Dominant negative effects on H3K27 methylation by Weaver syndrome-associated EZH2 variants

Heterozygous missense mutations in EZH2 cause Weaver syndrome (WS), a developmental disorder characterized by intellectual disability and overgrowth. EZH2 encodes the enzymatic subunit of Polycomb Repressive Complex 2 (PRC2), which mediates mono-, di-, and tri-methylation of histone H3 lysine residue 27 (H3K27me1/2/3). Although the functional characterization of most WS-associated EZH2 variants is lacking, they are presumed loss of function. However, the dearth of reported early truncating mutations in EZH2 led us to hypothesise that a dominant negative mutational mechanism may underlie the development of WS. To test this, we performed a detailed structural analysis of all known WS-associated EZH2 variants, which provided initial support that they are dominant negative. Next, we isogenically modelled 10 representative WS-associated EZH2 variants in embryonic stem cells and showed they induce global reductions in H3K27me2 and H3K27me3 with concomitant global increases in H3K27me1, H3K27ac, and chromatin decompaction. Importantly, the reductions in H3K27me2/3 methylation revealed a pattern of dominant-negative interference to PRC2 activity. Comparative analysis of a gain-of-function EZH2 variant causing growth restriction highlighted the reciprocal nature of the chromatin changes in these opposing growth syndromes. Our findings detail the molecular effects of developmental-syndrome-associated EZH2 variants in cells and implicate imbalanced landscapes of H3K27 modification in their pathology.