GO:1990352 BRE1 E3 ubiquitin ligase complex: Components, Assembly and Research Methods
Research-grade guide for scientists and biopharma professionals
Key Takeaways
• GO:1990352 describes the BRE1 E3 ubiquitin ligase complex, a homodimeric complex built around the BRE1/RNF20-RNF40 E3 ligase that monoubiquitinates histone H2B.
• The complex is recruited to active genes and regulates RNA polymerase II association, coupling transcription to histone modification.
• BRE1 works with the E2 conjugating enzyme Rad6 to catalyze H2B monoubiquitination, a prerequisite for H3K4 and H3K79 methylation.
• Loss of mammalian BRE1 (RNF20/RNF40) causes replication stress and chromosomal instability, linking the complex to genome maintenance.
• Structural studies have revealed how Bre1 dimerizes and engages Lge1/WAC to coordinate H2B ubiquitination.
• The complex has emerging roles beyond chromatin, including mitochondrial function and innate immune regulation.
Description
The BRE1 E3 ubiquitin ligase complex (GO:1990352) is a cellular component defined as a homodimeric protein complex composed of the E3 ubiquitin-protein ligase BRE1, which plays a role in regulating the association of RNA polymerase II with active genes. In budding yeast, Bre1 was originally identified as an E3 ligase required for recruitment and substrate selection of the E2 enzyme Rad6 at promoters, establishing a direct link between the ubiquitination machinery and transcriptional activation. The complex is conserved in mammals, where the orthologous RNF20/RNF40 complex performs similar functions in histone H2B monoubiquitination. Mechanistically, the BRE1 complex catalyzes the attachment of a single ubiquitin moiety to histone H2B at lysine 123 in yeast (or the equivalent residue in mammals), a modification that serves as a prerequisite for downstream methylation of H3K4 and H3K79. This cascade of histone modifications is critical for proper gene expression, and disruption of the complex leads to defects in transcription elongation, replication-coupled processes, and genome stability. Recent structural work has illuminated how Bre1 homodimers coordinate with accessory factors such as Lge1 in yeast and WAC in mammals to achieve efficient H2B ubiquitination. For researchers, GO:1990352 provides a precise annotation for studying the composition, assembly, and regulation of this conserved ubiquitin ligase module. The complex sits at the intersection of chromatin biology, DNA replication, and disease pathways, making it a compelling target for functional genomics and therapeutic exploration.
BRE1 E3 ubiquitin ligase complex At A Glance
| GO ID | GO:1990352 |
|---|---|
| GO term | BRE1 E3 ubiquitin ligase complex |
| Ontology | cellular_component |
| Synonym | BRE1 E3 ubiquitin-protein ligase complex; BRE1 oligomer |
| Major function | E3 ubiquitin ligase activity toward histone H2B; regulation of RNA polymerase II association with active genes |
| Composition | Homodimer of BRE1 (yeast) or RNF20/RNF40 heterodimer (mammals) |
| Associated E2 enzyme | Rad6 (yeast) / RAD6A/RAD6B (mammals) |
| Key substrate | Histone H2B (monoubiquitination) |
| Conservation | Conserved from yeast to humans |
What Is GO:1990352?
GO:1990352, the BRE1 E3 ubiquitin ligase complex, is a cellular component consisting of a homodimer of the BRE1 protein, which functions as an E3 ubiquitin-protein ligase. This complex is involved in regulating the association of RNA polymerase II with actively transcribed genes. The term is synonymous with BRE1 E3 ubiquitin-protein ligase complex and BRE1 oligomer, reflecting its dimeric architecture and catalytic activity.
Why Is BRE1 E3 ubiquitin ligase complex Important in Cell Biology?
The BRE1 E3 ubiquitin ligase complex is essential for epigenetic regulation because it catalyzes histone H2B monoubiquitination, a modification that primes chromatin for subsequent methylation events and influences transcription elongation. Its role in coupling sister chromatid cohesion to DNA replication highlights its importance in genome stability. In mammals, deficiency of the complex leads to replication stress and chromosomal instability, underscoring its relevance to cancer biology. Beyond chromatin, emerging evidence links BRE1 to mitochondrial function and innate immunity, expanding its physiological significance.
