The chromodomain of LIKE HETEROCHROMATIN PROTEIN 1 is essential for H3K27me3 binding and function during Arabidopsis development

Heterochromatin protein 1 (HP1) of Schistosoma mansoni: non-canonical chromatin landscape and oviposition effects

BACKGROUND

Heterochromatin protein 1 (HP1) is widespread in several organisms playing a role in control of gene expression by heterochromatin formation and maintenance of silent chromatin. Schistosoma mansoni is a human parasite that is responsible for Schistosomiasis, a tropical neglected disease in the tropical and subtropical areas in the world, where the intermediate host Biomphalaria glabrata is present.

OBJECTIVES

In this study we attempted to investigate if the SmHP1 is enriched in S. mansoni chromatin in cercariae larvae stage, compared with another larvae stage sporocysts and its importance for S. mansoni life cycle progression and parasite oviposition.

METHODS

We used ChIPmentation with commercial antibody ab109028 that passed in-house quality control. We also used RNA interference, mice infection and histology.

FINDINGS

Our data show that S. mansoni HP1 enrichment is non-canonical with a peak at the transcription end sites of protein coding genes. We did not find strong differences in SmHP1 chromatin landscapes between sporocysts and cercariae. Knock- down of SmHP1 in schistosomula and in vivo experiments in mice unexpectedly increased parasite oviposition.

MAIN CONCLUSIONS

Our results suggest that SmHP1 may influence chromatin structure in a non-canonical way in S. mansoni stages and may play a role in regulation of parasite oviposition.

The Impact of Polycomb Group Proteins on 3D Chromatin Structure and Environmental Stresses in Plants

The two multi-subunit complexes, Polycomb Repressive Complex 1 and 2 (PRC1/2), act synergistically during development to maintain the gene silencing state among different species. In contrast with mammals and Drosophila melanogaster, the enzyme activities and components of the PRC1 complex in plants are not fully conserved. In addition, the mutual recruitment of PRC1 and PRC2 in plants differs from that observed in mammals and Drosophila. Polycomb Group (PcG) proteins and their catalytic activity play an indispensable role in transcriptional regulation, developmental processes, and the maintenance of cellular identity. In plants, PRC1 and PRC2 deposit H2Aub and H3K27me3, respectively, and also play an important role in influencing three-dimensional (3D) chromatin structure. With the development of high-throughput sequencing techniques and computational biology, remarkable progress has been made in the field of plant 3D chromatin structure, and PcG has been found to be involved in the epigenetic regulation of gene expression by mediating the formation of 3D chromatin structures. At the same time, some genetic evidence indicates that PcG enables plants to better adapt to and resist a wide range of stresses by dynamically regulating gene expression. In the following review, we focus on the recruitment relationship between PRC1 and PRC2, the crucial role of PcG enzyme activity, the effect of PcG on 3D chromatin structure, and the vital role of PcG in environmental stress in plants.

LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) partially inhibits the transcriptional activation of FT by MYB73 and regulates flowering in Arabidopsis

Polycomb group (PcG) proteins are essential gene repressors in higher eukaryotes. However, how PcG proteins mediate transcriptional regulation of specific genes remains unknown. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), as a component of Polycomb Repression Complexes (PRC), epigenetically mediates several plant developmental processes together with PcG proteins. We observed physical interaction between MYB73 and LHP1 in vitro and in vivo. Genetic analysis indicated that myb73 mutants showed slightly late flowering, and the lhp1-3 myb73-2 double mutant exhibited delayed flowering and downregulated FT expression compared to lhp1-3. Chromatin immunoprecipitation and yeast one-hybrid assays revealed that MYB73 preferentially binds to the FT promoter. Additionally, our protoplast transient assays demonstrated that MYB73 activates to the FT promoter. Interestingly, the LHP1-MYB73 interaction is necessary to repress the FT promoter, suggesting that the LHP1-MYB73 interaction prevents FT activation by MYB73 in Arabidopsis. Our results show an example in which a chromatin regulator affects transcriptional regulation by negatively regulating a transcription factor through direct interaction.

Preventing too much of a good thing: epigenetic regulation limits sucrose-induced anthocyanin production in Arabidopsis

This article is a Commentary on Zhang et al. (2024), 243: 1374–1386.

Protein post-translational modifications in auxin signaling

Protein post-translational modifications (PTMs), such as ubiquitination, phosphorylation, and small ubiquitin-like modifier (SUMO)ylation, are crucial for regulating protein stability, activity, subcellular localization, and binding with cofactors. Such modifications remarkably increase the variety and complexity of proteomes, which are essential for regulating numerous cellular and physiological processes. The regulation of auxin signaling is finely tuned in time and space to guide various plant growth and development. Accumulating evidence indicates that PTMs play critical roles in auxin signaling regulations. Thus, a thorough and systematic review of the functions of PTMs in auxin signal transduction will improve our profound comprehension of the regulation mechanism of auxin signaling and auxin-mediated various processes. This review discusses the progress of protein ubiquitination, phosphorylation, histone acetylation and methylation, SUMOylation, and S-nitrosylation in the regulation of auxin signaling.

Leaf growth - complex regulation of a seemingly simple process

Understanding the underlying mechanisms of plant development is crucial to successfully steer or manipulate plant growth in a targeted manner. Leaves, the primary sites of photosynthesis, are vital organs for many plant species, and leaf growth is controlled by a tight temporal and spatial regulatory network. In this review, we focus on the genetic networks governing leaf cell proliferation, one major contributor to final leaf size. First, we provide an overview of six regulator families of leaf growth in Arabidopsis: DA1, PEAPODs, KLU, GRFs, the SWI/SNF complexes, and DELLAs, together with their surrounding genetic networks. Next, we discuss their evolutionary conservation to highlight similarities and differences among species, because knowledge transfer between species remains a big challenge. Finally, we focus on the increase in knowledge of the interconnectedness between these genetic pathways, the function of the cell cycle machinery as their central convergence point, and other internal and environmental cues.

Identification of vernalization-related genes and cold memory element (CME) required for vernalization response in radish (Raphanus sativus L.)

