Distinct chromatin signatures in the Arabidopsis male gametophyte

ASH1L in Hepatoma Cells and Hepatic Stellate Cells Promotes Fibrosis-Associated Hepatocellular Carcinoma by Modulating Tumor-Associated Macrophages

Hepatocellular carcinoma (HCC) often occurs in the context of fibrosis or cirrhosis. Methylation of histone is an important epigenetic mechanism, but it is unclear whether histone methyltransferases are potent targets for fibrosis-associated HCC therapy. ASH1L, an H3K4 methyltransferase, is found at higher levels in activated hepatic stellate cells (HSCs) and hepatoma cells. To determine the role of ASH1L in vivo, transgenic mice with conditional Ash1l depletion in the hepatocyte cell lineage (Ash1lflox/floxAlbcre) or HSCs (Ash1lflox/floxGFAPcreERT2) are generated, and these mice are challenged in a diethylnitrosamine (DEN)/carbon tetrachloride (CCl4)-induced model of liver fibrosis and HCC. Depleting Ash1l in both hepatocytes and HSCs mitigates hepatic fibrosis and HCC development. Multicolor flow cytometry, bulk, and single-cell transcriptomic sequencing reveal that ASH1L creates an immunosuppressive microenvironment. Mechanically, ASH1L-mediated H3K4me3 modification increases the expression of CCL2 and CSF1, which recruites and polarizes M2-like pro-tumorigenic macrophages. The M2-like macrophages further enhance tumor cell proliferation and suppress CD8+ T cell activation. AS-99, a small molecule inhibitor of ASH1L, demonstrates similar anti-fibrosis and tumor-suppressive effects. Of pathophysiological significance, the increased expression levels of mesenchymal ASH1L and M2 marker CD68 are associated with poor prognosis of HCC. The findings reveal ASH1L as a potential small-molecule therapeutic target against fibrosis-related HCC.

Nuclear-localized pyruvate kinases control phosphorylation of histone H3 on threonine 11

Phosphorylation of histone H3 at threonine 11 (H3T11ph) affects transcription and chromosome stability. However, the enzymes responsible for depositing H3T11ph and the functions of H3T11ph in plants remain unknown. Here we report that in Arabidopsis thaliana, PYRUVATE KINASE 6 (PK6), PK7 and PK8 enter the nucleus under conditions of sufficient glucose and light exposure, where they interact with SWI2/SNF2-RELATED 1 COMPLEX 4 (SWC4) and phosphorylate H3 at threonine 11. Mutations in these kinases or knockdown of SWC4 resulted in FLC-dependent early flowering, short hypocotyls and short pedicels. Genome-wide, H3T11ph is highly enriched at transcription start sites and transcription termination sites, and positively correlated with gene transcript levels. PK6 and SWC4 targeted FLC, MYB73, PRE1, TCP4 and TCP10, depositing H3T11ph at these loci and promoting their transcription, and PK6 occupancy at these loci requires SWC4. Together, our results reveal that nuclear-localized PK6, PK7 and PK8 modulate H3T11ph and plant growth.

A simple, robust, cost-effective, and low-input ChIP-seq method for profiling histone modifications and Pol II in plants

Chromatin immunoprecipitation and sequencing (vs ChIP-seq) is an essential tool for epigenetic and molecular genetic studies. Although being routinely used, ChIP-seq is expensive, requires grams of plant materials, and is challenging for samples that enrich fatty acids such as seeds. Here, we developed an Ultrasensitive Plant ChIP-seq (UP-ChIP) method based on native ChIP-seq combined with Tn5 tagmentation-based library construction strategy. UP-ChIP is generally applicable for profiling both histone modification and Pol II in a wide range of plant samples, such as a single Arabidopsis seedling, a few Arabidopsis seeds, and sorted nuclei. Compared with conventional ChIP-seq, UP-ChIP is much less labor intensive and only consumes 1 μg of antibody and 10 μl of Protein-A/G conjugated beads for each IP and can work effectively with the amount of starting material down to a few milligrams. By performing UP-ChIP in various conditions and genotypes, we showed that UP-ChIP is highly reliable, sensitive, and quantitative for studying histone modifications. Detailed UP-ChIP protocol is provided. We recommend UP-ChIP as an alternative to traditional ChIP-seq for profiling histone modifications and Pol II, offering the advantages of reduced labor intensity, decreased costs, and low-sample input.

