GO:0140955 histone H3K36 trimethyltransferase activity: Mechanism, Genes and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:0140955 describes the enzymatic activity that adds three methyl groups to lysine 36 of histone H3, producing the H3K36me3 mark.
• SETD2 is the primary histone H3K36 trimethyltransferase in humans, and its loss reduces H3K36me3 globally.
• H3K36me3 is recognized by reader proteins such as MutSα and is linked to DNA mismatch repair and double-strand break repair pathway choice.
• Oncohistone mutations such as H3K36M and H3G34V/R/D inhibit or block H3K36 methylation, contributing to tumorigenesis.
• SETD2 deficiency drives autoimmune, fibrotic, and malignant phenotypes in preclinical models.
• CRISPR knockout, point-mutation, and knock-in models are essential to dissect the causal roles of H3K36 trimethyltransferase activity in disease.
Description
Histone H3 lysine 36 trimethylation (H3K36me3) is a chromatin mark associated with active transcription and DNA repair. The enzyme responsible for depositing this mark is histone H3K36 trimethyltransferase, encoded by the GO term GO:0140955. This activity catalyzes the successive transfer of three methyl groups from S-adenosyl-L-methionine to lysine 36 of histone H3, yielding H3K36me3 and S-adenosyl-L-homocysteine. Researchers study this term because H3K36me3 is critical for transcriptional fidelity, splicing, and genome stability, and its dysregulation is implicated in cancer, autoimmune diseases, and fibrosis. Understanding the molecular players and regulatory mechanisms of H3K36 trimethyltransferase activity is therefore essential for both basic chromatin biology and translational medicine.
histone H3K36 trimethyltransferase activity At A Glance
| GO ID | GO:0140955 |
|---|---|
| GO term | histone H3K36 trimethyltransferase activity |
| Ontology | molecular_function |
| Synonym | histone H3K36 mono/di/trimethylase activity; histone H3K36 trimethylase activity; histone H3-K36 trimethylation; histone H3K36 trimethylation; histone lysine N-trimethyltransferase activity (H3-K36 specific) |
| Major function | Catalyzes the addition of three methyl groups to histone H3 lysine 36, forming H3K36me3 |
| Cofactor | S-adenosyl-L-methionine (SAM) as methyl donor |
| Reaction product | H3K36me3 and S-adenosyl-L-homocysteine |
| Primary enzyme | SETD2 (SET domain containing 2) in humans |
What Is GO:0140955?
GO:0140955 is a molecular function term defined as the catalysis of the reaction: L-lysyl36-[histone H3] + 3 S-adenosyl-L-methionine = 3 H+ + N6,N6,N6-trimethyl-L-lysyl36-[histone H3] + 3 S-adenosyl-L-homocysteine. In simpler terms, it is the enzyme activity that adds three methyl groups to the lysine residue at position 36 of histone H3, producing the trimethylated form known as H3K36me3.
Why Is histone H3K36 trimethyltransferase activity Important in Cell Biology?
Histone H3K36 trimethyltransferase activity is central to epigenetic regulation because H3K36me3 serves as a docking site for reader proteins that control transcription elongation, RNA splicing, and DNA repair. Loss of this activity leads to genome instability and altered gene expression, which can drive cancer, autoimmune disorders, and fibrosis. Thus, measuring and manipulating H3K36 trimethyltransferase activity is vital for understanding disease mechanisms and developing targeted therapies.
• H3K36me3 is a hallmark of actively transcribed gene bodies and is required for transcriptional fidelity.
• SETD2-mediated H3K36me3 recruits MutSα to chromatin, linking the mark to DNA mismatch repair.
• H3K36me3 influences DNA double-strand break repair pathway choice.
• Loss of SETD2 and H3K36me3 promotes Kras-induced pancreatic acinar-to-ductal metaplasia and epithelial-mesenchymal transition.
• SETD2 deficiency in T cells leads to autoimmune diseases via phospholipid remodeling.
• SETD2 loss in the absence of VHL promotes renal fibrosis through TGF-β/Smad signaling.
• Oncohistone H3K36M inhibits NSD2 and activates a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer.
• H3G34V/R/D mutations block H3K36 methylation and disrupt H3K36me3-MutSα interaction.
• SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis.
• H3K36 trimethyltransferase activity is a potential therapeutic target in cancers with SETD2 mutations.
What Happens During histone H3K36 trimethyltransferase activity?