Floral transition is accelerated by exposure to long-term cold like winter in plants, which is called as vernalization. Acceleration of floral transition by vernalization is observed in a diversity of biennial and perennial plants including Brassicaceae family plants. Scientific efforts to understand molecular mechanism underlying vernalization-mediated floral transition have been intensively focused in model plant Arabidopsis thaliana. To get a better understanding on floral transition by vernalization in radish (Raphanus sativus L.), we investigated transcriptomic changes taking place during vernalization in radish. Thousands of genes were differentially regulated along time course of vernalization compared to non-vernalization (NV) sample. Twelve major clusters of DEGs were identified based on distinctive expression profiles during vernalization. Radish FLC homologs were shown to exert an inhibition of floral transition when transformed into Arabidopsis plants. In addition, DNA region containing RY motifs located within a Raphanus sativus FLC homolog, RsFLC1 was found to be required for repression of RsFLC1 by vernalization. Transgenic plants harboring disrupted RY motifs were impaired in the enrichment of H3K27me3 on RsFLC1 chromatin, thus resulting in the delayed flowering in Arabidopsis. Taken together, we report transcriptomic profiles of radish during vernalization and demonstrate the requirement of RY motif for vernalization-mediated repression of RsFLC homologs in radish (Raphanus sativus L.).

Functions and mechanisms of RNA helicases in plants

RNA helicases (RHs) are a family of ubiquitous enzymes that alter RNA structures and remodel ribonucleoprotein complexes typically using energy from the hydrolysis of ATP. RHs are involved in various aspects of RNA processing and metabolism, exemplified by transcriptional regulation, pre-mRNA splicing, miRNA biogenesis, liquid-liquid phase separation, and rRNA biogenesis, among other molecular processes. Through these mechanisms, RHs contribute to vegetative and reproductive growth, as well as abiotic and biotic stress responses throughout the life cycle in plants. In this review, we systematically characterize RH-featured domains and signature motifs in Arabidopsis. We also summarize the functions and mechanisms of RHs in various biological processes in plants with a focus on DEAD-box and DEAH-box RNA helicases, aiming to present the latest understanding of RHs in plant biology.

Convergent evolution of the annual life history syndrome from perennial ancestors

Despite most angiosperms being perennial, once-flowering annuals have evolved multiple times independently, making life history traits among the most labile trait syndromes in flowering plants. Much research has focused on discerning the adaptive forces driving the evolution of annual species, and in pinpointing traits that distinguish them from perennials. By contrast, little is known about how 'annual traits' evolve, and whether the same traits and genes have evolved in parallel to affect independent origins of the annual syndrome. Here, we review what is known about the distribution of annuals in both phylogenetic and environmental space and assess the evidence for parallel evolution of annuality through similar physiological, developmental, and/or genetic mechanisms. We then use temperate grasses as a case study for modeling the evolution of annuality and suggest future directions for understanding annual-perennial transitions in other groups of plants. Understanding how convergent life history traits evolve can help predict species responses to climate change and allows transfer of knowledge between model and agriculturally important species.

The Phytophthora sojae nuclear effector PsAvh110 targets a host transcriptional complex to modulate plant immunity

Plants have evolved sophisticated immune networks to restrict pathogen colonization. In response, pathogens deploy numerous virulent effectors to circumvent plant immune responses. However, the molecular mechanisms by which pathogen-derived effectors suppress plant defenses remain elusive. Here, we report that the nucleus-localized RxLR effector PsAvh110 from the pathogen Phytophthora sojae, causing soybean (Glycine max) stem and root rot, modulates the activity of a transcriptional complex to suppress plant immunity. Soybean like-heterochromatin protein 1-2 (GmLHP1-2) and plant homeodomain finger protein 6 (GmPHD6) form a transcriptional complex with transcriptional activity that positively regulates plant immunity against Phytophthora infection. To suppress plant immunity, the nuclear effector PsAvh110 disrupts the assembly of the GmLHP1-2/GmPHD6 complex via specifically binding to GmLHP1-2, thus blocking its transcriptional activity. We further show that PsAvh110 represses the expression of a subset of immune-associated genes, including BRI1-associated receptor kinase 1-3 (GmBAK1-3) and pathogenesis-related protein 1 (GmPR1), via G-rich elements in gene promoters. Importantly, PsAvh110 is a conserved effector in different Phytophthora species, suggesting that the PsAvh110 regulatory mechanism might be widely utilized in the genus to manipulate plant immunity. Thus, our study reveals a regulatory mechanism by which pathogen effectors target a transcriptional complex to reprogram transcription.

Epigenetic marks for mitigating abiotic stresses in plants

Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.

The Importance of Networking: Plant Polycomb Repressive Complex 2 and Its Interactors

Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.

Altered H3K27 trimethylation contributes to flowering time variations in polyploid Arabidopsis thaliana ecotypes

Polyploidy is a widespread phenomenon in flowering plant species. Polyploid plants frequently exhibit considerable transcriptomic alterations after whole-genome duplication (WGD). It is known that the transcriptomic response to tetraploidization is ecotype-dependent in Arabidopsis; however, the biological significance and the underlying mechanisms are unknown. In this study, we found that 4x Col-0 presents a delayed flowering time whereas 4x Ler does not. The expression of FLOWERING LOCUS C (FLC), the major repressor of flowering, was significantly increased in 4x Col-0 but only a subtle change was present in 4x Ler. Moreover, the level of a repressive epigenetic mark, trimethylation of histone H3 at lysine 27 (H3K27me3), was significantly decreased in 4x Col-0 but not in 4x Ler, potentially leading to the differences in FLC transcription levels and flowering times. Hundreds of other genes in addition to FLC showed H3K27me3 alterations in 4x Col-0 and 4x Ler. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) and transcription factors required for H3K27me3 deposition presented transcriptional changes between the two ecotypes, potentially accounting for the different H3K27me3 alterations. We also found that the natural 4x Arabidopsis ecotype Wa-1 presented an early flowering time, which was associated with low expression of FLC. Taken together, our results demonstrate a role of H3K27me3 alterations in response to genome duplication in Arabidopsis autopolyploids, and that variation in flowering time potentially functions in autopolyploid speciation.

CmLHP1 proteins play a key role in plant development and sex determination in melon (Cucumis melo)

In monoecious melon (Cucumis melo), sex is determined by the differential expression of sex determination genes (SDGs) and adoption of sex-specific transcriptional programs. Histone modifications such as H3K27me3 have been previously shown to be a hallmark associated to unisexual flower development in melon; yet, no genetic approaches have been conducted for elucidating the roles of H3K27me3 writers, readers, and erasers in this process. Here we show that melon homologs to Arabidopsis LHP1, CmLHP1A and B, redundantly control several aspects of plant development, including sex expression. Cmlhp1ab double mutants displayed an overall loss and redistribution of H3K27me3, leading to a deregulation of genes involved in hormone responses, plant architecture, and flower development. Consequently, double mutants display pleiotropic phenotypes and, interestingly, a general increase of the male:female ratio. We associated this phenomenon with a general deregulation of some hormonal response genes and a local activation of male-promoting SDGs and MADS-box transcription factors. Altogether, these results reveal a novel function for CmLHP1 proteins in maintenance of monoecy and provide novel insights into the polycomb-mediated epigenomic regulation of sex lability in plants.

