SummaryPosttranslational modifications of histone tails are an important factor regulating chromatin structure and gene expression. Epigenetic memory systems have been predicted to involve mutually exclusive histone modifications that, through positive feedback mechanisms, generate bistable states [1, 2]. How the states are interconverted is not understood, and whether the histone modifications are sufficient for epigenetic memory is still greatly debated [3]. We have exploited the process of vernalization, the slow quantitative epigenetic silencing of Arabidopsis FLC induced by cold, to detail with fine temporal and spatial resolution the dynamics of histone modifications during an epigenetic switch. The profiles of H3K36me3, H3K4me3, and H3K4me2 at FLC throughout the vernalization process were compared to H3K27me3, which accumulates at a local nucleation region during the cold and spreads across the locus on return to the warm [2]. We find for many phases of the vernalization process that H3K36me3 and H3K27me3 show opposing profiles in the FLC nucleation region and gene body, that H3K36me3 and H3K27me3 rarely coexist on the same histone tail, and that this antagonism is functionally important. A lack of H3K36me3 results in a fully silenced state at FLC even in the absence of cold. We therefore propose that H3K36me3 is the opposing modification to H3K27me3 in the Polycomb-mediated silencing of FLC. However, the lack of an absolute mirror profile predicted from modeling suggests that their antagonistic roles contribute a necessary, but not sufficient, component of the mechanism enabling switching between and inheritance of epigenetic states.

Gene silencing by Polycomb complexes is central to eukaryotic development. Cold-induced epigenetic repression of () in the plant provides an opportunity to study initiation and maintenance of Polycomb silencing. Here, we show that a subset of Polycomb repressive complex 2 factors nucleate silencing in a small region within, locally increasing H3K27me3 levels. This nucleation confers a silenced state that is metastably inherited, with memory held in the local chromatin. Metastable memory is then converted to stable epigenetic silencing through separate Polycomb factors, which spread across the locus after cold to enlarge the domain that contains H3K27me3. Polycomb silencing at thus has mechanistically distinct phases, which involve specialization of distinct Polycomb components to deliver first metastable then long-term epigenetic silencing.

Reprogramming of epigenetic states in gametes and embryos is essential for correct development in plants and mammals1. In plants, the germ line arises from somatic tissues of the flower necessitating erasure of chromatin modifications accumulated at specific loci during development or in response to external stimuli. If this occurs inefficiently it can lead to epigenetic states being inherited from one generation to the next2-4. However, in most cases accumulated epigenetic modifications are efficiently erased before the next generation. An important example of epigenetic reprogramming in plants is the resetting of expression of the Arabidopsis thaliana floral repressor FLC locus. FLC is epigenetically silenced by prolonged cold in a process called vernalization. However, the locus is reactivated prior to completion of seed development to ensure a vernalization requirement every generation. In contrast to our detailed understanding of the Polycomb-mediated epigenetic silencing induced by vernalization, little is known about the mechanism involved in the re-activation of FLC. Here we show that a hypomorphic mutation in the jumonji domain protein ELF6 impaired the reactivation of FLC in reproductive tissues, leading to inheritance of a partially vernalized state. ELF6 has H3K27me3 demethylase activity and the mutation reduced this enzymatic activity in planta. Consistent with this, H3K27me3 levels at the FLC locus stayed higher and FLC expression remained lower, than in the wild type in the following generation. Our data reveal an ancient role for H3K27 demethylation in the reprogramming of epigenetic states in plant and mammalian embryos5-7.