BRWD3 promotes KDM5 degradation to maintain H3K4 methylation levels

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 120; no. 39; p. e2305092120
• Main Authors: Han, Dongsheng, Schaffner, Samantha H., Davies, Jonathan P., Benton, Mary Lauren, Plate, Lars, Nordman, Jared T.
• Format: Journal Article
• Language: English
• Published: Washington National Academy of Sciences 26.09.2023
• Subjects: Binding sites; Biological Sciences; Chromatin; Degradation; Depletion; DNA methylation; Gene expression; Genomes; Histones; Immunoprecipitation; Lysine; Mass spectrometry; Mass spectroscopy; Methylation; Proteins; Substrates; Ubiquitin-protein ligase
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.2305092120

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.