The Polycomb group (PcG) and trithorax group (trxG) genes play crucial roles in development by regulating expression of homeotic and other genes controlling cell fate. Both groups catalyse modifications of chromatin, particularly histone methylation, leading to epigenetic changes that affect gene activity. The trxG antagonizes the function of PcG genes by activating PcG target genes, and consequently trxG mutants suppress PcG mutant phenotypes. We previously identified the ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN1 (ALP1) gene as a genetic suppressor of mutants in the Arabidopsis PcG gene LIKE HETEROCHROMATIN PROTEIN1 (LHP1). Here, we show that ALP1 interacts genetically with several other PcG and trxG components and that it antagonizes PcG silencing. Transcriptional profiling reveals that when PcG activity is compromised numerous target genes are hyper-activated in seedlings and that in most cases this requires ALP1. Furthermore, when PcG activity is present ALP1 is needed for full activation of several floral homeotic genes that are repressed by the PcG. Strikingly, ALP1 does not encode a known chromatin protein but rather a protein related to PIF/Harbinger class transposases. Phylogenetic analysis indicates that ALP1 is broadly conserved in land plants and likely lost transposase activity and acquired a novel function during angiosperm evolution. Consistent with this, immunoprecipitation and mass spectrometry (IP-MS) show that ALP1 associates, in vivo, with core components of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a widely conserved PcG protein complex which functions as a H3K27me3 histone methyltransferase. Furthermore, in reciprocal pulldowns using the histone methyltransferase CURLY LEAF (CLF), we identify not only ALP1 and the core PRC2 components but also plant-specific accessory components including EMBRYONIC FLOWER 1 (EMF1), a transcriptional repressor previously associated with PRC1-like complexes. Taken together our data suggest that ALP1 inhibits PcG silencing by blocking the interaction of the core PRC2 with accessory components that promote its HMTase activity or its role in inhibiting transcription. ALP1 is the first example of a domesticated transposase acquiring a novel function as a PcG component. The antagonistic interaction of a modified transposase with the PcG machinery is novel and may have arisen as a means for the cognate transposon to evade host surveillance or for the host to exploit features of the transposition machinery beneficial for epigenetic regulation of gene activity.

Molecular mechanisms enabling the switching and maintenance of epigenetic states are not fully understood. Distinct histone modifications are often associated with ON/OFF epigenetic states, but how these states are stably maintained through DNA replication, yet in certain situations switch from one to another remains unclear. Here, we address this problem through identification ofArabidopsisINCURVATA11 (ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER 1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS (TRBs).ICU11encodes a 2-oxoglutarate–dependent dioxygenase, an activity associated with histone demethylation in other organisms, and mutant plants show defects in multiple aspects of theArabidopsisepigenome. To investigate its primary molecular function we identified theArabidopsis FLOWERING LOCUS C(FLC) as a direct target and foundicu11disrupted the cold-induced, Polycomb-mediated silencing underlying vernalization.icu11prevented reduction in H3K36me3 levels normally seen during the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This was coincident with an attenuation of H3K27me3 at the internal nucleation site inFLC, and reduction in H3K27me3 levels across the body of the gene after plants were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic switching between the mutually exclusive chromatin states atFLC, from the active H3K36me3 state to the silenced H3K27me3 state. These data support the importance of physical coupling of histone modification activities to promote epigenetic switching between opposing chromatin states.

A large fraction of plant genomes is composed of transposable elements (TE), which provide a potential source of novel genes through "domestication"-the process whereby the proteins encoded by TE diverge in sequence, lose their ability to catalyse transposition and instead acquire novel functions for their hosts. In Arabidopsis, ANTAGONIST OF LIKE HETEROCHROMATIN PROTEIN 1 (ALP1) arose by domestication of the nuclease component of Harbinger class TE and acquired a new function as a component of POLYCOMB REPRESSIVE COMPLEX 2 (PRC2), a histone H3K27me3 methyltransferase involved in regulation of host genes and in some cases TE. It was not clear how ALP1 associated with PRC2, nor what the functional consequence was. Here, we identify ALP2 genetically as a suppressor of Polycomb-group (PcG) mutant phenotypes and show that it arose from the second, DNA binding component of Harbinger transposases. Molecular analysis of PcG compromised backgrounds reveals that ALP genes oppose silencing and H3K27me3 deposition at key PcG target genes. Proteomic analysis reveals that ALP1 and ALP2 are components of a variant PRC2 complex that contains the four core components but lacks plantspecific accessory components such as the H3K27me3 reader LIKE HETEROCHROMA-TION PROTEIN 1 (LHP1). We show that the N-terminus of ALP2 interacts directly with ALP1, whereas the C-terminus of ALP2 interacts with MULTICOPY SUPPRESSOR OF

Although all cells in a multicellular organism contain the same set of genes, the spatiotemporal expression of these genes needs to be dynamically regulated for proper development (i.e. morphogenesis and life cycle transitions) to take place. Epigenetic mechanisms (i.e. heritable but reversible changes to chromatin) are important to maintain such gene expression patterns. Polycomb‐group proteins are evolutionarily conserved epigenetic regulators that function – via epigenetic marks such as histone modifications and alterations to chromatin structure – to maintain the repression of developmentally important genes so that these genes are expressed appropriately. Although they maintain specific patterns of gene repression, Polycomb‐group proteins are ubiquitously expressed. How their activity is regulated is a largely unexplored area but recent research in both metazoans and plants suggests myriad methods of regulation, including control of mRNA (messenger ribonucleic acid) and protein abundance and stability, post‐translational modifications and interactions with proteins and noncoding RNAs . Key Concepts Chromatin comprises of DNA folded up to form higher order structures, the basic unit of which is a nucleosome, which consists of DNA wrapped around histone proteins. Epigenetic changes can regulate transcription and include alterations to DNA packaging and covalent modifications of histones or DNA. Epigenetic changes are important for development because they can cause gene expression patterns that are heritable through cell divisions but more easily reversible than changes to DNA sequence. Polycomb‐group proteins are conserved epigenetic regulators that maintain the repression of developmentally important genes in plants and animals. Polycomb‐group proteins form various complexes that can modify chromatin (by adding epigenetic marks such as H3K27me3 and H2Aub to histones and altering chromatin structure and accessibility). Polycomb‐group proteins are expressed ubiquitously and therefore need to be finely regulated to allow for specific and dynamic repression of their target genes. Polycomb‐group protein levels or activity may be regulated by post‐translational modifications and controlled degradation. Polycomb‐group proteins associate with other proteins or long noncoding RNAs that may regulate their activity or recruitment to specific targets. Polycomb‐group repression can be reversed by antagonistic transcriptional activators and removers of Polycomb‐group epigenetic marks, some of which are part of the evolutionarily conserved trithorax‐group of proteins.

No abstract