Arabidopsis REF6 is a histone H3 lysine 27 demethylase

Abstract

Polycomb group (PcG)-mediated histone H3 lysine 27 trimethylation (H3K27me3) has a key role in gene repression and developmental regulation. There is evidence that H3K27me3 is actively removed in plants, but it is not known how this occurs. Here we show that RELATIVE OF EARLY FLOWERING 6 (REF6), also known as Jumonji domain-containing protein 12 (JMJ12), specifically demethylates H3K27me3 and H3K27me2, whereas its metazoan counterparts, the KDM4 proteins, are H3K9 and H3K36 demethylases. Plants overexpressing REF6 resembled mutants defective in H3K27me3-mediated gene silencing. Genetic interaction tests indicated that REF6 acts downstream of H3K27me3 methyltransferases. Mutations in REF6 caused ectopic and increased H3K27me3 level and decreased mRNA expression of hundreds of genes involved in regulating developmental patterning and responses to various stimuli. Our work shows that plants and metazoans use conserved mechanisms to regulate H3K27me3 dynamics but use distinct subfamilies of enzymes.

Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis

“…47) showed that REF6-6HA was associated with SOC1, and that this association was significantly attenuated in nf-yb2-1 nf-yb3-1 and under SD conditions (Fig. 6b,d), but enhanced by GA treatment (Fig.…”

“…Because H3K27me3 is deposited by H3K27me3 methyltransferases of the polycomb repressive complex 2 and removed by H3K27 demethylases, we then examined whether NF-Y modulates H3K27me3 dynamics at SOC1 through its interaction with CURLY LEAF (CLF), a main H3K27me3 methyltransferase, or REF6, a H3K27 demethylase, both of which affect flowering in Arabidopsis (Table 1) [46][47][48][49] .…”

“…As both clf and REF6-YFP-HA overexpression (REF6ox) plants exhibit global changes in H3K27me3 levels 46,47 , we performed ChIP assays on these two types of plants and found that overexpression of REF6 dramatically reduced H3K27me3 levels at SOC1, whereas there was no significant change in H3K27me3 levels in clf (Fig. 5d).…”

Efficient targeted mutagenesis in potato by the CRISPR/Cas9 system

“…The A. tumefaciens-mediated transient expression in N. benthamiana was performed according to our previous paper (Lu et al 2011). A. tumefaciens-mediated transformations of potato double-haploid DM were performed as following.…”

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

“…Notably, epigenomic profiling in Arabidopsis has established that trimethylation of histone H3 lysine 27 (H3K27me3) is associated with the transcriptional repression of numerous genes and depends on the evolutionary conserved Polycomb Repressive Complex 2 (PRC2) (Turck et al 2007;Zhang et al 2007;Bouyer et al 2011;Lafos et al 2011). As in other eukaryotes, PRC2-mediated repression is antagonized by the activity of demethylases (Lu et al 2011) and Trithorax proteins including histone methyl transferases that catalyse trimethylation of H3K4 (Pien & Grossniklaus 2007) (H3K4me3). Thus, H3K27me3 and H3K4me3 represent two antagonist chromatin marks that were shown to be diagnostic for two major chromatin states along the Arabidopsis epigenome .…”