Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes

Abstract

BackgroundPolycomb Repressive Complex 2 (PRC2) is an essential regulator of gene expression that maintains genes in a repressed state by marking chromatin with trimethylated Histone H3 lysine 27 (H3K27me3). In Arabidopsis, loss of PRC2 function leads to pleiotropic effects on growth and development thought to be due to ectopic expression of seed and embryo-specific genes. While there is some understanding of the mechanisms by which specific genes are targeted by PRC2 in animal systems, it is still not clear how PRC2 is recruited to specific regions of plant genomes.ResultsWe used ChIP-seq to determine the genome-wide distribution of hemagglutinin (HA)-tagged FERTLIZATION INDEPENDENT ENDOSPERM (FIE-HA), the Extra Sex Combs homolog protein present in all Arabidopsis PRC2 complexes. We found that the FIE-HA binding sites co-locate with a subset of the H3K27me3 sites in the genome and that the associated genes were more likely to be de-repressed in mutants of PRC2 components. The FIE-HA binding sites are enriched for three sequence motifs including a putative GAGA factor binding site that is also found in Drosophila Polycomb Response Elements (PREs).ConclusionsOur results suggest that PRC2 binding sites in plant genomes share some sequence features with Drosophila PREs. However, unlike Drosophila PREs which are located in promoters and devoid of H3K27me3, Arabidopsis FIE binding sites tend to be in gene coding regions and co-localize with H3K27me3.

The Arabidopsis GAGA-Binding Factor BASIC PENTACYSTEINE6 Recruits the POLYCOMB-REPRESSIVE COMPLEX1 Component LIKE HETEROCHROMATIN PROTEIN1 to GAGA DNA Motifs

“…It might also be possible that group II BBR/BPCs, PRC1 and PRC2 members, participate together in the same complex at GAGA motif-containing PREs. This concept is consistent with a function of the PRC2 member FIE in a possible BBR/BPC-dependent H3K27me3 at plant PRE-like elements (Deng et al, 2013).…”

“…In animals, PREs were defined by their importance for gene repression by PcG proteins (Schwartz and Pirrotta, 2008). Previous bioinformatics analyses of the in vivo target loci of the PRC2 member FIE identified an enrichment of GAGA motifs at putative PRE-like elements (Deng et al, 2013). Our work directly supports the existence of such PRE-like elements in plants by identifying a DNA-binding protein, BPC6, that can mediate the specific interaction of the PRC1 component LHP1 with GAGA DNA motifs.…”

Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation

“…Altogether, our data provide evidence that transcriptional control of the PRC2 component CLF, and likely of other PRC2 components, plays an important role in determining H3K27me3 levels and the corresponding expression of H3K27me3 targets in a spatiotemporal manner. This regulation is likely complemented by other previously described modes of regulation in Arabidopsis, including cis-regulatory regions similar to the Polycomb repressive element in Drosophila (Deng et al, 2013), long noncoding RNAs, and protein-protein interactions via PRC1 and PRC1-like genes to determine target specificity and chromatin compaction (Margueron and Reinberg, 2011).…”

Complementary Activities of TELOMERE REPEAT BINDING Proteins and Polycomb Group Complexes in Transcriptional Regulation of Target Genes

“…A genome-wide survey of binding sites for the PRC2 component FERTILIZATION INDEPENDENT ENDOSPERM (FIE) reported an enrichment of teloboxes as well as GAGA and GAAGAA repeat motifs at FIE-enriched peaks (Deng et al, 2013). Furthermore, a recent study reports an overrepresentation of teloboxes particularly at those PcG target genes that show strongly reduced H3K27me3 levels in the clf mutant background (Wang et al, 2016).…”