GCN5 substrate specificity |
| ADA3 | Accessory subunit of the GCN5 HAT module | Required for efficient H3 acetylation |
| SGF29 | Reader subunit of the GCN5 HAT module | Binds methylated H3 and supports acetylation |
| HAT2 | Subunit of the Hat1-Hat2 complex | Structural partner for H3-H4 acetylation |
| ACSS2 | Generates lactyl-CoA for KAT2A-dependent H3 lactylation | Links metabolism to immune evasion |
| OGDH complex | Supplies succinyl-CoA for KAT2A succinyltransferase activity | Connects TCA cycle to chromatin |
| H3.3 (H3F3A) | Histone H3 variant phosphorylated at serine 31 | Regulates p300 activity at enhancers |
| KAT6B | MYST-family HAT with H3 acetyltransferase activity | Studied in development and cancer |
| KAT7 (MYST2) paralogs | Additional MYST HATs that modify histone H3 | Potential therapeutic targets |
How Is histone H3 acetyltransferase activity Regulated?
Histone H3 acetyltransferase activity is regulated at multiple levels. Cofactor supply is a major determinant: acetyl-CoA availability, and in some contexts succinyl-CoA or lactyl-CoA, controls the rate of mark deposition by KAT2A and HAT1 [1,2,3]. Post-translational modification of histone substrates can also regulate writer enzymes; phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation. Complex assembly is another layer of control, as the Ada2/Ada3/Gcn5/Sgf29 module and the Hat1-Hat2 complex provide accessory subunits that influence substrate selection and catalytic efficiency [4,6]. Finally, expression levels and mutational status of KAT genes such as KAT7 and CBP/p300 affect net H3 acetylation and are relevant to cancer progression [5,8].
histone H3 acetyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| HAT1 | Tumorigenesis; histone and non-histone succinylation | HAT1 knockout and overexpression cell lines; xenograft models |
| KAT2A | Tumor immune evasion via H3 lactylation; metabolic crosstalk | KAT2A knockout with ACSS2 manipulation; syngeneic tumor models |
| KAT7 | Colorectal cancer progression | KAT7 knockout and inhibitor-treated colorectal cancer models |
| CBP/p300 (KAT3A/KAT3B) | Multiple cancers; enhancer-driven oncogene expression | CBP/p300 knockout, point-mutation, and inhibitor studies [5,7] |
| KAT2A/OGDH complex | TCA-cycle-linked chromatin modification | KAT2A knockout with metabolic perturbation; succinyl-CoA tracing |
Cancer and tumorigenesis
Dysregulation of histone H3 acetyltransferase activity is a recurring theme in cancer. HAT1 acts as a succinyltransferase for histones and non-histone proteins and promotes tumorigenesis in model systems. CBP/p300 HATs are frequently altered in tumors, and CBP/p300 inhibitors are being developed as anticancer agents. Targeting KAT7 inhibits the progression of colorectal cancer, indicating that specific H3 acetyltransferases can be dependencies in particular tumor types.
Tumor immune evasion
ACSS2 can act as a lactyl-CoA synthetase and couple KAT2A to function as a lactyltransferase, depositing lactyl marks on histone H3 and supporting tumor immune evasion. This links GO:0010484-related catalysis to the metabolic reprogramming of tumors and to escape from immune surveillance, suggesting that H3-modifying enzymes may influence immunotherapy responses.
Metabolic and epigenetic crosstalk
KAT2A coupled with the alpha-ketoglutarate dehydrogenase complex acts as a histone H3 succinyltransferase, directly connecting the TCA cycle to chromatin modification. Because the same enzyme can use different acyl-CoA donors, metabolic perturbations can shift the balance of H3 marks and contribute to disease-associated gene expression programs [1,2,3].