• Catalyzes histone H2B monoubiquitination, a prerequisite for H3K4 and H3K79 methylation.
• Regulates RNA polymerase II association with active genes, impacting transcription.
• Couples sister chromatid cohesion establishment to DNA replication.
• Deficiency causes replication stress and chromosomal instability in mammalian cells.
• Implicated in cancer through RNF20/RNF40 loss.
• Plays a protective role in mitochondrial function and energy metabolism in Parkinson's disease models.
• Participates in innate immune response regulation via a Toll-dependent feedback loop.
• Conserved from yeast to humans, enabling cross-species mechanistic studies.
• Structural insights inform drug discovery targeting the complex.
• Serves as a model for studying E3 ligase-substrate selection.
BRE1 E3 ubiquitin ligase complex: Components, Assembly and Research Methods
What Happens During BRE1 E3 ubiquitin ligase complex?
In simple terms: The BRE1 complex acts as a molecular tagger that marks histones to control gene activity.
The BRE1 E3 ubiquitin ligase complex functions primarily in the nucleus, where it monoubiquitinates histone H2B. This modification is a key step in a signaling cascade that leads to methylation of histones H3K4 and H3K79, which are associated with active transcription. The complex is recruited to promoters and coding regions of active genes, where it regulates the association of RNA polymerase II, thereby influencing transcription elongation. In yeast, Bre1 couples this histone modification to sister chromatid cohesion during DNA replication, ensuring proper chromosome segregation.
Structure and Composition of BRE1 E3 ubiquitin ligase complex
In simple terms: The complex is made of two BRE1 proteins joined together, forming a homodimer.
The BRE1 E3 ubiquitin ligase complex is a homodimeric protein complex composed of the E3 ubiquitin-protein ligase BRE1. In Saccharomyces cerevisiae, Bre1 forms a homodimer and interacts with the E2 enzyme Rad6 to catalyze ubiquitin transfer. In mammals, the complex is a heterodimer of RNF20 and RNF40, which are orthologs of yeast Bre1. Structural studies have revealed that Bre1 dimerization is critical for its function and that it interacts with accessory proteins such as Lge1 in yeast and WAC in mammals to coordinate H2B ubiquitination.
Molecular Mechanism of BRE1 E3 ubiquitin ligase complex
In simple terms: BRE1 helps attach a small protein called ubiquitin to histones, which acts like a switch for gene expression.
The catalytic mechanism of the BRE1 complex involves the transfer of ubiquitin from the E2 enzyme Rad6 to histone H2B. Bre1 acts as a scaffold that recruits Rad6 to specific promoters and selects the substrate, ensuring monoubiquitination rather than polyubiquitination. Recent structural and biochemical studies have shown that Bre1 dimerization and its interaction with Lge1/WAC are essential for efficient ubiquitin transfer. The modification of H2B then serves as a platform for the recruitment of methyltransferases that deposit H3K4me and H3K79me, further modulating chromatin structure.
Regulation of BRE1 E3 ubiquitin ligase complex
In simple terms: The activity of the BRE1 complex is controlled by other proteins and signals to ensure it acts at the right time and place.
The BRE1 complex is regulated at multiple levels. Its recruitment to chromatin is dependent on transcriptional activators and the phosphorylation state of Bre1. In yeast, the complex is cell-cycle regulated, with peak activity during S phase to coordinate cohesion with replication. In mammals, the RNF20/RNF40 complex is regulated by interactions with WAC and other factors that modulate its stability and activity. Additionally, a Toll-dependent feedback loop controls Bre1/Rad6 expression in the context of innate immunity.