Substrate recognition and binding
In simple terms: The enzyme first finds and binds to histone H3.
The trimethyltransferase enzyme, primarily SETD2, recognizes the histone H3 tail and binds to it in a sequence-specific manner. This interaction positions lysine 36 (K36) within the active site for methylation.
Successive methyl group transfer
In simple terms: The enzyme adds three methyl groups one by one to the same lysine.
Using S-adenosyl-L-methionine (SAM) as the methyl donor, the enzyme catalyzes three sequential methylation reactions: first to monomethylated H3K36me1, then dimethylated H3K36me2, and finally trimethylated H3K36me3. Each step releases S-adenosyl-L-homocysteine (SAH).
Formation of H3K36me3 mark
In simple terms: The final product is a trimethylated mark on histone H3.
The end product, H3K36me3, remains on the histone and serves as a binding platform for reader proteins such as MutSα and other chromatin modifiers.
Recruitment of reader proteins
In simple terms: Other proteins read the mark and carry out downstream functions.
H3K36me3 is recognized by proteins containing PWWP, Tudor, or chromodomains. For example, MutSα binds H3K36me3 to facilitate DNA mismatch repair, and this interaction is disrupted by H3G34 mutations. The mark also influences double-strand break repair pathway choice.
Key Genes Involved in GO:0140955 histone H3K36 trimethyltransferase activity
The following genes encode enzymes, reader proteins, and regulatory factors directly linked to histone H3K36 trimethyltransferase activity.
| Gene | Major Role | Research Relevance |
|---|---|---|
| SETD2 | Primary histone H3K36 trimethyltransferase | Most studied enzyme for H3K36me3; loss causes cancer, autoimmune, and fibrotic phenotypes |
| NSD1 | Histone H3K36 methyltransferase (mono/di) | Contributes to H3K36me2, which can be substrate for SETD2; inhibited by H3K36M |
| NSD2 | Histone H3K36 methyltransferase (di) | Inhibited by H3K36M oncohistone; involved in antiviral-like immune response |
| NSD3 | Histone H3K36 methyltransferase | Potential redundant roles in H3K36 methylation; less studied |
| ASH1L | Histone H3K36 methyltransferase | Implicated in transcriptional regulation; context-dependent |
| SETMAR | Histone H3K36 methyltransferase | Fusion protein with methyltransferase activity; role in DNA repair |
| H3-3A (H3F3A) | Histone H3 variant | Mutations at G34 block H3K36 methylation and disrupt MutSα binding |
| H3C1 (HIST1H3A) | Histone H3 | K36M mutation inhibits H3K36 trimethylation and drives tumorigenesis |
| MUTSα (MSH2/MSH6) | Reader of H3K36me3 | Binds H3K36me3 for mismatch repair; interaction blocked by H3G34V/R/D |
| MSH2 | Component of MutSα | Required for H3K36me3-mediated mismatch repair |
| MSH6 | Component of MutSα | Required for H3K36me3-mediated mismatch repair |
| TP53 | Tumor suppressor | Cooperates with SETD2 loss in tumorigenesis |
| KRAS | Oncogene | SETD2 loss promotes KRAS-driven pancreatic and lung cancer |
| VHL | Tumor suppressor | SETD2 deficiency promotes renal fibrosis in VHL-absent context |
| SMAD2/3 | TGF-β signaling effectors | Mediate SETD2-deficiency-induced renal fibrosis |
| POLR2A | RNA polymerase II subunit | Interacts with H3K36me3 during transcription elongation |
| BRCA1 | DNA repair protein | Involved in repair pathway choice influenced by H3K36me3 |
| 53BP1 | DNA repair protein | Involved in repair pathway choice influenced by H3K36me3 |
How Is histone H3K36 trimethyltransferase activity Regulated?
Histone H3K36 trimethyltransferase activity is regulated at multiple levels. SETD2 recruitment to chromatin is coupled to RNA polymerase II elongation, and its activity can be modulated by interacting proteins and post-translational modifications. The oncohistone H3K36M inhibits NSD2 and other H3K36 methyltransferases, leading to global loss of H3K36me3 and activation of a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer. Additionally, H3G34V/R/D mutations block H3K36 methylation and disrupt the interaction between H3K36me3 and MutSα. These examples illustrate how genetic alterations in histones and regulatory proteins can directly impact H3K36 trimethyltransferase activity.