Structural basis for the recognition of methylated histone H3 by the Arabidopsis LHP1 chromodomain

Arabidopsis LHP1 (LIKE HETEROCHROMATIN PROTEIN 1), a unique homolog of HP1 in Drosophila, plays important roles in plant development, growth, and architecture. In contrast to specific binding of the HP1 chromodomain to methylated H3K9 histone tails, the chromodomain of LHP1 has been shown to bind to both methylated H3K9 and H3K27 histone tails, and LHP1 carries out its function mainly via its interaction with these two epigenetic marks. However, the molecular mechanism for the recognition of methylated histone H3K9/27 by the LHP1 chromodomain is still unknown. In this study, we characterized the binding ability of LHP1 to histone H3K9 and H3K27 peptides and found that the chromodomain of LHP1 binds to histone H3K9me2/3 and H3K27me2/3 peptides with comparable affinities, although it exhibited no binding or weak binding to unmodified or monomethylated H3K9/K27 peptides. Our crystal structures of the LHP1 chromodomain in peptide-free and peptide-bound forms coupled with mutagenesis studies reveal that the chromodomain of LHP1 bears a slightly different chromodomain architecture and recognizes methylated H3K9 and H3K27 peptides via a hydrophobic clasp, similar to the chromodomains of human Polycomb proteins, which could not be explained only based on primary structure analysis. Our binding and structural studies of the LHP1 chromodomain illuminate a conserved ligand interaction mode between chromodomains of both animals and plants, and shed light on further functional study of the LHP1 protein.

Polycomb Repressive Complex 2 in Eukaryotes-An Evolutionary Perspective

Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.

Post-Embryonic Phase Transitions Mediated by Polycomb Repressive Complexes in Plants

Correct timing of developmental phase transitions is critical for the survival and fitness of plants. Developmental phase transitions in plants are partially promoted by controlling relevant genes into active or repressive status. Polycomb Repressive Complex1 (PRC1) and PRC2, originally identified in Drosophila, are essential in initiating and/or maintaining genes in repressive status to mediate developmental phase transitions. Our review summarizes mechanisms in which the embryo-to-seedling transition, the juvenile-to-adult transition, and vegetative-to-reproductive transition in plants are mediated by PRC1 and PRC2, and suggests that PRC1 could act either before or after PRC2, or that they could function independently of each other. Details of the exact components of PRC1 and PRC2 in each developmental phase transitions and how they are recruited or removed will need to be addressed in the future.

A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies

Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1-another PcG protein interacting with the EZL1 complex-reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome.

Biological role and mechanism of chromatin readers in plants

Epigenetic modifications are important gene regulatory mechanisms conserved in plants, animals, and fungi. Chromatin reader domains are protein-protein/DNA interaction modules acting within the chromatin-modifying complex to function as molecular interpreters of the epigenetic code. Understanding how reader proteins recognize specific epigenetic modifications and mediate downstream chromatin and transcriptional events is fundamental to many biological processes. Recent studies have uncovered a number of novel reader proteins with diverse functions and mechanisms in plants. Here, we provide an overview of the recent progress on reader-mark recognition modes, the mechanisms by which reader proteins influence chromatin dynamics, and how reader-chromatin interactions regulate biological function. Because of space limitations, this review focuses on reader domains in plants that specifically bind histone methylation, histone acetylation, and DNA methylation.

One factor, many systems: the floral homeotic protein AGAMOUS and its epigenetic regulatory mechanisms

Tissue-specific transcription factors allow cells to specify new fates by exerting control over gene regulatory networks and the epigenetic landscape of a cell. However, our knowledge of the molecular mechanisms underlying cell fate decisions is limited. In Arabidopsis, the MADS-box transcription factor AGAMOUS (AG) plays a central role in regulating reproductive organ identity and meristem determinacy during flower development. During the vegetative phase, AG transcription is repressed by Polycomb complexes and intronic noncoding RNA. Once AG is transcribed in a spatiotemporally regulated manner during the reproductive phase, AG functions with chromatin regulators to change the chromatin structure at key target gene loci. The concerted actions of AG and the transcription factors functioning downstream of AG recruit general transcription machinery for proper cell fate decision. In this review, we describe progress in AG research that has provided important insights into the regulatory and epigenetic mechanisms underlying cell fate determination in plants.

MeCP2: latest insights fundamentally change our understanding of its interactions with chromatin and its functional attributes

Methyl CpG binding protein 2 (MeCP2) was initially isolated as an exclusive reader of DNA methylated at CpG. This recognition site, was subsequently extended to other DNA methylated residues and it has been the persisting dogma that binding to methylated DNA constitutes its physiologically relevant role. As we review here, two very recent papers fundamentally change our understanding of the interactions of this protein with chromatin, as well as its functional attributes. In the first one, the protein has been shown to bind to tri-methylated histone H3 (H3K27me3), providing a hint for what might turn out to be the first described chromodomain-containing protein reader in the animal kingdom, and unequivocally demonstrates the ability of MeCP2 to bind to nonmethylated CpG regions of the genome. The second paper reports how the protein dynamically participates in the formation of constitutive heterochromatin condensates. Histone H3K27me3 is a critical component of this form of chromatin.

Mapping Influenza-Induced Posttranslational Modifications on Histones from CD8+ T Cells

T cell function is determined by transcriptional networks that are regulated by epigenetic programming via posttranslational modifications (PTMs) to histone proteins and DNA. Bottom-up mass spectrometry (MS) can identify histone PTMs, whereas intact protein analysis by MS can detect species missed by bottom-up approaches. We used a novel approach of online two-dimensional liquid chromatography-tandem MS with high-resolution reversed-phase liquid chromatography (RPLC), alternating electron transfer dissociation (ETD) and collision-induced dissociation (CID) on precursor ions to maximize fragmentation of uniquely modified species. The first online RPLC separation sorted histone families, then RPLC or weak cation exchange hydrophilic interaction liquid chromatography (WCX-HILIC) separated species heavily clad in PTMs. Tentative identifications were assigned by matching proteoform masses to predicted theoretical masses that were verified with tandem MS. We used this innovative approach for histone-intact protein PTM mapping (HiPTMap) to identify and quantify proteoforms purified from CD8 T cells after in vivo influenza infection. Activation significantly altered PTMs following influenza infection, histone maps changed as T cells migrated to the site of infection, and T cells responding to secondary infections had significantly more transcription enhancing modifications. Thus, HiPTMap identified and quantified proteoforms and determined changes in CD8 T cell histone PTMs over the course of infection.

