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BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels
Dongsheng Han1, Samantha H Schaffner1, Jonathan P Davies1
1Department of Biological Sciences, Vanderbilt University, Nashville, TN 37212.
Abstract:
Histone modifications are critical for regulating chromatin structure and gene expression. Dysregulation of histone modifications likely contributes to disease states and cancer. Depletion of the chromatin-binding protein BRWD3 (Bromodomain and WD repeat-containing protein 3), a known substrate-specificity factor of the Cul4-DDB1 E3 ubiquitin ligase complex, results in increased H3K4me1 (H3 lysine 4 monomethylation) levels. The underlying mechanism linking BRWD3 and H3K4 methylation, however, has yet to be defined. Here, we show that depleting BRWD3 not only causes an increase in H3K4me1 levels but also causes a decrease in H3K4me3 (H3 lysine 4 trimethylation) levels, indicating that BRWD3 influences H3K4 methylation more broadly. Using immunoprecipitation coupled to quantitative mass spectrometry, we identified an interaction between BRWD3 and the H3K4-specific lysine demethylase 5 (KDM5/Lid), an enzyme that removes tri- and dimethyl marks from H3K4. Moreover, analysis of ChIP-seq (chromatin immunoprecipitation sequencing) data revealed that BRWD3 and KDM5 are significantly colocalized throughout the genome and H3K4me3 are highly enriched at BRWD3 binding sites. We show that BRWD3 promotes K48-linked polyubiquitination and degradation of KDM5 and that KDM5 degradation is dependent on both BRWD3 and Cul4. Critically, depleting KDM5 fully restores altered H3K4me3 levels and partially restores H3K4me1 levels upon BRWD3 depletion. Together, our results demonstrate that BRWD3 regulates KDM5 activity to balance H3K4 methylation levels.
Insights
Bromodomain and WD repeat-containing protein 3 (BRWD3) regulates histone methylation by controlling the degradation of KDM5, an enzyme that removes H3K4 methylation marks. This finding reveals a new mechanism for maintaining chromatin structure and gene expression balance.
Area of Science:
- Epigenetics and Gene Regulation
- Molecular Biology
- Biochemistry
Background:
- Histone modifications are crucial for chromatin structure and gene expression.
- Dysregulation of these modifications is linked to diseases like cancer.
- The precise mechanisms controlling specific histone marks, such as H3K4 methylation, are not fully understood.
Purpose of the Study:
- To elucidate the mechanism by which BRWD3 (Bromodomain and WD repeat-containing protein 3) influences H3K4 methylation levels.
- To investigate the interaction between BRWD3 and enzymes involved in H3K4 methylation.
- To determine the role of BRWD3 in regulating the stability and activity of H3K4-modifying enzymes.
Main Methods:
- Depletion of BRWD3 and analysis of H3K4me1 and H3K4me3 levels.
- Immunoprecipitation coupled with quantitative mass spectrometry to identify protein interactions.
- Chromatin immunoprecipitation sequencing (ChIP-seq) to assess genomic colocalization.
- Analysis of KDM5 ubiquitination and degradation pathways.
Main Results:
- BRWD3 depletion alters H3K4me1 and H3K4me3 levels, indicating a broader role in H3K4 methylation.
- BRWD3 interacts with KDM5 (lysine demethylase 5), an enzyme that removes H3K4 methylation marks.
- BRWD3 promotes KDM5 degradation via K48-linked polyubiquitination, dependent on Cul4.
- Depletion of KDM5 rescues the H3K4 methylation changes caused by BRWD3 depletion.
Conclusions:
- BRWD3 acts as a regulator of KDM5 activity, controlling its degradation.
- This regulation by BRWD3 is essential for maintaining balanced H3K4 methylation levels.
- The BRWD3-KDM5 axis represents a novel mechanism influencing chromatin states and gene expression.
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