"To remember or forget: Insights into the mechanisms of epigenetic reprogramming and priming in early plant embryos"

Chromatin is dynamically modified throughout the plant life cycle to regulate gene expression in response to environmental and developmental cues. Although such epigenetic information can be inherited across generations in plants, chromatin features that regulate gene expression are typically reprogrammed during plant gametogenesis and directly after fertilization. Nevertheless, environmentally induced epigenetic marks on genes can be transmitted across generations. Moreover, epigenetic information installed on early embryonic chromatin can be stably inherited during subsequent growth and influence how plants respond to environmental conditions much later in development. Here, we review recent breakthroughs towards deciphering mechanisms underlying epigenetic reprogramming and transcriptional priming during early plant embryogenesis.

Dynamics of DNA methylation and its impact on plant embryogenesis

Flowering plants exhibit unique DNA methylation dynamics during development. Particular attention can be focused on seed development and the embryo, which represents the starting point of the sporophytic life cycle. A build-up of CHH methylation is now recognized as highly characteristic of embryo development. This process is thought to occur in order to silence potentially harmful transposable element expression, though roles in promoting seed dormancy and dessication tolerance have also been revealed. Recent studies show that increased CHH methylation in embryos inhabits both novel loci, unmethylated elsewhere in the plant, as well as shared loci, exhibiting more dense methylation. The role of DNA methylation in cis-regulatory gene regulation in plants is less well established compared to mammals, and here we discuss both transposable element regulation and the potential role of DNA methylation in dynamic gene expression.

Bivalent histone modifications: how phytopathogens evade plant immunity

Bivalent histone modifications regulate gene expression during development, but little is known about their function in plant-microbe interactions. In a recent report, Zhao et al. showed that expression of bivalent chromatin-marked gene 1 (BCG1), containing a pathogen-associated molecular pattern (PAMP) motif, is epigenetically regulated by trimethylation of lysine 4 (H3K4me3) and lysine 27 (H3K27me3) of histone H3 to evade plant immunity.

ARID1 is required to regulate and reinforce H3K9me2 in sperm cells in Arabidopsis

Heterochromatin de-condensation in companion gametic cells is conserved in both plants and animals. In plants, microspore undergoes asymmetric pollen mitosis (PMI) to produce a vegetative cell (VC) and a generative cell (GC). Subsequently, the GC undergoes pollen mitosis (PMII) to produce two sperm cells (SC). Consistent with heterochromatin de-condensation in the VC, H3K9me2, a heterochromatin mark, is barely detected in VC. However, how H3K9me2 is differentially regulated during pollen mitosis remains unclear. Here, we show that H3K9me2 is gradually evicted from the VC since PMI but remain unchanged in the GC and SC. ARID1, a pollen-specific transcription factor that facilitates PMII, promotes H3K9me2 maintenance in the GC/SC but slows down its eviction in the VC. The genomic targets of ARID1 mostly overlaps with H3K9me2 loci, and ARID1 recruits H3K9 methyltransferase SUVH6. Our results uncover that differential pattern of H3K9me2 between two cell types is regulated by ARID1 during pollen mitosis.

Interplay between histone variants and chaperones in plants

Histone chaperones and histone variants play crucial roles in DNA replication, gene transcription, and DNA repair in eukaryotes. Histone chaperones reversibly promote nucleosome assembly and disassembly by incorporating or evicting histones and histone variants to modulate chromatin accessibility, thereby altering the chromatin states and modulating DNA-related biological processes. Cofactors assist histone chaperones to target specific chromatin regions to regulate the exchange of histones and histone variants. In this review, we summarize recent progress in the interplay between histone variants and chaperones in plants. We discuss the structural basis of chaperone-histone complexes and the mechanisms of their cooperation in regulating gene transcription and plant development.