Tidying-up the plant nuclear space: domains, functions, and dynamics

Understanding how the packaging of chromatin in the nucleus is regulated and organized to guide complex cellular and developmental programmes, as well as responses to environmental cues is a major question in biology. Technological advances have allowed remarkable progress within this field over the last years. However, we still know very little about how the 3D genome organization within the cell nucleus contributes to the regulation of gene expression. The nuclear space is compartmentalized in several domains such as the nucleolus, chromocentres, telomeres, protein bodies, and the nuclear periphery without the presence of a membrane around these domains. The role of these domains and their possible impact on nuclear activities is currently under intense investigation. In this review, we discuss new data from research in plants that clarify functional links between the organization of different nuclear domains and plant genome function with an emphasis on the potential of this organization for gene regulation.

Knowing When to Silence: Roles of Polycomb-Group Proteins in SAM Maintenance, Root Development, and Developmental Phase Transition

Polycomb repressive complex 1 (PRC1) and PRC2 are the major complexes composed of polycomb-group (PcG) proteins in plants. PRC2 catalyzes trimethylation of lysine 27 on histone 3 to silence target genes. Like Heterochromatin Protein 1/Terminal Flower 2 (LHP1/TFL2) recognizes and binds to H3K27me3 generated by PRC2 activities and enrolls PRC1 complex to further silence the chromatin through depositing monoubiquitylation of lysine 119 on H2A. Mutations in PcG genes display diverse developmental defects during shoot apical meristem (SAM) maintenance and differentiation, seed development and germination, floral transition, and so on so forth. PcG proteins play essential roles in regulating plant development through repressing gene expression. In this review, we are focusing on recent discovery about the regulatory roles of PcG proteins in SAM maintenance, root development, embryo development to seedling phase transition, and vegetative to reproductive phase transition.

HSI2/VAL1 and HSL1/VAL2 function redundantly to repress DOG1 expression in Arabidopsis seeds and seedlings

DELAY OF GERMINATION1 (DOG1) is a primary regulator of seed dormancy. Accumulation of DOG1 in seeds leads to deep dormancy and delayed germination in Arabidopsis. B3 domain-containing transcriptional repressors HSI2/VAL1 and HSL1/VAL2 silence seed dormancy and enable the subsequent germination and seedling growth. However, the roles of HSI2 and HSL1 in regulation of DOG1 expression and seed dormancy remain elusive. Seed dormancy was analysed by measurement of maximum germination percentage of freshly harvested Arabidopsis seeds. In vivo protein-protein interaction analysis, ChIP-qPCR and EMSA were performed and suggested that HSI2 and HSL1 can form dimers to directly regulate DOG1. HSI2 and HSL1 dimers interact with RY elements at DOG1 promoter. Both B3 and PHD-like domains are required for enrichment of HSI2 and HSL1 at the DOG1 promoter. HSI2 and HSL1 recruit components of polycomb-group proteins, including CURLY LEAF (CLF) and LIKE HETERCHROMATIN PROTEIN 1 (LHP1), for consequent deposition of H3K27me3 marks, leading to repression of DOG1 expression. Our findings suggest that HSI2- and HSL1-dependent histone methylation plays critical roles in regulation of seed dormancy during seed germination and early seedling growth.

Nuclear import of LIKE HETEROCHROMATIN PROTEIN1 is redundantly mediated by importins α-1, α-2 and α-3

LIKE HETEROCHROMATIN PROTEIN1 (LHP1) encodes the only plant homologue of the metazoan HETEROCHROMATIN PROTEIN1 (HP1) protein family. The LHP1 protein is necessary for proper epigenetic regulation of a range of developmental processes in plants. LHP1 is a transcriptional repressor of flowering-related genes, such as FLOWERING LOCUS T (FT), FLOWERING LOCUS C (FLC), AGAMOUS (AG) and APETALA 3 (AP3). We found that LHP1 interacts with importin α-1 (IMPα-1), importin α-2 (IMPα-2) and importin α-3 (IMPα-3) both in vitro and in vivo. A genetic approach revealed that triple mutation of impα-1, impα-2 and impα-3 resulted in Arabidopsis plants with a rapid flowering phenotype similar to that of plants with mutations in lhp1 due to the upregulation of FT expression. Nuclear targeting of LHP1 was severely impaired in the impα triple mutant, resulting in the de-repression of LHP1 target genes AG, AP3 and SHATTERPROOF 1 as well as FT. Therefore, the importin proteins IMPα-1, -2 and -3 are necessary for the nuclear import of LHP1.

Shedding light on the chromatin changes that modulate shade responses

Perception of vegetation proximity or plant shade informs of potential competition for resources by the neighboring vegetation. As vegetation proximity impacts on both light quantity and quality, perception of this cue by plant photoreceptors reprograms development to result in responses that allow plants to compete with the neighboring vegetation. Developmental reprogramming involves massive and rapid changes in gene expression, with the concerted action of photoreceptors and downstream transcription factors. Changes in gene expression can be modulated by epigenetic processes that alter chromatin compaction, influencing the accessibility and binding of transcription factors to regulatory elements in the DNA. However, little is known about the epigenetic regulation of plant responses to the proximity of other plants. In this manuscript, we review what is known about plant shade effects on chromatin changes at the cytological level, that is, changes in nuclear morphology and high order chromatin density. We address which are the specific histone post-transcriptional modifications that have been associated with changes in shade-regulated gene expression, such as histone acetylation and histone methylation. Furthermore, we explore the possible mechanisms that integrate shade signaling components and chromatin remodelers to settle epigenetic marks at specific loci. This review aims to be a starting point to understand how a specific environmental cue, plant shade, integrates with chromatin dynamics to implement the proper acclimation responses.

