GO:0031151 histone H3K79 methyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0031151 describes the enzymatic activity that transfers a methyl group from S-adenosyl-L-methionine to lysine 79 of histone H3, producing S-adenosyl-L-homocysteine and H3K79me.
• In humans, this activity is primarily carried out by DOT1L, the sole known histone H3K79 methyltransferase, which lacks a SET domain and instead adopts a class I methyltransferase fold.
• H3K79 methylation is a conserved epigenetic mark enriched in actively transcribed chromatin and is deposited co-transcriptionally.
• The activity is regulated by histone ubiquitination, phosphorylation by proline-directed kinases, and crosstalk with other histone post-translational modifications.
• DOT1L-mediated H3K79 methylation is implicated in mixed-lineage leukemia, other cancers, and epigenetic therapy resistance, making it a drug target.
• CRISPR knockout, point-mutation, knock-in, and overexpression models are essential to dissect the causal roles of H3K79 methyltransferase activity in development and disease.
Description
Histone H3K79 methyltransferase activity (GO:0031151) is a molecular function that catalyzes the transfer of a methyl group from S-adenosyl-L-methionine (SAM) to the epsilon-amino group of lysine 79 on histone H3, yielding S-adenosyl-L-homocysteine (SAH) and methylated H3K79. This activity is conserved from yeast to humans and is unique among histone lysine methyltransferases because the target residue lies within the globular core of the nucleosome rather than the flexible N-terminal tail. In humans, the principal enzyme responsible for this activity is DOT1L (disruptor of telomeric silencing 1-like), a non-SET domain methyltransferase that belongs to the class I methyltransferase superfamily. The H3K79 methylation mark deposited by this activity is associated with actively transcribed genes and is thought to influence chromatin accessibility, transcriptional elongation, and DNA damage responses. Because H3K79 methylation is dynamically regulated and frequently misregulated in leukemia and other cancers, understanding GO:0031151 is critical for both basic chromatin biology and therapeutic development. Researchers study this activity using biochemical assays, chromatin immunoprecipitation, and CRISPR-based genetic models to define its substrates, regulators, and downstream effects.
histone H3K79 methyltransferase activity At A Glance
| GO ID | GO:0031151 |
|---|---|
| GO term | histone H3K79 methyltransferase activity |
| Ontology | molecular_function |
| Synonym | histone H3K79 methylase activity; histone-H3K79 methyltransferase activity; histone lysine N-methyltransferase activity (H3-K79 specific); histone methylase activity (H3-K79 specific); histone methyltransferase activity (H3-K79 specific) |
| Major function | Catalyzes the methylation of histone H3 at lysine 79 using S-adenosyl-L-methionine as the methyl donor |
| Major enzyme | DOT1L in humans; Dot1p in yeast |
| Substrate | Histone H3 (lysine 79) and S-adenosyl-L-methionine |
| Product | Histone H3 N6-methyl-L-lysine (H3K79me) and S-adenosyl-L-homocysteine |
| Cofactor | S-adenosyl-L-methionine (SAM) as the methyl donor |
| Regulation | Regulated by histone ubiquitination, phosphorylation, and crosstalk with other histone modifications |
What Is GO:0031151?
GO:0031151, histone H3K79 methyltransferase activity, is defined as the catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 79) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 79). In other words, it is the enzymatic addition of a methyl group to the lysine residue at position 79 of the histone H3 protein, using SAM as the methyl donor. This activity is a molecular function and is distinct from other histone methyltransferase activities because of its unique substrate specificity for H3K79.
Why Is histone H3K79 methyltransferase activity Important in Cell Biology?
Histone H3K79 methyltransferase activity is essential for normal development and genome stability, and its dysregulation is directly linked to human disease. The mark it deposits, H3K79 methylation, is enriched in actively transcribed genes and is involved in transcriptional elongation, cell cycle progression, and DNA damage repair. In mixed-lineage leukemia (MLL), fusion proteins recruit DOT1L to aberrant genomic loci, leading to abnormal H3K79 methylation and leukemogenesis. Beyond leukemia, DOT1L activity has been implicated in solid tumors, fibrosis, and epigenetic therapy resistance. Because this activity is a druggable epigenetic target, understanding its mechanism and regulation is critical for developing new therapeutics.
• H3K79 methylation is a conserved epigenetic mark associated with active transcription and is deposited co-transcriptionally.
• DOT1L is the sole known histone H3K79 methyltransferase in humans, making it a unique therapeutic target.