The roles of epigenetic regulators in plant regeneration: Exploring patterns amidst complex conditions

Plants possess remarkable capability to regenerate upon tissue damage or optimal environmental stimuli. This ability not only serves as a crucial strategy for immobile plants to survive through harsh environments, but also made numerous modern plant improvements techniques possible. At the cellular level, this biological process involves dynamic changes in gene expression that redirect cell fate transitions. It is increasingly recognized that chromatin epigenetic modifications, both activating and repressive, intricately interact to regulate this process. Moreover, the outcomes of epigenetic regulation on regeneration are influenced by factors such as the differences in regenerative plant species and donor tissue types, as well as the concentration and timing of hormone treatments. In this review, we focus on several well-characterized epigenetic modifications and their regulatory roles in the expression of widely studied morphogenic regulators, aiming to enhance our understanding of the mechanisms by which epigenetic modifications govern plant regeneration.

Plant histone variants at the nexus of chromatin readouts, stress and development

Histones are crucial proteins that are involved in packaging the DNA as condensed chromatin inside the eukaryotic cell nucleus. Rather than being static packaging units, these molecules undergo drastic variations spatially and temporally to facilitate accessibility of DNA to replication, transcription as well as wide range of gene regulatory machineries. In addition, incorporation of paralogous variants of canonical histones in the chromatin is ascribed to specific functions. Given the peculiar requirement of plants to rapidly modulate gene expression levels on account of their sessile nature, histones and their variants serve as additional layers of gene regulation. This review summarizes the mechanisms and implications of distribution, modifications and differential incorporation of histones and their variants across plant genomes, and outlines emerging themes.

Histone Variant H3.3 Controls Arabidopsis Fertility by Regulating Male Gamete Development

Reprograming of chromatin structures and changes in gene expression are critical for plant male gamete development, and epigenetic marks play an important role in these processes. Histone variant H3.3 is abundant in euchromatin and is largely associated with transcriptional activation. The precise function of H3.3 in gamete development remains unclear in plants. Here, we report that H3.3 is abundantly expressed in Arabidopsis anthers and its knockout mutant h3.3-1 is sterile due to male sterility. Transcriptome analysis of young inflorescence has identified 2348 genes downregulated in h3.3-1 mutant, among which 1087 target genes are directly bound by H3.3, especially at their 3' ends. As a group, this set of H3.3 targets is enriched in the reproduction-associated processes including male gamete generation, pollen sperm cell differentiation and pollen tube growth. The function of H3.3 in male gamete development is dependent on the Anti-Silencing Factor 1A/1B (ASF1A/1B)-Histone regulator A (HIRA)-mediated pathway. Our results suggest that ASF1A/1B-HIRA-mediated H3.3 deposition at its direct targets for transcription activation forms the regulatory networks responsible for male gamete development.

Temporally-coordinated bivalent histone modifications of BCG1 enable fungal invasion and immune evasion

Bivalent histone modifications, including functionally opposite H3K4me3 and H3K27me3 marks simultaneously on the same nucleosome, control various cellular processes by fine-tuning the gene expression in eukaryotes. However, the role of bivalent histone modifications in fungal virulence remains elusive. By mapping the genome-wide landscape of H3K4me3 and H3K27me3 dynamic modifications in Fusarium graminearum (Fg) during invasion, we identify the infection-related bivalent chromatin-marked genes (BCGs). BCG1 gene, which encodes a secreted Fusarium-specific xylanase containing a G/Q-rich motif, displays the highest increase of bivalent modification during Fg infection. We report that the G/Q-rich motif of BCG1 is a stimulator of its xylanase activity and is essential for the full virulence of Fg. Intriguingly, this G/Q-rich motif is recognized by pattern-recognition receptors to trigger plant immunity. We discover that Fg employs H3K4me3 modification to induce BCG1 expression required for host cell wall degradation. After breaching the cell wall barrier, this active chromatin state is reset to bivalency by co-modifying with H3K27me3, which enables epigenetic silencing of BCG1 to escape from host immune surveillance. Collectively, our study highlights how fungal pathogens deploy bivalent epigenetic modification to achieve temporally-coordinated activation and suppression of a critical fungal gene, thereby facilitating successful infection and host immune evasion.