Like Heterochromatin Protein 1b represses fruit ripening via regulating the H3K27me3 levels in ripening-related genes in tomato

Polycomb group (PcG) proteins play vital roles in plant development via epigenetically repressing the transcription of target genes. However, to date, their function in fruit ripening is largely unknown. Combining reverse genetic approaches, physiological methods, yeast two-hybrid, co-immunoprecipitation, and chromatin immunoprecipitation assays, we show that Like Heterochromatin Protein 1b (SlLHP1b), a tomato Polycomb Repressive Complex 1 (PRC1)-like protein with a ripening-related expression pattern, represses fruit ripening via colocalization with epigenetic mark H3K27me3. RNA interference (RNAi)-mediated downregulation of SlLHP1b advanced ripening initiation, climacteric ethylene production, and fruit softening, whereas SlLHP1b overexpression delayed these events. Ripening-related genes were significantly upregulated in SlLHP1b RNAi fruits and downregulated in overexpressing fruits compared with wild-type. Furthermore, SlLHP1b protein interacts with ripening regulator MSI1, a subunit of the PRC2 complex. Moreover, SlLHP1b also binds the epigenetic histone mark H3K27me3 in vivo and chromatin immunoprecipitation-quantitative PCR results showed binding occurs preferentially to regions of ripening-associated chromatin marked by histone H3K27me3. Furthermore, the H3K27me3 levels in chromatin of ripening-related genes is negatively correlated with accumulation of their transcripts in SlLHP1b down or upregulated fruits during ripening. Our findings reveal a novel regulatory function of SlLHP1b in fruit and provide new insights into the PcG-mediated epigenetic regulation of climacteric fruit ripening.

Arabidopsis PEAPODs function with LIKE HETEROCHROMATIN PROTEIN1 to regulate lateral organ growth

In higher plants, lateral organs are usually of determinate growth. It remains largely elusive how the determinate growth is achieved and maintained. Previous reports have shown that Arabidopsis PEAPOD (PPD) proteins suppress proliferation of dispersed meristematic cells partly through a TOPLESS corepressor complex. Here, we identified a new PPD-interacting partner, LIKE HETEROCHROMATIN PROTEIN1 (LHP1), using the yeast two-hybrid system, and their interaction is mediated by the chromo shadow domain and the Jas domain in LHP1 and PPD2, respectively. Our genetic data demonstrate that the phenotype of ppd2 lhp1 is more similar to lhp1 than to ppd2, indicating epistasis of lhp1 to ppd2. Microarray analysis reveals that PPD2 and LHP1 can regulate expression of a common set of genes directly or indirectly. Consistently, chromatin immunoprecipitation results confirm that PPD2 and LHP1 are coenriched at the promoter region of their targets such as D3-TYPE CYCLINS and HIGH MOBILITY GROUP A, which are upregulated in ppd2, lhp1 and ppd2 lhp1 mutants, and that PPDs mediate repressive histone 3 lysine-27 trimethylation at these loci. Taken together, our data provide evidence that PPD and LHP1 form a corepressor complex that regulates lateral organ growth.

Genetic and molecular basis of floral induction in Arabidopsis thaliana

Many plants synchronize their life cycles in response to changing seasons and initiate flowering under favourable environmental conditions to ensure reproductive success. To confer a robust seasonal response, plants use diverse genetic programmes that integrate environmental and endogenous cues and converge on central floral regulatory hubs. Technological advances have allowed us to understand these complex processes more completely. Here, we review recent progress in our understanding of genetic and molecular mechanisms that control flowering in Arabidopsis thaliana.

Writing and Reading Histone H3 Lysine 9 Methylation in Arabidopsis

In eukaryotes, histone H3 lysine 9 methylation (H3K9me) mediates the silencing of invasive and repetitive sequences by preventing the expression of aberrant gene products and the activation of transposition. In Arabidopsis, while it is well known that dimethylation of histone H3 at lysine 9 (H3K9me2) is maintained through a feedback loop between H3K9me2 and DNA methylation, the details of the H3K9me2-dependent silencing pathway have not been fully elucidated. Recently, the regulation and the function of H3K9 methylation have been extensively characterized. In this review, we summarize work from the recent studies regarding the regulation of H3K9me2, emphasizing the process of deposition and reading and the biological significance of H3K9me2 in Arabidopsis.

The vernalisation regulator FLOWERING LOCUS C is differentially expressed in biennial and annual Brassica napus

Plants in temperate areas evolved vernalisation requirement to avoid pre-winter flowering. In Brassicaceae, a period of extended cold reduces the expression of the flowering inhibitor FLOWERING LOCUS C (FLC) and paves the way for the expression of downstream flowering regulators. As with all polyploid species of the Brassicaceae, the model allotetraploid Brassica napus (rapeseed, canola) is highly duplicated and carries 9 annotated copies of Bna.FLC. To investigate whether these multiple homeologs and paralogs have retained their original function in vernalisation or undergone subfunctionalisation, we compared the expression patterns of all 9 copies between vernalisation-dependent (biennial, winter type) and vernalisation-independent (annual, spring type) accessions, using RT-qPCR with copy-specific primers and RNAseq data from a diversity set. Our results show that only 3 copies – Bna.FLC.A03b, Bna.FLC.A10 and to some extent Bna.FLC.C02 – are differentially expressed between the two growth types, showing that expression of the other 6 copies does not correlate with growth type. One of those 6 copies, Bna.FLC.C03b, was not expressed at all, indicating a pseudogene, while three further copies, Bna.FLC.C03a and Bna.FLC.C09ab, did not respond to cold treatment. Sequence variation at the COOLAIR binding site of Bna.FLC.A10 was found to explain most of the variation in gene expression. However, we also found that Bna.FLC.A10 expression is not fully predictive of growth type.

Evolution and conservation of polycomb repressive complex 1 core components and putative associated factors in the green lineage

Background

Polycomb group (PcG) proteins play important roles in animal and plant development and stress response. Polycomb repressive complex 1 (PRC1) and PRC2 are the key epigenetic regulators of gene expression, and are involved in almost all developmental stages. PRC1 catalyzes H2A monoubiquitination resulting in transcriptional silencing or activation. The PRC1 components in the green lineage were identified and evolution and conservation was analyzed by bioinformatics techniques. RING Finger Protein 1 (RING1), B lymphoma Mo-MLV insertion region 1 homolog (BMI1), Like Heterochromatin Protein 1 (LHP1) and Embryonic Flower 1 (EMF1) are the PRC1 core components and Vernalization 1 (VRN1), VP1/ABI3-Like 1/2/3 (VAL1/2/3), Alfin-like 1–7 (AL1–7), Inhibitor of growth 1/2 (ING1/2), and Early Bolting in Short Days (EBS) / Short Life (SHL) are the associated factors.