Key Genes Involved in GO:1990352 BRE1 E3 ubiquitin ligase complex
The following genes and proteins are key components or regulators of the BRE1 E3 ubiquitin ligase complex and its associated pathways.
| Gene | Major Role | Research Relevance |
|---|---|---|
| BRE1 (yeast) | E3 ubiquitin ligase; core component of the complex | Model for studying H2B ubiquitination and transcription |
| RNF20 (human) | E3 ubiquitin ligase; mammalian ortholog of Bre1 | Implicated in cancer and genome stability |
| RNF40 (human) | E3 ubiquitin ligase; partner of RNF20 | Forms heterodimer with RNF20; cancer relevance |
| RAD6 (yeast) | E2 ubiquitin-conjugating enzyme | Essential for Bre1-mediated H2B ubiquitination |
| RAD6A (human) | E2 ubiquitin-conjugating enzyme | Mammalian counterpart of Rad6 |
| RAD6B (human) | E2 ubiquitin-conjugating enzyme | Mammalian counterpart of Rad6 |
| LGE1 (yeast) | Accessory factor for Bre1 | Required for efficient H2B ubiquitination |
| WAC (human) | Accessory factor for RNF20/RNF40 | Regulates H2B ubiquitination and complex stability |
| H2B (histone) | Substrate of Bre1-mediated ubiquitination | Key chromatin modification linked to transcription |
| H3 (histone) | Downstream methylation target | H3K4 and H3K79 methylation depend on H2B ubiquitination |
| RNA polymerase II | Transcription machinery | Association with active genes regulated by Bre1 |
| CACT (Drosophila) | Immune signaling regulator | Bre1/Rad6-cact feedback loop in innate immunity |
| Parkin (Drosophila) | Mitochondrial function | Bre1 protective role in Parkinson's models |
| PINK1 (Drosophila) | Mitochondrial function | Bre1 protective role in Parkinson's models |
| Rad6 (Drosophila) | E2 enzyme | Partner of Bre1 in immune and mitochondrial contexts |
| Bre1 (Drosophila) | E3 ligase | Studied in Parkinson's and immunity models |
| RNF20/RNF40 (mouse) | Mammalian complex | Knockout models show replication stress |
How Is BRE1 E3 ubiquitin ligase complex Regulated?
The BRE1 E3 ubiquitin ligase complex is regulated by cell cycle cues, transcriptional activators, and protein-protein interactions. In yeast, Bre1 recruitment to promoters is dependent on transcriptional activation and is coupled to DNA replication to ensure sister chromatid cohesion. In mammals, the RNF20/RNF40 complex interacts with WAC, which is required for efficient H2B ubiquitination and complex stability. Additionally, a Toll-dependent feedback loop controls Bre1/Rad6 expression during innate immune responses.
BRE1 E3 ubiquitin ligase complex and Human Disease
| Gene | Disease / Biology | Potential Experimental Model |
|---|---|---|
| RNF20/RNF40 | Cancer, replication stress, chromosomal instability | RNF20/RNF40 knockout cell lines |
| Bre1 (Drosophila) | Parkinson's disease, mitochondrial dysfunction | Drosophila models with Bre1 knockout or overexpression |
| Bre1/Rad6 (Drosophila) | Innate immune response | Drosophila genetic models with Toll pathway activation |
| BRE1 (yeast) | Sister chromatid cohesion defects | Yeast mutants and cohesion assays |
| RAD6 (yeast) | Defective H2B ubiquitination | Yeast rad6 mutants |
Cancer and Genome Instability
Deficiency in the mammalian BRE1 complex components RNF20/RNF40 leads to replication stress and chromosomal instability, hallmarks of cancer. Loss of RNF20/RNF40 function has been observed in various cancers, suggesting a tumor suppressor role. The complex's involvement in DNA replication and repair pathways makes it a potential target for cancer therapy.
Neurodegeneration
In Drosophila models of Parkinson's disease, Bre1 plays a protective role in mitochondrial function and energy metabolism. This suggests that the BRE1 complex may have neuroprotective functions beyond its canonical chromatin role, potentially linking epigenetic regulation to mitochondrial health.