A molecular mechanism for embryonic resetting of winter memory and restoration of winter annual growth habit in wheat

The staple food crop winter bread wheat (Triticum aestivum) acquires competence to flower in late spring after experiencing prolonged cold in temperate winter seasons, through the physiological process of vernalization. Prolonged cold exposure results in transcriptional repression of the floral repressor VERNALIZATION 2 (TaVRN2) and activates the expression of the potent floral promoter VERNALIZATION 1 (TaVRN1). Cold-induced TaVRN1 activation and TaVRN2 repression are maintained in post-cold vegetative growth and development, leading to an epigenetic 'memory of winter cold', enabling spring flowering. When and how the cold memory is reset in wheat is essentially unknown. Here we report that the cold-induced TaVRN1 activation is inherited by early embryos, but reset in subsequent embryo development, whereas TaVRN2 remains silenced through seed development, but is reactivated rapidly by light during seed germination. We further found that a chromatin reader mediates embryonic resetting of TaVRN1 and that chromatin modifications play an important role in the regulation of TaVRN1 expression and thus the floral transition, in response to developmental state and environmental cues. The findings define a two-step molecular mechanism for re-establishing vernalization requirement in common wheat, ensuring that each generation must experience winter cold to acquire competence to flower in spring.

Evidence of a novel silencing effect on transgenes in the Arabidopsis thaliana sperm cell

We encountered unexpected transgene silencing in Arabidopsis thaliana sperm cells; transgenes encoding proteins with no specific intracellular localization (cytoplasmic proteins) were silenced transcriptionally or posttranscriptionally. The mRNA of cytoplasmic protein transgenes tagged with a fluorescent protein gene was significantly reduced, resulting in undetectable fluorescent protein signals in the sperm cell. Silencing of the cytoplasmic protein transgenes in the sperm cell did not affect the expression of either its endogenous homologous genes or cotransformed transgenes encoding a protein with targeted intracellular localization. This transgene silencing in the sperm cell persisted in mutants of the major gene silencing machinery including DNA methylation. The incomprehensible, yet real, transgene silencing phenotypes occurring in the sperm cell could mislead the interpretation of experimental results in plant reproduction, and this Commentary calls attention to that risk and highlights details of this novel cytoplasmic protein transgene silencing.

Epigenetic processes in plant stress priming: Open questions and new approaches

Priming reflects the capacity of plants to memorise environmental stress experience and improve their response to recurring stress. Epigenetic modifications in DNA and associated histone proteins may carry short-term and long-term memory in the same plant or mediate transgenerational effects, but the evidence is still largely circumstantial. New experimental tools now enable scientists to perform targeted manipulations that either prevent or generate a particular epigenetic modification in a particular location of the genome. Such 'reverse epigenetics' approaches allow for the interrogation of causality between individual priming-induced modifications and their role for altering gene expression and plant performance under recurring stress. Furthermore, combining site-directed epigenetic manipulation with conditional and cell-type specific promoters creates novel opportunities to test and engineer spatiotemporal patterns of priming.

The sporophyte-to-gametophyte transition: The haploid generation comes of age

Flowering plants alternate between two multicellular generations: the diploid sporophyte and haploid gametophyte. Despite its small size, the gametophyte has significant impacts on plant genetics, evolution, and breeding. Each male pollen grain and female embryo sac is a multicellular organism with independent gene expression, a functioning metabolism, and specialized cell types. In this review, we describe recent progress in understanding the process in which the haploid genome takes over expression from its diploid parent - the sporophyte-to-gametophyte transition. The focus is on pollen, but similar concepts may also apply to the female gametophyte. Technological advances in single-cell genomics offer the opportunity to characterize haploid gene expression in unprecedented detail, positioning the field to make rapid progress.

Application of single-cell multi-omics approaches in horticulture research

Cell heterogeneity shapes the morphology and function of various tissues and organs in multicellular organisms. Elucidation of the differences among cells and the mechanism of intercellular regulation is essential for an in-depth understanding of the developmental process. In recent years, the rapid development of high-throughput single-cell transcriptome sequencing technologies has influenced the study of plant developmental biology. Additionally, the accuracy and sensitivity of tools used to study the epigenome and metabolome have significantly increased, thus enabling multi-omics analysis at single-cell resolution. Here, we summarize the currently available single-cell multi-omics approaches and their recent applications in plant research, review the single-cell based studies in fruit, vegetable, and ornamental crops, and discuss the potential of such approaches in future horticulture research.