PWO proteins are associated with PRC2 since their emergence in vascular plants

The Polycomb repressive complex 2 (PRC2), a conserved histone methyltransferase complex, plays a central role in transcriptional silencing across eukaryotes. Here, we investigate the evolution of PWWP-DOMAIN INTERACTORS OF POLYCOMBS (PWOs), which interact with PRC2, and examine the conservation of the PWOs-PRC2 interaction across plant evolution by comparing orthologs from the lycophyte Selaginella moellendorffii (Sm) and the flowering plant Arabidopsis thaliana (Arabidopsis; At). Phylogenetic data traced the presence of PWO proteins across plant lineages, while protein-protein interaction assays and AlphaFold predictions assessed PWO-PRC2 interactions and structural conservation. Functional complementation assays confirmed PWOs' conserved functions. PWO proteins are present in vascular plants but absent in bryophytes and green algae. The ancestral clade of PWO proteins includes the spikemoss Selaginella moellendorffii (Sm) PWO orthologs SmPWOa and SmPWOb. PWO proteins from vascular plants can interact with PRC2 components from multiple species, including bryophytes, which naturally lack PWOs. The PWO-PRC2 interaction is mediated by a conserved short C-motif. Functional and molecular assays further demonstrate that SmPWOs retain their conserved functions in Arabidopsis. Our data suggest an evolutionarily conserved role for PWOs in modulating PRC2 activity and emphasize how lineage-specific proteins associated with conserved chromatin-modifying complexes may shape epigenetic control mechanisms during evolution.