Innate Immunity
A Toll-dependent Bre1/Rad6-cact feedback loop controls host innate immune responses, indicating that the BRE1 complex is involved in immune signaling. This expands the physiological roles of the complex beyond chromatin regulation.
From BRE1 E3 ubiquitin ligase complex-Related Genes to Experimental Models
| Research Question | Suitable Model |
|---|---|
| What is the role of BRE1 in transcription? | Knockout of BRE1 in yeast or mammalian cells followed by RNA-seq |
| How does BRE1 affect histone modifications? | Point mutations in catalytic residues of BRE1 |
| What are the interaction partners of BRE1? | Knock-in of tagged BRE1 for proteomics |
| Does BRE1 overexpression affect genome stability? | Overexpression of RNF20/RNF40 in mammalian cells |
| What is the role of BRE1 in immunity? | Knockout of Bre1 in Drosophila immune models |
| How does BRE1 protect mitochondria? | Overexpression or knockout of Bre1 in Parkinson's disease models |
How to Study the BRE1 E3 ubiquitin ligase complex Process
| Method | What It Measures | Typical Application |
|---|---|---|
| ChIP-seq | Genomic binding sites of BRE1 complex | Mapping recruitment to active genes |
| In vitro ubiquitination | Catalytic activity and substrate specificity | Mechanistic studies of H2B ubiquitination |
| Cryo-EM | 3D structure of the complex | Understanding assembly and interactions |
| CRISPR knockout screens | Genetic dependencies and pathways | Identifying synthetic lethal interactions |
| RNA-seq | Transcriptional changes upon BRE1 loss | Assessing impact on gene expression |
| Proteomics | Interaction partners of BRE1 | Identifying accessory factors like WAC |
| Cohesion assays | Sister chromatid cohesion | Linking BRE1 to replication |
| Mitochondrial function assays | Energy metabolism and ROS | Studying Bre1 in Parkinson's models |
Chromatin Immunoprecipitation (ChIP)
ChIP assays using antibodies against BRE1 or its subunits can map the genomic binding sites of the complex. ChIP followed by sequencing (ChIP-seq) has been used to show that Bre1 localizes to active genes and regulates RNA polymerase II association.
Ubiquitination Assays
In vitro ubiquitination assays with purified Bre1, Rad6, and histone substrates can measure the catalytic activity of the complex. Such assays have been instrumental in defining the enzymatic mechanism and substrate specificity.
Structural Biology
Cryo-EM and X-ray crystallography have provided insights into the architecture of the Bre1 complex and its interactions with Lge1/WAC. These studies reveal how dimerization and accessory factors coordinate H2B ubiquitination.
Genome-wide Screens
CRISPR knockout screens targeting BRE1 complex components can identify genetic interactions and pathways that depend on the complex. Such screens have been used to link RNF20/RNF40 to replication stress responses.
How CRISPR Can Be Used to Study GO:1990352 BRE1 E3 ubiquitin ligase complex
Knockout
CRISPR knockout of BRE1 or its mammalian orthologs RNF20/RNF40 can abolish H2B ubiquitination and lead to replication stress, making it a powerful tool to study the complex's role in genome stability. Knockout models in yeast have been used to dissect cohesion defects.
Point Mutation
Introducing point mutations in the catalytic domain of BRE1 can separate its ligase activity from scaffolding functions. Such mutants have been used to show that H2B ubiquitination is essential for downstream H3 methylation.
Knock-in
Knock-in of epitope-tagged BRE1 allows for affinity purification and proteomic identification of interacting proteins, such as Lge1 and WAC. Tagged knock-in models also enable live-cell imaging of complex dynamics.
Overexpression
Overexpression of RNF20/RNF40 can enhance H2B ubiquitination and may protect against replication stress. Overexpression studies in Drosophila have revealed a protective role for Bre1 in mitochondrial function.
How EDITGENE Supports BRE1 E3 ubiquitin ligase complex Research
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Frequently Asked Questions About BRE1 E3 ubiquitin ligase complex
What is the BRE1 E3 ubiquitin ligase complex?
