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Abstract

Epigenetic silencing is essential for regulating gene expression and cellular diversity in eukaryotes. While transposable elements (TEs) are mostly silenced with DNA and H3K9 methylation, gene silencing is mediated by H3K27me3, an epigenetic mark deposited by the Polycomb repressive complex 2 (PRC2). Despite the major role epigenetic silencing plays in the development of multicellular eukaryotes, little is known about how epigenetically-controlled regulatory networks were shaped over evolutionary time. Here, we analyse epigenomes from a diverse group of species across the green lineage and infer the chronological epigenetic recruitment of genes that occurred during land plant evolution. We first reveal the nature of plant heterochromatin in the unicellular green microalga Chlorella sorokiniana and identify a substantial number of genes marked with H3K27me3, highlighting the deep origin of PRC2-regulated genes in the green lineage. By incorporating genomic phylostratigraphy, we show how genes of differing evolutionary age are partitioned into distinct epigenetic states in plants, with evolutionarily young genes incorporated into developmental programs controlled by H3K9 methylation in Arabidopsis. We further reveal a major wave of PRC2 recruitment to genes that emerged during land terrestrialisation and flowering plant evolution, and identify an ancestral PRC2 network with a shared functional topology in green algae through to land plants, providing a glimpse of the earliest types of genes regulated by PRC2 during the course of plant evolution. Finally, we analyse the potential regulation of these ancestral PRC2 target genes and find a strong enrichment of motifs bound by ancient AP2/ERF transcription factors (TFs) known to interact with PRC2, which we hypothesise were key determinants in shaping some of the first gene regulatory networks controlled by PRC2 in plants. Our data thus reveal pivotal epigenetic adaptations that occurred during a significant period in the evolutionary history of plants, which likely contributed to key regulatory innovations that influenced major morphological and developmental change into the modern-day. More broadly, our findings offer insight into the evolutionary dynamics and molecular triggers that drive the adaptation and elaboration of epigenetic regulation, laying the groundwork for its future consideration in other major eukaryotic lineages.