Opposing Chromatin Signals Direct and Regulate the Activity of Lysine Demethylase 4C (KDM4C)

Abstract

Histone H3 lysine 4 trimethylation (H3K4me3) and histone H3 lysine 9 trimethylation (H3K9me3) are epigenetic marks with opposing roles in transcription regulation. Whereas colocalization of these modifications is generally excluded in the genome, how this preclusion is established remains poorly understood. Lysine demethylase 4C (KDM4C), an H3K9me3 demethylase, localizes predominantly to H3K4me3-containing promoters through its hybrid tandem tudor domain (TTD) (1, 2), providing a model for how these modifications might be excluded. We quantitatively investigated the contribution of the TTD to the catalysis of H3K9me3 demethylation by KDM4C and demonstrated that TTD-mediated recognition of H3K4me3 stimulates demethylation of H3K9me3 in cis on peptide and mononucleosome substrates. Our findings support a multivalent interaction mechanism, by which an activating mark, H3K4me3, recruits and stimulates KDM4C to remove the repressive H3K9me3 mark, thus facilitating exclusion. In addition, our work suggests that differential TTD binding properties across the KDM4 demethylase family may differentiate their targets in the genome.Post-translational modifications of histone proteins regulate chromatin structure and accessibility and act as part of the chromatin scaffold to control many nuclear processes. Lysine methylation, one of the most functionally diverse histone modifications, has a regulatory role in a range of processes, including heterochromatin formation, transcriptional regulation, and DNA repair (3, 4). Both the extent of methylation (mono-, di-, or trimethylation) and the position of the lysine within the histone tail determine the functional effect of the modification by recruiting different effector proteins. Of particular interest are two modifications with opposing effects on transcription, histone H3 lysine 9 trimethylation (H3K9me3) 3 and histone H3 lysine 4 trimethylation (H3K4me3). H3K9me3 is a major component of silent heterochromatin and in euchromatic promoters is generally associated with repressed transcription (5-9). In contrast, H3K4me3 is found at euchromatic promoters and correlates with active transcription (10 -13). These chromatin modifications have critical and opposing roles in regulating gene expression, and colocalization of H3K9me3 and H3K4me3 on the same nucleosome is generally excluded in the genome (14,15). Although this exclusivity must be tightly controlled, the mechanisms that preclude colocalization of these histone marks are poorly understood. The spatial and temporal localization of histone lysine methylation are regulated by the opposing activities of histone modifying enzymes. Histone lysine methyltransferases are "writers" that deposit methyl groups on lysines, whereas histone lysine demethylases are "erasers" that remove the methylation. In principle, the exclusion of colocalized modifications could be explained by a methyltransferase that functions at H3K9 only in the absence of H3K4me3 (or vice versa). Indeed, several H3K9 methyltransferases are partially inhibited by H3...

Reader domain specificity and lysine demethylase-4 family function

“…The functional analyses reported here demonstrate that the distinct mode of H3K23me3 binding stimulates the demethyalse activity of KDM4B towards H3K36me3. These results are in accord with such ‘cross-talk' between a histone methylation ‘reader' and ‘eraser', leading to cis -histone demethylation reported for PHF8, KDM7A4647, KDM4A and KDM4C2848. In the case of PHF8, biochemical and structural characterization indicates H3K4me3 strongly promotes H3K9 demethylation46.…”

The histone demethylase KDM4B regulates peritoneal seeding of ovarian cancer

“…KDM4A is stabilized by hypoxia independently of HIF to facilitate gene amplification (24). KDM4 family members interact with H3K4me3 and H4K20me2 through tandem TUDOR domains, indicating that KDM4B may be recruited to specific regions of transcriptional activation or DNA damage (33, 34). The KDM4 family is generally inhibited by hypoxic conditions (9, 35).…”

Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation

“…H3K4me3 has been proposed to regulate H3K9 methylation by inhibiting binding of the H3K9 HMTs, preventing its deposition, and also by stabilising binding of H3K9 demethylases, thereby promoting its removal from gene promoters ( Fig. 4 B) [ [158] , [159] , [160] , [161] , [162] , [163] , [164] , [165] , [166] , [167] , [168] , [169] , [170] , [171] , [172] , [173] ].…”