Results

Each PRC1 subunit possesses special domain organizations, such as RING and the ring finger and WD40-associated ubiquitin-like (RAWUL) domains for RING1 and BMI1, chromatin organization modifier (CHROMO) and chromo shadow (ChSh) domains for LHP1, one or two B3 DNA binding domain(s) for VRN1, B3 and zf-CW domains for VAL1/2/3, Alfin and Plant HomeoDomain (PHD) domains for AL1–7, ING and PHD domains for ING1/2, Bromoadjacent homology (BAT) and PHD domains for EBS/SHL. Six new motifs are uncovered in EMF1.

The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1–7, ING1/2, and EBS/SHL exist from alga to higher plants, whereas LHP1 only occurs in higher plants. EMF1 and VRN1 are present only in eudicots. PRC1 components undergo duplication in the plant evolution. Most of plants carry the homologous core component LHP1, the associated factor EMF1, and several homologs in RING1, BMI1, VRN1, AL1–7, ING1/2/3, and EBS/SHL. Cabbage, cotton, poplar, orange and maize often exhibit more gene copies than other species. Domain organization analysis shows that duplicated gene functions may be of diverse.

Conclusions

The PRC1 core components RING1 and BMI1, and the associated factors VAL1/2/3, AL1–7, ING1/2, and EBS/SHL originate from algae. The core component LHP1 is from moss and the associated factors EMF1 and VRN1 are from dicotyledon. PRC1 components are of functional redundancy and diversity in evolution.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5905-9) contains supplementary material, which is available to authorized users.

Polycomb repressive complex 2 attenuates ABA-induced senescence in Arabidopsis

The phytohormone abscisic acid (ABA)-induced leaf senescence facilitates nutrient reuse and potentially contributes to enhancing plant stress tolerance. However, excessive senescence causes serious reductions in crop yield, and the mechanism by which senescence is finely tuned at different levels is still insufficiently understood. Here, we found that the double mutant of core enzymes of the polycomb repressive complex 2 (PRC2) is hypersensitive to ABA in Arabidopsis thaliana. To elucidate the interplay between ABA and PRC2 at the genome level, we extensively profiled the transcriptomic and epigenomic changes triggered by ABA. We observed that H3K27me3 preferentially targets ABA-induced senescence-associated genes (SAGs). In the double, but not single, mutant of PRC2 enzymes, these SAGs were derepressed and could be more highly induced by ABA compared with the wild-type, suggesting a redundant role for the PRC2 enzymes in negatively regulating ABA-induced senescence. Contrary to the rapid transcriptomic changes triggered by ABA, the reduction of H3K27me3 at these SAGs falls far behind the induction of their expression, indicating that PRC2-mediated H3K27me3 contributed to long-term damping of ABA-induced senescence to prevent an oversensitive response. The findings of this study may serve as a paradigm for a global understanding of the interplay between the rapid effects of a phytohormone such as ABA and the long-term effects of the epigenetic machinery in regulating plant senescence processes and environmental responses.

The Arabidopsis thaliana CONSTANS-LIKE 4 (COL4) - A Modulator of Flowering Time

Appropriate control of flowering time is crucial for crop yield and the reproductive success of plants. Flowering can be induced by a number of molecular pathways that respond to internal and external signals. In Arabidopsis, expression of the key florigenic signal FLOWERING LOCUS T (FT) is positively regulated by CONSTANS (CO) a BBX protein sharing high sequence similarity with 16 CO-like proteins. Within this study, we investigated the role of the Arabidopsis CONSTANS-LIKE 4 (COL4), whose role in flowering control was unknown. We demonstrate that, unlike CO, COL4 is a flowering repressor in long days (LD) and short days (SD) and acts on the expression of FT and FT-like genes as well as on SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1). Reduction of COL4 expression level leads to an increase of FT and APETALA 1 (AP1) expression and to accelerated flowering, while the increase of COL4 expression causes a flowering delay. Further, the observed co-localization of COL4 protein and CO in nuclear speckles supports the idea that the two act as an antagonistic pair of transcription factors. This interaction may serve the fine-tuning of flowering time control and other light dependent plant developmental processes.

Retrospective and perspective of plant epigenetics in China

Epigenetics refers to the study of heritable changes in gene function that do not involve changes in the DNA sequence. Such effects on cellular and physiological phenotypic traits may result from external or environmental factors or be part of normal developmental program. In eukaryotes, DNA wraps on a histone octamer (two copies of H2A, H2B, H3 and H4) to form nucleosome, the fundamental unit of chromatin. The structure of chromatin is subjected to a dynamic regulation through multiple epigenetic mechanisms, including DNA methylation, histone posttranslational modifications (PTMs), chromatin remodeling and noncoding RNAs. As conserved regulatory mechanisms in gene expression, epigenetic mechanisms participate in almost all the important biological processes ranging from basal development to environmental response. Importantly, all of the major epigenetic mechanisms in mammalians also occur in plants. Plant studies have provided numerous important contributions to the epigenetic research. For example, gene imprinting, a mechanism of parental allele-specific gene expression, was firstly observed in maize; evidence of paramutation, an epigenetic phenomenon that one allele acts in a single locus to induce a heritable change in the other allele, was firstly reported in maize and tomato. Moreover, some unique epigenetic mechanisms have been evolved in plants. For example, the 24-nt siRNA-involved RNA-directed DNA methylation (RdDM) pathway is plant-specific because of the involvements of two plant-specific DNA-dependent RNA polymerases, Pol IV and Pol V. A thorough study of epigenetic mechanisms is of great significance to improve crop agronomic traits and environmental adaptability. In this review, we make a brief summary of important progress achieved in plant epigenetics field in China over the past several decades and give a brief outlook on future research prospects. We focus our review on DNA methylation and histone PTMs, the two most important aspects of epigenetic mechanisms.

