Coordinated regulation of active and repressive histone methylations by a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

Abstract

H3K9me2 and H3K27me2 are important epigenetic marks associated with transcription repression, whileH3K4me3 is associated with transcription activation. It has been shown that active and repressive histone methylations distribute in a mutually exclusive manner, but the underlying mechanism was poorly understood. Here we identified ceKDM7A, a PHD (plant homeodomain)-and JmjC domain-containing protein, as a histone demethylase specific for H3K9me2 and H3K27me2. We further demonstrated that the PHD domain of ceKDM7A bound H3K4me3 and H3K4me3 co-localized with ceKDM7A at the genome-wide level. Disruption of the PHD domain binding to H3K4me3 reduced the demethylase activity in vivo, and loss of ceKDM7A reduced the expression of its associated target genes. These results indicate that ceKDM7A is recruited to the promoter to demethylate H3K9me2 and H3K27me2 and activate gene expression through the binding of the PHD domain to H3K4me3. Thus, our study identifies a dual-specificity histone demethylase and provides novel insights into the regulation of histone methylation.

Features of the PHF8/KIAA1718 histone demethylase

“…Thus, substrate binding is not required to maintain its structure. Lin et al addressed the role of the PHD of ceKIAA1718 in vivo [10]. The PHD deletion mutant expressed in Tn5 cells using a baculovirus system does not show demethylase activity against H3K9me2 and H3K27me2 [10], which is not consistent with the crystal structure data.…”

Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans

“…Cocrystal structures of ceKDM7A with H3K4me3-containing peptides bound to the PHD finger and H3K9me2 or H3K27me2 peptides bound to the JmjC domain indicate that binding of the peptides does not cause significant conformational changes (Supplementary information, Figure S2A-S2C), suggesting that each domain can perform their biochemical functions independently. Consistently, a fragment containing only the PHD finger can bind to H3K4me3-containing peptide, and disrupting the interaction between the PHD finger and H3K4me3 did not affect the demethylase activity of the JmjC domain in vitro (Lin et al, accompanying paper in this issue [33]). However, the PHD finger binding to H3K4me3 is required for demethylation by the JmjC domain in vivo.…”

“…We also found that its C. elegans ortholog ceKDM7A, a PHDand JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo (Lin et al, accompanying paper in this issue [33]). However, the molecular mechanisms for both the enzymatic activity and the function of the PHD finger remain unknown.…”

“…However, the PHD finger binding to H3K4me3 is required for demethylation by the JmjC domain in vivo. Further analyses indicate that the PHD finger binding to H3K4me3 guides the demethylation by the JmjC domain in physiological conditions, indicating a cross-regulation between the two domains (Lin et al, accompanying paper in this issue [33]). Geometrical measurement of the structures revealed that H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting that the cross-regulation could be a trans-histone event.…”

“…The PHD finger binds H3K4me3, and the binding directs the demethylation by the JmjC domain in vivo (Lin et al, accompanying paper in this issue [33]). To gain insights into the substrate specificity of the enzyme and the molecular mechanism of the cross-regulation between the PHD finger and the JmjC domain, we solved cocrystal structures of the enzyme in complex with a histone H3 peptide with dual methylation marks H3K4me3K9me2 and H3K4me3K27me2 (Figure 1 and Supplementary information, Figure S1).…”