The BRE1 E3 ubiquitin ligase complex (GO:1990352) is a homodimeric protein complex composed of the E3 ubiquitin-protein ligase BRE1. It monoubiquitinates histone H2B and regulates RNA polymerase II association with active genes.
What genes are involved in the BRE1 E3 ubiquitin ligase complex?
Key genes include BRE1 (yeast) and its mammalian orthologs RNF20 and RNF40, as well as the E2 enzyme Rad6 (RAD6A/RAD6B in humans) and accessory factors like LGE1 and WAC.
What is the function of BRE1 in histone modification?
BRE1 catalyzes the monoubiquitination of histone H2B, which is a prerequisite for subsequent methylation of H3K4 and H3K79, thereby influencing transcription.
How is the BRE1 complex linked to cancer?
Deficiency in mammalian BRE1 components RNF20/RNF40 leads to replication stress and chromosomal instability, which are hallmarks of cancer.
What is the role of Bre1 in Parkinson's disease?
In Drosophila models, Bre1 plays a protective role in mitochondrial function and energy metabolism, suggesting a link to Parkinson's disease.
How does the BRE1 complex regulate RNA polymerase II?
The complex is recruited to active genes where it modifies histones, thereby regulating the association of RNA polymerase II with chromatin.
What are the structural features of the BRE1 complex?
The complex is a homodimer of Bre1 in yeast, while mammals have a heterodimer of RNF20/RNF40. Structural studies show interactions with Lge1/WAC are critical for function.
What experimental models are used to study BRE1?
Common models include yeast genetics, mammalian cell lines with CRISPR knockouts, and Drosophila models for immunity and neurodegeneration.
How does BRE1 couple sister chromatid cohesion to DNA replication?
In yeast, Bre1 is required for establishing sister chromatid cohesion during S phase, linking histone modification to replication.
What is the role of Bre1 in innate immunity?
A Toll-dependent Bre1/Rad6-cact feedback loop controls host innate immune responses in Drosophila.
Conclusion
The BRE1 E3 ubiquitin ligase complex (GO:1990352) is a conserved chromatin-modifying machine that monoubiquitinates histone H2B to regulate transcription, DNA replication, and genome stability. Its roles extend to cancer, neurodegeneration, and innate immunity, making it a compelling subject for basic and translational research. Understanding its structure, regulation, and disease connections will continue to reveal new therapeutic opportunities.
References
- 1. Zhang W et al.. 2017. E3 ubiquitin ligase Bre1 couples sister chromatid cohesion establishment to DNA replication in Saccharomyces cerevisiae.. Elife 6 PMID: 29058668
- 2. Wood A et al.. 2003. Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.. Mol Cell 11(1):267-74 PMID: 12535539
- 3. Shukla PK et al.. 2023. Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex.. Nucleic Acids Res 51(5):2117-2136 PMID: 36715322
- 4. Wei Z et al.. 2025. Protective role of Bre1 in mitochondrial function and energy metabolism in Drosophila models of Parkinson's disease.. Free Radic Biol Med 240:663-673 PMID: 40914324
- 5. Chernikova SB et al.. 2012. Deficiency in mammalian histone H2B ubiquitin ligase Bre1 (Rnf20/Rnf40) leads to replication stress and chromosomal instability.. Cancer Res 72(8):2111-9 PMID: 22354749
- 6. Shi M et al.. 2026. Structural insights into the Bre1-Lge1 and RNF20/RNF40-WAC interactions critical for H2B ubiquitination.. Nucleic Acids Res 54(2) PMID: 41533567
- 7. Zhao F et al.. 2023. Mechanism of histone H2B monoubiquitination by Bre1.. Nat Struct Mol Biol 30(11):1623-1627 PMID: 37872231
- 8. Cai Q et al.. 2022. A Toll-dependent Bre1/Rad6-cact feedback loop in controlling host innate immune response.. Cell Rep 41(11):111795 PMID: 36516751