Structural Analysis of the Arabidopsis AL2-PAL and PRC1 Complex Provides Mechanistic Insight into Active-to-Repressive Chromatin State Switch

Polycomb group proteins play essential roles in transcriptional gene repression during both animal and plant development. Polycomb repression complex 1 (PRC1) is one of the key functional modules in polycomb group silencing. It acts as both a reader of H3K27me3 (histone H3 lysine 27 trimethylation) and a writer of H2Aub1 (histone H2A monoubiquitination) in establishing stable repression chromatin state. Intriguingly, a recent study showed that Arabidopsis PRC1 contains the H3K4me3-binding proteins of the ALFIN-like (AL) family, pointing to a chromatin state switch from active to repressive transcription of embryonic genes required for vegetative plant development. However, molecular and structural basis of AL-PRC1 complexes are lacking, which harmed insightful mechanistic understanding of AL-PRC1 complex function. In the present study, we report the crystal structures of the PAL domain (DUF3594 domain) of AL2 and AL7 proteins as well as their mechanistic binding to the PRC1 ring-finger proteins (RING1 and BMI1). We found that the PAL domain exists as a homodimer and represents a novel protein fold. We further determined the crystal structures of the PAL domain of AL2 (AL2-PAL) in complex with AtRING1a and AtBMI1b, the two core components of Arabidopsis PRC1. Interestingly, two PAL-binding sites were found on AtRING1a. Each of them can bind AL but with different affinities and distinct structural bases. Based on our results, we propose a mechanistic model to understand how AL proteins target PRC1 to active chromatin to undergo the transition from H3K4me3 to H2Aub1/H3K27me3 in establishing gene silencing.

LHP1 Interacts with ATRX through Plant-Specific Domains at Specific Loci Targeted by PRC2

Heterochromatin Protein 1 (HP1) is a major regulator of chromatin structure and function. In animals, the network of proteins interacting with HP1 is mainly associated with constitutive heterochromatin marked by H3K9me3. HP1 physically interacts with the putative ortholog of the SNF2 chromatin remodeler ATRX, which controls deposition of histone variant H3.3 in mammals. In this study, we show that the Arabidopsis thaliana ortholog of ATRX participates in H3.3 deposition and possesses specific conserved domains in plants. We found that plant Like HP1 (LHP1) protein interacts with ATRX through domains that evolved specifically in land plant ancestors. Loss of ATRX function in Arabidopsis affects the expression of a limited subset of genes controlled by PRC2 (POLYCOMB REPRESSIVE COMPLEX 2), including the flowering time regulator FLC. The function of ATRX in regulation of flowering time requires novel LHP1-interacting domain and ATPase activity of the ATRX SNF2 helicase domain. Taken together, these results suggest that distinct evolutionary pathways led to the interaction between ATRX and HP1 in mammals and its counterpart LHP1 in plants, resulting in distinct modes of transcriptional regulation.

Chromatin modulation and gene regulation in plants: insight about PRC1 function

In plant and metazoan, Polycomb Group (PcG) proteins play key roles in regulating developmental processes by repression of gene expression. PcG proteins function as multi-protein complexes; among them the best characterized ones are Polycomb Repressive Complex 1 (PRC1) and PRC2. PRC2 catalyzes histone H3 lysine 27 trimethylation (H3K27me3), and PRC1 can bind H3K27me3 and catalyzes H2A monoubiquitination. While the PRC2 components and molecular functions are evolutionarily conserved, varied PRC1 complexes are found and they show high divergences between animals and plants. In addition to the core subunits, an exponentially increasing number of PRC1-associated factors have been identified in Arabidopsis thaliana. Recent studies have also unraveled cross-component interactions and intertwined roles of PRC1 and PRC2 in chromatin modulation. In addition, complexities of interactions and functions between PcG and Trithorax Group proteins have been observed. This short review summarizes up current knowledge to provide insight about repressive functional mechanism of PRC1 and its interplay with other factors.

Arabidopsis PWWP domain proteins mediate H3K27 trimethylation on FLC and regulate flowering time

LHP1 mediates recruitment of the PRC2 histone methyltransferase complex to chromatin and thereby facilitates maintenance of H3K27me3 on FLC, a key flowering repressor gene. Here, we report that the PWWP domain proteins (PDPs) interact with FVE and MSI5 to suppress FLC expression and thereby promote flowering. We demonstrated that FVE, MSI5, and PDP3 were co-purified with LHP1. The H3K27me3 level on FLC was decreased in the pdp mutants as well as in the fve/msi5 double mutant. This study suggests that PDPs function together with FVE and MSI5 to regulate the function of the PRC2 complex on FLC.

Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression

In this study, Berry et al. investigated the functions of the different domains of LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in Arabidopsis. They show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region and show that both the hinge region and H3K27me3 recognition facilitate LHP1 localization and H3K27me3 maintenance.

Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNA-binding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression.

A Histone Code Reader and a Transcriptional Activator Interact to Regulate Genes for Salt Tolerance

Plant homeodomain (PHD) finger proteins are involved in various developmental processes and stress responses. They recognize and bind to epigenetically modified histone H3 tail and function as histone code readers. Here we report that GmPHD6 reads low methylated histone H3K4me0/1/2 but not H3K4me3 with its N-terminal domain instead of the PHD finger. GmPHD6 does not possess transcriptional regulatory ability but has DNA-binding ability. Through the PHD finger, GmPHD6 interacts with its coactivator, LHP1-1/2, to form a transcriptional activation complex. Using a transgenic hairy root system, we demonstrate that overexpression of GmPHD6 improves stress tolerance in soybean (Glycinemax) plants. Knocking down the LHP1 expression disrupts this role of GmPHD6, indicating that GmPHD6 requires LHP1 functions during stress response. GmPHD6 influences expression of dozens of stress-related genes. Among these, we identified three targets of GmPHD6, including ABA-stress-ripening-induced CYP75B1 and CYP82C4 Overexpression of each gene confers stress tolerance in soybean plants. GmPHD6 is recruited to H3K4me0/1/2 marks and recognizes the G-rich elements in target gene promoters, whereas LHP1 activates expression of these targets. Our study reveals a mechanism involving two partners in a complex. Manipulation of the genes in this pathway should improve stress tolerance in soybean or other legumes/crops.