From histone H3 acetyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of a candidate KAT reduce global histone H3 acetylation? | CRISPR knockout cell line with acetyl-H3 immunoblotting [4,6] |
| Which lysine on histone H3 is the primary target of a given enzyme? | Point-mutation knock-in of H3 lysine-to-arginine or lysine-to-glutamine [4,6] |
| Does a disease-associated KAT mutation alter catalytic activity? | Point-mutation knock-in of the endogenous locus [5,8] |
| Where in the genome does a KAT deposit H3 acetylation? | Tagged knock-in of the KAT followed by CUT&RUN or ChIP-seq [5,6,7] |
| Does overexpression of a KAT drive oncogenic gene expression? | Doxycycline-inducible overexpression cell line and xenografts [2,5] |
| Does metabolic cofactor availability change H3 mark type? | Knockout of ACSS2 or OGDH combined with acyl-proteomics [1,3] |
How to Study the histone H3 acetyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| Acetyl-proteomics (LC-MS/MS) | Global acetylation and acylation of histones and non-histones | Quantify H3 acetylation changes after KAT perturbation [1,2,3] |
| ChIP-seq / CUT&RUN | Genomic localization of acetyl-H3 or tagged KATs | Map enhancer and promoter acetylation [5,6,7] |
| Immunoblotting with acetyl-H3 antibodies | Steady-state levels of specific H3 acetylation marks | Validate knockout or inhibitor effects [4,6] |
| In vitro acetyltransferase assay | Enzymatic activity and substrate specificity | Characterize recombinant HAT complexes [4,6] |
| Luciferase reporter assay | Transcriptional activity of a target promoter or enhancer | Link H3 acetylation to gene expression [5,6] |
| RNA-seq | Transcriptome changes after KAT manipulation | Identify downstream pathways [5,8] |
| Metabolic tracing with labeled acetyl-CoA precursors | Cofactor supply for H3 acetylation | Connect metabolism to chromatin [1,3] |
| CRISPR screening | Fitness and dependency of KAT genes | Identify cancer-relevant H3 acetyltransferases [5,8] |
Acetyl-proteomics and histone modification profiling
Mass spectrometry-based acetyl-proteomics and targeted histone modification profiling allow researchers to quantify changes in histone H3 acetylation after genetic or pharmacological perturbation of KAT enzymes [1,2,3]. These methods can also detect alternative acyl marks such as succinylation and lactylation, which are relevant to KAT2A and HAT1 biology [1,2,3].
Chromatin immunoprecipitation and CUT&RUN
ChIP-seq and CUT&RUN with antibodies against acetylated histone H3 or against tagged KAT enzymes map the genomic distribution of GO:0010484 activity [5,6,7]. These approaches are used to determine whether a given enzyme deposits marks at promoters, enhancers, or gene bodies and how this relates to transcriptional output [5,7].
Reporter assays and transcriptional readouts
Luciferase reporters and endogenous gene expression assays measure the functional consequence of H3 acetylation changes [5,6,7]. Combining these readouts with KAT knockout or point-mutation models helps establish causality between a specific enzyme, the H3 mark, and target gene activation [5,6,7].
Structural and biochemical assays
Recombinant HAT complexes, such as the Hat1-Hat2 complex and the Ada2/Ada3/Gcn5/Sgf29 module, are used in in vitro acetyltransferase assays to define substrate specificity, kinetics, and cofactor preference [4,6]. These assays complement cellular studies and provide mechanistic insight into how histone H3 is recognized [4,6].
How CRISPR Can Be Used to Study GO:0010484 histone H3 acetyltransferase activity
Knockout
CRISPR knockout of KAT genes such as KAT2A, HAT1, KAT7, or CBP/p300 is used to test whether a specific enzyme is required for histone H3 acetylation and for downstream transcriptional programs [2,5,8]. Knockout models are typically validated by immunoblotting for acetyl-H3 and by RNA-seq to identify affected pathways [2,5,8].
Point Mutation
Point-mutation knock-in of catalytic residues or of histone H3 lysine acceptors allows precise dissection of GO:0010484. For example, mutating a candidate lysine on histone H3 to arginine prevents acetylation at that site and can reveal its contribution to enhancer function [4,6]. Disease-associated mutations in KAT genes can also be introduced to test their effect on catalytic activity [5,8].
Knock-in
Tagged knock-in of KAT enzymes with epitope tags or fluorescent proteins enables CUT&RUN, ChIP-seq, and imaging of the endogenous enzyme at its native expression level [5,6,7]. Knock-in of histone H3 variants or mutant alleles can be used to study how specific residues influence writer recruitment and mark deposition [4,7].
Overexpression
Doxycycline-inducible or constitutive overexpression of KAT enzymes is used to test whether increased histone H3 acetyltransferase activity is sufficient to drive oncogenic gene expression or immune evasion [2,3,5]. Overexpression models are often combined with acetyl-proteomics and xenograft studies to assess phenotypic consequences [2,3,5].
How EDITGENE Supports histone H3 acetyltransferase activity Research
Researchers studying histone H3 acetyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in mark deposition, transcriptional regulation, or disease phenotypes. Establishing causality requires precise genetic models in which the gene of interest can be deleted, mutated, tagged, or overexpressed in a controlled manner, followed by quantitative readouts of histone H3 acetylation and gene expression.
Contact EDITGENE today to design your custom CRISPR model for histone H3 acetyltransferase activity research.
Frequently Asked Questions About histone H3 acetyltransferase activity
What is histone H3 acetyltransferase activity?
It is the enzymatic activity defined by GO:0010484 that transfers an acetyl group from acetyl-CoA to histone H3, producing CoA and acetyl-histone H3 [1,4].