• Aberrant DOT1L activity drives MLL-rearranged leukemia through fusion protein recruitment.
• H3K79 methylation crosstalks with histone ubiquitination and phosphorylation, integrating signaling pathways.
• DOT1L inhibitors are in clinical trials for leukemia and other cancers, highlighting the importance of this activity.
• The activity is involved in DNA damage response and cell cycle regulation, affecting genome stability.
• Dysregulation of H3K79 methylation has been linked to liver fibrosis through epigenetic activation of the NLRP3 inflammasome.
• CRISPR-based models are essential to study the causal role of H3K79 methyltransferase activity in disease.
• The activity is regulated by proline-directed kinases, connecting it to cellular signaling networks.
• Understanding this activity can inform the development of epigenetic therapies targeting histone lysine methylation.
What Happens During histone H3K79 methyltransferase activity?
Substrate recognition and binding
In simple terms: The enzyme finds and grabs the histone protein and the methyl donor.
The methyltransferase enzyme, primarily DOT1L in humans, recognizes the nucleosome core and binds to histone H3, positioning lysine 79 near the catalytic site. It also binds the cofactor S-adenosyl-L-methionine (SAM), which serves as the methyl donor. This step is influenced by the ubiquitination state of histone H2B, which can stimulate the enzyme's activity.
Methyl group transfer
In simple terms: The enzyme moves a methyl group from SAM onto the lysine.
Once bound, the enzyme catalyzes the transfer of a methyl group from SAM to the epsilon-amino group of lysine 79 on histone H3, forming S-adenosyl-L-homocysteine (SAH) and methylated H3K79. This reaction can occur in mono-, di-, or tri-methylated forms, with the degree of methylation influencing downstream readout.
Product release and chromatin modification
In simple terms: The modified histone stays in place, and the mark is read by other proteins.
After catalysis, SAH is released and the methylated H3K79 mark becomes part of the chromatin landscape. This mark is recognized by effector proteins that regulate transcription elongation and DNA repair. The presence of H3K79 methylation is associated with actively transcribed regions and can affect nucleosome dynamics.
Crosstalk with other histone modifications
In simple terms: Other chemical tags on histones can turn this enzyme up or down.
Histone ubiquitination, particularly H2B ubiquitination, stimulates Dot1 methyltransferase activity, while phosphorylation of DOT1L by proline-directed kinases can modulate its function. This crosstalk ensures that H3K79 methylation is coordinated with other chromatin events.
Key Genes Involved in GO:0031151 histone H3K79 methyltransferase activity
The following genes and proteins are central to histone H3K79 methyltransferase activity, including the enzyme itself, its regulators, and downstream effectors.
| Gene | Major Role | Research Relevance |
|---|---|---|
| DOT1L | Sole known histone H3K79 methyltransferase in humans; catalyzes H3K79 methylation | Target for leukemia and epigenetic therapy; knockout and inhibitor studies |
| H3-3A | Histone H3 variant that can be methylated at K79 | Substrate for in vitro methyltransferase assays |
| H3-3B | Histone H3 variant that can be methylated at K79 | Substrate for in vitro methyltransferase assays |
| HIST1H3A | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3B | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3C | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3D | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3E | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3F | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3G | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3H | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3I | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| HIST1H3J | Replication-dependent histone H3 | Substrate for H3K79 methylation in chromatin |
| MLLT3 | Component of MLL fusion proteins that recruit DOT1L | Model for MLL-rearranged leukemia |
| AFF1 | Component of MLL fusion proteins that recruit DOT1L | Model for MLL-rearranged leukemia |
| MLLT1 | Component of MLL fusion proteins that recruit DOT1L | Model for MLL-rearranged leukemia |
| RNF20 | E3 ubiquitin ligase that ubiquitinates H2B, stimulating Dot1 activity | Regulator of H3K79 methylation |
| RNF40 | E3 ubiquitin ligase that ubiquitinates H2B, stimulating Dot1 activity | Regulator of H3K79 methylation |
How Is histone H3K79 methyltransferase activity Regulated?