Functional characterization of rice CW-domain containing zinc finger proteins involved in histone recognition

Histone recognition is important for understanding the mechanisms of histone modification, which play a pivotal role in transcriptional regulation during plant development. Here, we identified three cysteine-tryptophan (CW)-domain containing zinc finger (ZF) proteins involved in histone recognition, namely OsCW-ZF3, OsCW-ZF5 and OsCW-ZF7. Protein sequence analysis showed that they have two unknown motifs in addition to the CW domain. All three OsCW-ZFs were expressed in aerial tissues, with relatively high levels in developing panicles. Subcellular localization revealed that the OsCW-ZFs target the cell nucleus and CW domains are not necessary for their nuclear localization. In contrast to OsCW-ZF3 and OsCW-ZF5 where the CW domains bind histone H3 lysine 4 with different methylated forms (H3K4me), the CW domain from OsCW-ZF7 recognizes only trimethylated histone H3 lysine 4 (H3K4me3). Analysis of mutant suggested that three conserved tryptophan residues in the CW domain are essential for binding to H3K4me. Further study found that OsCW-ZF7 interacts with TAFII20, a transcription initiation factor TFIID 20kDa subunit. Knockout of OsCW-ZF7 caused defective development of awns. This study provides new insights into our understanding of the CW domain and lays a foundation for further investigation of its roles in rice.

Protein folding, misfolding and aggregation: The importance of two-electron stabilizing interactions

Proteins associated with neurodegenerative diseases are highly pleiomorphic and may adopt an all-α-helical fold in one environment, assemble into all-β-sheet or collapse into a coil in another, and rapidly polymerize in yet another one via divergent aggregation pathways that yield broad diversity of aggregates’ morphology. A thorough understanding of this behaviour may be necessary to develop a treatment for Alzheimer’s and related disorders. Unfortunately, our present comprehension of folding and misfolding is limited for want of a physicochemical theory of protein secondary and tertiary structure. Here we demonstrate that electronic configuration and hyperconjugation of the peptide amide bonds ought to be taken into account to advance such a theory. To capture the effect of polarization of peptide linkages on conformational and H-bonding propensity of the polypeptide backbone, we introduce a function of shielding tensors of the C^α atoms. Carrying no information about side chain-side chain interactions, this function nonetheless identifies basic features of the secondary and tertiary structure, establishes sequence correlates of the metamorphic and pH-driven equilibria, relates binding affinities and folding rate constants to secondary structure preferences, and manifests common patterns of backbone density distribution in amyloidogenic regions of Alzheimer’s amyloid β and tau, Parkinson’s α-synuclein and prions. Based on those findings, a split-intein like mechanism of molecular recognition is proposed to underlie dimerization of Aβ, tau, αS and PrP^C, and divergent pathways for subsequent association of dimers are outlined; a related mechanism is proposed to underlie formation of PrP^Sc fibrils. The model does account for: (i) structural features of paranuclei, off-pathway oligomers, non-fibrillar aggregates and fibrils; (ii) effects of incubation conditions, point mutations, isoform lengths, small-molecule assembly modulators and chirality of solid-liquid interface on the rate and morphology of aggregation; (iii) fibril-surface catalysis of secondary nucleation; and (iv) self-propagation of infectious strains of mammalian prions.

H3K23me1 is an evolutionarily conserved histone modification associated with CG DNA methylation in Arabidopsis

Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a histone modification not previously described in plants. H3K23me1 is an evolutionarily conserved mark in diverse species of flowering plants. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms. In transposable elements it co-localized with CG, CHG and CHH DNA methylation as well as with the heterochromatic histone mark H3K9me2. Transposable elements are often rich in H3K23me1 but different families vary in their enrichment: LTR-Gypsy elements are most enriched and RC/Helitron elements are least enriched. The histone methyltransferase KRYPTONITE and normal DNA methylation were required for normal levels of H3K23me1 on transposable elements. Immunostaining experiments confirmed the pericentromeric localization and also showed mild enrichment in less condensed regions. Accordingly, gene bodies of protein-coding genes had intermediate H3K23me1 levels, which coexisted with CG DNA methylation. Enrichment of H3K23me1 along gene bodies did not correlate with transcription levels. Together, this work establishes H3K23me1 as a so far undescribed component of the plant histone code.

Governing the Silencing State of Chromatin: The Roles of Polycomb Repressive Complex 1 in Arabidopsis

Polycomb group proteins form multiple protein complexes such as Polycomb Repressive Complex (PRC) 1 and PRC2, which repress the expression of thousands of genes. PRC1 and PRC2 are essential for normal development in Arabidopsis. Recently, significant progress has been made in understanding the functions and regulatory mechanisms of PRC1. In this review, we focus on the discovery of the composition of PRC1, functions of its components, the recruitment of PRC1 to target genes and the control of PRC1 function in Arabidopsis. Perspectives on dissecting the roles of PRC1 in plant gene expression and development are also given.

LHP1 Could Act as an Activator and a Repressor of Transcription in Plants

Polycomb group (PcG) proteins within the polycomb repressive complex 1 (PRC1) and PRC2 are significant epigenetic regulatory factors involved in important cellular and developmental processes in eukaryotes. In Arabidopsis, LIKE HETEROCHROMATIN PROTEIN 1 (LHP1), also known as TERMINAL FLOWER 2, has been proposed as a plant specific subunit of PRC1 that could bind the trimethylated lysine 27 of histone H3 (H3K27me3), which is established by PRC2 and is required for a functional plant PcG system. LHP1 not only interacts with PRC1 to catalyze monoubiquitination at lysine 119 of histone H2A but also functions with PRC2 to establish H3K27me3. This review is about the interaction of LHP1 with PRC1 and PRC2, in which LHP1 may act as a bridge between the two. Meantime, this review highlights that LHP1 could act as an activator and a repressor of transcription.

H2A deubiquitinases UBP12/13 are part of the Arabidopsis polycomb group protein system

Polycomb group (PcG) proteins form an epigenetic memory system in plants and animals, but interacting proteins are poorly known in plants. Here, we have identified Arabidopsis UBIQUITIN SPECIFIC PROTEASES (USP; UBP in plant and yeasts) 12 and 13 as partners of the plant-specific PcG protein LIKE HETEROCHROMATIN PROTEIN 1 (LHP1). UBP12 binds to chromatin of PcG target genes and is required for histone H3 lysine 27 trimethylation and repression of a subset of PcG target genes. Plants lacking UBP12 and UBP13 developed autonomous endosperm in the absence of fertilization. We have identified UBP12 and UBP13 as new proteins in the plant PcG regulatory network. UBP12 and UBP13 belong to an ancient gene family and represent plant homologues of metazoan USP7. We have found that Drosophila USP7 shares a function in heterochromatic gene repression with UBP12/13 and their homologue UBP26. In summary, we demonstrate that USP7-like proteins are essential for gene silencing in diverse genomic contexts.