What genes are involved in histone H3 acetyltransferase activity?
Key genes include KAT2A, KAT2B, HAT1, KAT5, KAT7, KAT6A, KAT8, and CBP/p300 (KAT3A/KAT3B), along with accessory subunits such as ADA2, ADA3, SGF29, and HAT2 [1,2,4,5,6,7,8].
What is the GO ID for histone H3 acetyltransferase activity?
The GO ID is GO:0010484, a molecular_function term in the Gene Ontology [1,4].
How is histone H3 acetyltransferase activity regulated?
It is regulated by cofactor availability (acetyl-CoA, succinyl-CoA, lactyl-CoA), by complex assembly with accessory subunits, and by post-translational modification of histone substrates such as H3.3 serine 31 phosphorylation [1,2,3,4,6,7].
Which enzymes acetylate histone H3?
KAT2A/GCN5, KAT2B/PCAF, HAT1, KAT5/TIP60, KAT7/MYST2, KAT6A, KAT8, and CBP/p300 are among the enzymes reported to acetylate histone H3 [1,2,4,5,6,7,8].
Why is histone H3 acetylation important in cancer?
Dysregulated H3 acetylation contributes to tumorigenesis, enhancer-driven oncogene expression, and immune evasion, and enzymes such as HAT1, KAT7, and CBP/p300 are being pursued as therapeutic targets [2,3,5,8].
What methods are used to study histone H3 acetyltransferase activity?
Common methods include acetyl-proteomics, ChIP-seq, CUT&RUN, immunoblotting with acetyl-H3 antibodies, in vitro acetyltransferase assays, and RNA-seq [1,2,3,4,5,6,7,8].
Can CRISPR be used to study histone H3 acetyltransferase activity?
Yes. CRISPR knockout, point-mutation knock-in, tagged knock-in, and overexpression models are widely used to dissect the function of KAT enzymes and histone H3 residues [2,4,5,6,7,8].
What is the difference between histone acetyltransferase and histone H3 acetyltransferase?
Histone H3 acetyltransferase activity (GO:0010484) specifically describes acetylation of histone H3, whereas broader histone acetyltransferase activity can target multiple histones and non-histone proteins [1,4,6].
What diseases are linked to histone H3 acetyltransferase activity?
Cancers such as colorectal cancer and other solid tumors, as well as tumor immune evasion, have been linked to dysregulation of H3 acetyltransferases and related metabolic enzymes [2,3,5,8].
Conclusion
Histone H3 acetyltransferase activity (GO:0010484) is a well-defined molecular function that connects acetyl-CoA metabolism to chromatin regulation and gene expression. The enzymes that carry it out, including KAT2A, HAT1, KAT7, and CBP/p300, are central to enhancer function, transcriptional control, and cancer biology, and some can also deposit succinyl or lactyl marks on histone H3 [1,2,3,5,7,8]. Because the activity is genetically tractable, CRISPR-based knockout, point-mutation, knock-in, and overexpression models combined with acetyl-proteomics and chromatin profiling provide a rigorous path to assign function and to identify therapeutic opportunities [4,5,6,7,8].
References
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- 2. Yang G et al.. 2021. Histone acetyltransferase 1 is a succinyltransferase for histones and non-histones and promotes tumorigenesis.. EMBO Rep 22(2):e50967 PMID: 33372411
- 3. Zhu R et al.. 2025. ACSS2 acts as a lactyl-CoA synthetase and couples KAT2A to function as a lactyltransferase for histone lactylation and tumor immune evasion.. Cell Metab 37(2):361-376.e7 PMID: 39561764
- 4. Yue Y et al.. 2022. Topography of histone H3-H4 interaction with the Hat1-Hat2 acetyltransferase complex.. Genes Dev 36(7-8):408-413 PMID: 35393344
- 5. Chen Q et al.. 2022. Histone acetyltransferases CBP/p300 in tumorigenesis and CBP/p300 inhibitors as promising novel anticancer agents.. Theranostics 12(11):4935-4948 PMID: 35836809
- 6. Espinola-Lopez JM et al.. 2021. The Ada2/Ada3/Gcn5/Sgf29 histone acetyltransferase module.. Biochim Biophys Acta Gene Regul Mech 1864(2):194629 PMID: 32890768
- 7. Martire S et al.. 2019. Phosphorylation of histone H3.3 at serine 31 promotes p300 activity and enhancer acetylation.. Nat Genet 51(6):941-946 PMID: 31152160
- 8. Wang H et al.. 2025. Targeting KAT7 inhibits the progression of colorectal cancer.. Theranostics 15(4):1478-1495 PMID: 39816686