Histone H3K79 methyltransferase activity is regulated at multiple levels. Histone ubiquitination, particularly H2B ubiquitination by the RNF20/RNF40 complex, stimulates Dot1 methyltransferase activity. Phosphorylation of DOT1L by proline-directed kinases such as CDK and MAP kinases can modulate its function and stability. Additionally, crosstalk with other histone post-translational modifications, such as H3K4 methylation and H3K27 acetylation, can influence the recruitment and activity of DOT1L. These regulatory mechanisms ensure that H3K79 methylation is properly coordinated with transcription and other chromatin processes.
histone H3K79 methyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| DOT1L | MLL-rearranged leukemia | CRISPR knockout of DOT1L in leukemia cell lines; point mutation of catalytic residue |
| DOT1L | Liver fibrosis | Knockout of DOT1L in hepatocytes; overexpression of DOT1L in liver fibrosis models |
| MLLT3 | MLL-rearranged leukemia | Knock-in of MLL-AF9 fusion; CRISPR knockout of MLLT3 |
| AFF1 | MLL-rearranged leukemia | Knock-in of MLL-AF9 fusion; CRISPR knockout of AFF1 |
| RNF20 | Regulation of H3K79 methylation | Knockout of RNF20 to reduce H2B ubiquitination and H3K79 methylation |
Mixed-lineage leukemia (MLL)
In MLL-rearranged leukemia, fusion proteins recruit DOT1L to aberrant genomic loci, leading to abnormal H3K79 methylation and activation of leukemogenic gene expression programs. DOT1L inhibitors have shown efficacy in preclinical models and are being tested in clinical trials.
Solid tumors and epigenetic therapy resistance
Dysregulated H3K79 methylation has been observed in various solid tumors, and DOT1L activity can contribute to resistance to epigenetic therapies targeting histone lysine methylation. Targeting DOT1L may overcome resistance in some cancers.
Liver fibrosis
DOT1L-mediated H3K79 methylation epigenetically activates the NLRP3 inflammasome in hepatocytes, contributing to liver fibrosis through pyroptosis. This links H3K79 methyltransferase activity to inflammatory and fibrotic diseases.
Longevity and aging
Lysosomal signaling can influence the epigenome, including H3K79 methylation, to regulate longevity across generations in model organisms. This suggests a role for this activity in aging and age-related diseases.
From histone H3K79 methyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does DOT1L catalytic activity drive leukemia? | CRISPR knockout of DOT1L or point mutation of catalytic residue in MLL-rearranged cell lines |
| What is the role of H3K79 methylation in transcription? | Knock-in of H3K79A mutant histone H3 to prevent methylation |
| How does H2B ubiquitination regulate Dot1 activity? | Knockout of RNF20/RNF40 to abolish H2B ubiquitination |
| Does DOT1L overexpression promote fibrosis? | Overexpression of DOT1L in hepatocytes or liver tissue |
| Can DOT1L inhibition overcome epigenetic therapy resistance? | CRISPR knockout of DOT1L combined with epigenetic drug treatment |
| What is the effect of DOT1L phosphorylation on activity? | Point mutation of phosphorylation sites in DOT1L |
How to Study the histone H3K79 methyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| In vitro methyltransferase assay | Catalytic activity of DOT1L using SAM and histone H3 | Screening for inhibitors or testing mutant enzymes |
| ChIP-seq | Genome-wide distribution of H3K79 methylation | Mapping active chromatin and changes upon DOT1L inhibition |
| Mass spectrometry | Quantification of histone modifications including H3K79me | Detecting crosstalk and global changes |
| Western blot | Protein levels of DOT1L and H3K79me | Validating knockout or overexpression |
| CRISPR screen | Identification of genes regulating H3K79 methylation or DOT1L dependency | Discovering new therapeutic targets |
| Immunofluorescence | Nuclear localization of DOT1L and H3K79me | Visualizing chromatin changes |
| qRT-PCR | Expression of DOT1L target genes | Assessing transcriptional effects |
| Co-immunoprecipitation | Protein-protein interactions of DOT1L | Identifying regulatory complexes |
Biochemical methyltransferase assays
In vitro methyltransferase assays using recombinant DOT1L and histone H3 substrates measure the catalytic activity of H3K79 methyltransferase directly. These assays typically use radiolabeled SAM or fluorescent-coupled reactions to quantify methyl group transfer.
Chromatin immunoprecipitation (ChIP)
ChIP with antibodies specific for H3K79me2 or H3K79me3 allows mapping of the mark across the genome, revealing its association with actively transcribed genes. This method is used to assess changes in H3K79 methylation upon genetic or pharmacological perturbations.
Mass spectrometry-based proteomics
Mass spectrometry can identify and quantify histone modifications, including H3K79 methylation, in a global and site-specific manner. This approach is useful for detecting crosstalk with other modifications.
