EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development

EMBRYONIC FLOWER1 (EMF1) is a plant-specific gene crucial to Arabidopsis vegetative development. Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein (PcG) genes, which encode epigenetic repressors that regulate many aspects of eukaryotic development. In Arabidopsis, Polycomb Repressor Complex 2 (PRC2), made of PcG proteins, catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3) and PRC1-like proteins catalyze H2AK119 ubiquitination. Despite functional similarity to PcG proteins, EMF1 lacks sequence homology with known PcG proteins; thus, its role in the PcG mechanism is unclear. To study the EMF1 functions and its mechanism of action, we performed genome-wide mapping of EMF1 binding and H3K27me3 modification sites in Arabidopsis seedlings. The EMF1 binding pattern is similar to that of H3K27me3 modification on the chromosomal and genic level. ChIPOTLe peak finding and clustering analyses both show that the highly trimethylated genes also have high enrichment levels of EMF1 binding, termed EMF1_K27 genes. EMF1 interacts with regulatory genes, which are silenced to allow vegetative growth, and with genes specifying cell fates during growth and differentiation. H3K27me3 marks not only these genes but also some genes that are involved in endosperm development and maternal effects. Transcriptome analysis, coupled with the H3K27me3 pattern, of EMF1_K27 genes in emf1 and PRC2 mutants showed that EMF1 represses gene activities via diverse mechanisms and plays a novel role in the PcG mechanism.
Author Summary Polycomb group (PcG) proteins are epigenetic repressors maintaining developmental states in eukaryotic organisms. Plant PcG proteins are expected to be general epigenetic repressors; however, their overall impact on growth and differentiation and their mechanism of repression are still unclear. Here we identified several thousand target genes of the EMBRYONIC FLOWER 1 (EMF1) protein, which shares no sequence homology with known PcG proteins. EMF1 regulates developmental phase transitions as well as specifies cell fates during vegetative development. Trimethylation of histone 3 lysine 27 (H3K27me3) and ubiqutination of lysine 119 of histone H2A are carried out by different PcG protein complexes. EMF1 is required for both histone modifications on genes specifying stem cell fate in plants, thus revealing a novel role of EMF1 in linking the PcG protein complexes. Our results have important implications for the evolution of PcG regulatory mechanisms.