Silencing by plant Polycomb-group genes requires dispersed trimethylation of histone H3 at lysine 27

Abstract

The plant Polycomb-group (Pc-G) protein CURLY LEAF (CLF) is required to repress targets such as AGAMOUS (AG) and SHOOTMERISTEMLESS (STM). Using chromatin immunoprecipitation, we identify AG and STM as direct targets for CLF and show that they carry a characteristic epigenetic signature of dispersed histone H3 lysine 27 trimethylation (H3K27me3) and localised H3K27me2 methylation. H3K27 methylation is present throughout leaf development and consistent with this, CLF is required persistently to silence AG. However, CLF is not itself an epigenetic mark as it is lost during mitosis. We suggest a model in which Pc-G proteins are recruited to localised regions of targets and then mediate dispersed H3K27me3. Analysis of transgenes carrying AG regulatory sequences confirms that H3K27me3 can spread to novel sequences in a CLF-dependent manner and further shows that H3K27me3 methylation is not sufficient for silencing of targets. We suggest that the spread of H3K27me3 contributes to the mitotic heritability of Pc-G silencing, and that the loss of silencing caused by transposon insertions at plant Pc-G targets reflects impaired spreading.

KNOX genes: versatile regulators of plant development and diversity

“…Consistent with an epigenetic mode of KNOX gene repression, a second pathway confining KNOX activity to meristems requires the polycomb-group proteins CURLY LEAF (CLF), SWINGER (SWN) and FERTILISATION INDEPENDENT ENDOSPERM (Katz et al, 2004;Schubert et al, 2006). The SET domains of CLF and SWN have histone methyltransferase activity, which facilitates the maintenance of silenced target gene expression states through cell divisions.…”

“…Recent work has shown how the combined actions of two polycomb repressive complexes (PRCs) repress KNOX transcription (Xu and Shen, 2008). CLF-containing PRC2 marks KNOX genes by trimethylation of histone H3 at lysine 27 (H3K27me3) (Schubert et al, 2006). A PRC1-like complex, which contains the chromodomain protein LIKE HETEROCHROMATIN PROTEIN1 and two RING domain proteins, then binds to these methylated histones, resulting in the transcriptional repression of KNOX genes (Fig.…”

Plant SET domain-containing proteins: Structure, function and regulation

“…CLF was the first identified plant SET domain-containing protein within this class [50]. In Arabidopsis, CLF controls leaf and flower morphology as well as flowering time through repression of the floral homeotic genes AGAMOUS (AG) and SHOOTMERISTEMLESS (STM) [51,52]. Its close relative, SWN, acts redundantly in mediating tri-methylation of histone H3K27 at both AG and STM loci [52,53].…”

“…In Arabidopsis, CLF controls leaf and flower morphology as well as flowering time through repression of the floral homeotic genes AGAMOUS (AG) and SHOOTMERISTEMLESS (STM) [51,52]. Its close relative, SWN, acts redundantly in mediating tri-methylation of histone H3K27 at both AG and STM loci [52,53]. MEA plays a role in maintaining its own imprinting during endosperm development and methylation of H3K27 is associated with MEA silencing during vegetative development and male gametogenesis [54][55][56].…”

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

“…Among the many transcription factor families over-represented in profile 3, we found the MIKC subclass of the MADS box family that was previously shown to be regulated by PRC2 ). In addition, this family contains two wellcharacterized members FLC and AG, whose transcriptional regulation strongly relies on the presence of a large first intron that harbours activating as well as repressive ciselements that are required for PRC2 action (Schubert et al 2006;Sung et al 2006;Angel et al 2011) (Figure S1 in supplemental material online). This prompted us to investigate systematically the exon-intron organization of the genes in each profile.…”