histone H3K36 trimethyltransferase activity and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| SETD2 | Pancreatic cancer, lung cancer, renal fibrosis, autoimmune diseases | Conditional knockout mouse models, CRISPR KO cell lines |
| H3-3A (H3F3A) | Giant cell tumor of bone, pediatric glioblastoma | Point mutation knock-in (G34V/R/D) in cell lines |
| H3C1 (HIST1H3A) | Chondroblastoma, lung cancer | Point mutation knock-in (K36M) in cell lines |
| KRAS | Pancreatic and lung cancer | Oncogenic KRAS knock-in with SETD2 KO |
| VHL | Renal cell carcinoma and fibrosis | VHL KO with SETD2 KO in renal cells |
Cancer
SETD2 loss and H3K36me3 depletion are frequent in renal cell carcinoma, lung cancer, and pancreatic cancer. In pancreatic carcinogenesis, loss of Setd2 promotes Kras-induced acinar-to-ductal metaplasia and epithelial-mesenchymal transition. In lung cancer, SETD2 regulates chromatin accessibility and transcription to suppress tumorigenesis. Oncohistone H3K36M inhibits NSD2 and activates a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer. H3G34V/R/D mutations block H3K36 methylation and disrupt H3K36me3-MutSα interaction, contributing to mutagenesis.
Autoimmune diseases
Methyltransferase Setd2 prevents T cell-mediated autoimmune diseases via phospholipid remodeling. Loss of Setd2 in T cells leads to autoimmune phenotypes, highlighting the importance of H3K36me3 in immune regulation.
Renal fibrosis
SETD2 deficiency promotes renal fibrosis through the TGF-β/Smad signalling pathway in the absence of VHL. This suggests that H3K36 trimethyltransferase activity is protective against fibrotic remodeling in the kidney.
From histone H3K36 trimethyltransferase activity-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| Does loss of SETD2 affect H3K36me3 levels and gene expression? | SETD2 knockout cell lines (e.g., HEK293T, HeLa) |
| Does H3K36M mutation inhibit H3K36 trimethyltransferase activity? | H3K36M point mutation knock-in cell lines |
| Does H3G34V mutation block H3K36 methylation and MutSα binding? | H3G34V knock-in cell lines |
| Does SETD2 deficiency promote renal fibrosis? | SETD2 conditional knockout mouse with VHL deletion |
| Does Setd2 loss in T cells cause autoimmune disease? | T cell-specific Setd2 knockout mouse |
| Does SETD2 loss cooperate with KRAS to drive pancreatic cancer? | KrasG12D; Setd2 knockout mouse model |
How to Study the histone H3K36 trimethyltransferase activity Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ChIP-seq | Genome-wide H3K36me3 enrichment | Mapping active transcription and SETD2 targets |
| Western blot | Global H3K36me3 protein levels | Validating SETD2 knockout or overexpression |
| Immunofluorescence | Nuclear H3K36me3 pattern | Assessing changes in chromatin marks |
| Mass spectrometry | Histone modification stoichiometry | Detecting oncohistone effects |
| RNA-seq | Transcriptional changes | Linking H3K36me3 loss to gene expression |
| CRISPR screen | Gene essentiality and modifier identification | Discovering regulators of H3K36me3 |
| ATAC-seq | Chromatin accessibility | Assessing SETD2-dependent chromatin state |
| Co-immunoprecipitation | Protein-protein interactions | Studying H3K36me3 reader proteins |
Chromatin immunoprecipitation sequencing (ChIP-seq)
ChIP-seq using anti-H3K36me3 antibodies measures the genome-wide distribution of H3K36me3, providing a readout of histone H3K36 trimethyltransferase activity.
Western blot and immunofluorescence
Western blot with anti-H3K36me3 antibodies quantifies global H3K36me3 levels, while immunofluorescence can visualize nuclear patterns in cells.
Mass spectrometry
Mass spectrometry can detect and quantify histone modifications, including H3K36me3, and identify changes in response to genetic perturbations.
CRISPR-based genetic screens
CRISPR knockout screens targeting epigenetic modifiers can identify genes that regulate H3K36me3 levels and associated phenotypes.
How CRISPR Can Be Used to Study GO:0140955 histone H3K36 trimethyltransferase activity
Knockout
CRISPR knockout of SETD2 or other H3K36 methyltransferases eliminates enzyme activity, leading to loss of H3K36me3 and enabling functional studies in cancer and autoimmune models.