CRISPR-based genetic screens
CRISPR knockout or activation screens can identify genes that regulate H3K79 methyltransferase activity or that are required for the growth of DOT1L-dependent cancer cells. These screens provide unbiased insights into pathways that modulate this activity.
How CRISPR Can Be Used to Study GO:0031151 histone H3K79 methyltransferase activity
Knockout
CRISPR knockout of DOT1L completely abolishes histone H3K79 methyltransferase activity, providing a clean genetic model to study its loss-of-function effects in leukemia, fibrosis, and development. Knockout cell lines are used to validate inhibitor specificity and to identify pathways that compensate for loss of H3K79 methylation.
Point Mutation
Point mutations in the catalytic domain of DOT1L, such as substitution of the catalytic aspartate, can selectively eliminate methyltransferase activity without affecting protein stability or interactions. These models are valuable for distinguishing catalytic-dependent from scaffolding functions of DOT1L.
Knock-in
Knock-in of mutant histone H3 with lysine 79 substituted by alanine (H3K79A) prevents methylation at this site, allowing researchers to study the specific contribution of H3K79 methylation to chromatin function and disease. Knock-in of tagged DOT1L enables localization and interaction studies.
Overexpression
Overexpression of wild-type or mutant DOT1L in cell lines or animal models can drive aberrant H3K79 methylation and has been used to model leukemia and fibrosis. Overexpression models help define the oncogenic potential of DOT1L and test targeted therapies.
How EDITGENE Supports histone H3K79 methyltransferase activity Research
Researchers studying histone H3K79 methyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in a specific phenotype, such as leukemia cell proliferation or fibrosis. This requires precise genetic models that can knockout, mutate, knock-in, or overexpress the gene of interest. EDITGENE provides a comprehensive suite of CRISPR-based services to accelerate these studies, from custom cell line generation to high-throughput library screening and bioinformatics analysis.
Contact EDITGENE today to design your custom CRISPR model for histone H3K79 methyltransferase activity research.
Frequently Asked Questions About histone H3K79 methyltransferase activity
What is histone H3K79 methyltransferase activity?
It is the enzymatic activity that adds a methyl group to lysine 79 of histone H3, using S-adenosyl-L-methionine as the methyl donor, as defined by GO:0031151.
What genes are involved in histone H3K79 methyltransferase activity?
The primary gene is DOT1L in humans, which encodes the sole known H3K79 methyltransferase. Other genes include histone H3 variants and regulators like RNF20 and RNF40.
What is the role of DOT1L in leukemia?
DOT1L is recruited by MLL fusion proteins to aberrantly methylate H3K79, driving leukemogenic gene expression in MLL-rearranged leukemia.
How is H3K79 methylation regulated?
It is regulated by histone ubiquitination, phosphorylation of DOT1L by proline-directed kinases, and crosstalk with other histone modifications.
What diseases are associated with H3K79 methyltransferase activity?
It is associated with MLL-rearranged leukemia, solid tumors, liver fibrosis, and potentially aging-related processes.
What methods are used to study H3K79 methyltransferase activity?
Common methods include in vitro methyltransferase assays, ChIP-seq, mass spectrometry, and CRISPR-based genetic screens.
Can CRISPR be used to study H3K79 methyltransferase activity?
Yes, CRISPR knockout, point mutation, knock-in, and overexpression models are widely used to dissect the function of DOT1L and H3K79 methylation.
What is the difference between H3K79 methylation and other histone methylations?
H3K79 is located in the globular core of the nucleosome, unlike most other methylated lysines in histone tails, and its methylation is deposited by a non-SET domain enzyme.
Is DOT1L a good drug target?
Yes, DOT1L inhibitors are in clinical trials for leukemia and other cancers, and targeting DOT1L is a promising epigenetic therapy strategy.
How does H2B ubiquitination affect H3K79 methylation?
H2B ubiquitination stimulates Dot1 methyltransferase activity, linking ubiquitin signaling to H3K79 methylation.
Conclusion
Histone H3K79 methyltransferase activity (GO:0031151) is a fundamental epigenetic function carried out by DOT1L, with critical roles in transcription, development, and disease. Its unique substrate specificity and regulation by crosstalk mechanisms make it a fascinating subject for chromatin biology and a promising target for cancer therapy. Continued research using advanced CRISPR models and biochemical assays will further illuminate its mechanistic details and therapeutic potential.
References
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