EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development

Abstract

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.

Deciphering the Role of POLYCOMB REPRESSIVE COMPLEX1 Variants in Regulating the Acquisition of Flowering Competence in Arabidopsis

“…Consistent with the misexpression of FLC, MAF4, and MAF5 in the mutants, it has been shown previously that the levels of H3K27me3 marks at these genes were altered in PRC2 mutants (Jiang et al, 2008), emf1, and atring1a (Kim et al, 2012b;Shen et al, 2014). Therefore, to investigate whether AtBMI1 loss of function also affected the levels of H3K27me3 marks at FLC, MAF4, and MAF5, we examined the levels of this histone modification in atbmi1a/b mutants at the first intron of the genes, which has been shown to display an enrichment of H3K27me3 marks in wild-type seedlings at 9 to 10 DAG (Shen et al, 2014; Fig.…”

“…Recent findings regarding the PcG mechanism have shown that PRC1 is required for H3K27me3 marking at some target genes in both Arabidopsis (Yang et al, 2013a;Calonje, 2014) and animals (Comet and Helin, 2014;Schwartz and Pirrotta, 2014), placing PRC1 in a decisive position for the repression of some genes. In addition, several lines of evidence have suggested the existence of different mechanisms for PRC1-mediated repression in Arabidopsis (Kim et al, 2012b;Yang et al, 2013a;Calonje, 2014); however, it is not known whether a combination of different PRC1 subunits is required to exert the different mechanisms.…”

“…Interestingly, a recent report showed that SPL9 is a target of EMF1 (Kim et al, 2012b); thus, derepression of SPL9 may cause the activation of pri-MIR172b in emf1-2 mutants. Also, SPL3 is up-regulated in transgenic plants expressing an EMF1 antisense complementary DNA under the control of the floral meristem identity gene LFY promoter (LFY:asEMF1; Pu et al, 2013).…”

“…Also, SPL3 is up-regulated in transgenic plants expressing an EMF1 antisense complementary DNA under the control of the floral meristem identity gene LFY promoter (LFY:asEMF1; Pu et al, 2013). Moreover, it has been shown that several MIR172 genes are direct targets of EMF1 (Kim et al, 2012b). emf2-2 also displayed increased expression levels of SPL3, SPL9, and pri-MIR172b, although the levels of the transcripts were not as high as in emf1-2, probably due to a redundant role of VRN2 in regulating these genes, as EMF2 and VRN2 regulate a common subset of targets (Lafos et al, 2011).…”

EMBRYONIC FLOWER1 and ULTRAPETALA1 Act Antagonistically on Arabidopsis Development and Stress Response

“…Genomewide investigation of EMF1 targets has revealed that EMF1 mediates gene expression via diverse mechanisms. It acts along with PRC2 to repress the flower MADS box genes as well as with PRC1 to regulate the expression of many other genes (Kim et al, 2012).…”