Point Mutation
Point mutation knock-in of H3K36M or H3G34V/R/D in histone genes mimics oncohistone mutations that inhibit H3K36 trimethyltransferase activity and disrupt reader interactions.
Knock-in
Knock-in of tagged SETD2 or reporter constructs allows tracking of enzyme localization and activity in live cells.
Overexpression
Overexpression of SETD2 or other H3K36 methyltransferases can elevate H3K36me3 levels and test sufficiency in suppressing tumorigenic phenotypes.
How EDITGENE Supports histone H3K36 trimethyltransferase activity Research
Researchers studying histone H3K36 trimethyltransferase activity-related genes often need to determine whether a candidate gene is causally involved in H3K36me3 deposition, chromatin regulation, or disease phenotypes. EDITGENE provides custom CRISPR cell models and screening services to accelerate this discovery.
Contact EDITGENE today to design your custom CRISPR model for histone H3K36 trimethyltransferase activity research.
Frequently Asked Questions About histone H3K36 trimethyltransferase activity
What is histone H3K36 trimethyltransferase activity?
It is the enzymatic activity that adds three methyl groups to lysine 36 of histone H3, producing H3K36me3, as defined by GO:0140955.
What genes are involved in histone H3K36 trimethyltransferase activity?
The primary gene is SETD2, but NSD1, NSD2, NSD3, ASH1L, and SETMAR also have H3K36 methyltransferase activity.
Which enzyme catalyzes H3K36me3 formation?
SETD2 is the major histone H3K36 trimethyltransferase in humans.
What diseases are associated with loss of H3K36 trimethyltransferase activity?
Loss is linked to pancreatic cancer, lung cancer, renal fibrosis, and autoimmune diseases.
How is H3K36me3 detected in the lab?
Common methods include ChIP-seq, Western blot, immunofluorescence, and mass spectrometry.
What is the role of H3K36me3 in DNA repair?
H3K36me3 recruits MutSα for mismatch repair and influences double-strand break repair pathway choice.
What are oncohistone mutations affecting H3K36 methylation?
H3K36M and H3G34V/R/D are oncohistone mutations that inhibit H3K36 trimethylation or block reader binding.
Can CRISPR be used to study H3K36 trimethyltransferase activity?
Yes, CRISPR knockout, point mutation knock-in, and overexpression models are widely used to dissect its function.
What is the relationship between SETD2 and H3K36me3?
SETD2 deposits H3K36me3, and its loss leads to global reduction of this mark.
Why is H3K36me3 important for transcription?
H3K36me3 is associated with active gene bodies and helps maintain transcriptional fidelity.
Conclusion
Histone H3K36 trimethyltransferase activity, defined by GO:0140955, is a critical epigenetic function mediated primarily by SETD2. It deposits H3K36me3, a mark essential for transcription, DNA repair, and cellular differentiation. Dysregulation of this activity contributes to cancer, autoimmune diseases, and fibrosis, making it a compelling target for basic and translational research. CRISPR-based models and advanced sequencing methods continue to unravel its mechanistic roles and therapeutic potential.
References
- 1. Chen Y et al.. 2024. Methyltransferase Setd2 prevents T cell-mediated autoimmune diseases via phospholipid remodeling.. Proc Natl Acad Sci U S A 121(8):e2314561121 PMID: 38359295
- 2. Niu N et al.. 2020. Loss of Setd2 promotes Kras-induced acinar-to-ductal metaplasia and epithelia-mesenchymal transition during pancreatic carcinogenesis.. Gut 69(4):715-726 PMID: 31300513
- 4. Gladstein AC et al.. 2025. The H3 (K36M) oncohistone inhibits NSD2 to activate a SETD2-dependent antiviral-like immune response in KRAS-driven lung cancer.. bioRxiv PMID: 40501771
- 5. Xie Y et al.. 2023. SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis.. JCI Insight 8(4) PMID: 36810256
- 6. Fang J et al.. 2018. Cancer-driving H3G34V/R/D mutations block H3K36 methylation and H3K36me3-MutSα interaction.. Proc Natl Acad Sci U S A 115(38):9598-9603 PMID: 30181289
- 7. Liu C et al.. 2023. SETD2 deficiency promotes renal fibrosis through the TGF-β/Smad signalling pathway in the absence of VHL.. Clin Transl Med 13(11):e1468 PMID: 37933774
- 8. Clouaire T et al.. 2015. DNA double strand break repair pathway choice: a chromatin based decision?. Nucleus 6(2):107-13 PMID: 25675367
