Epigenetic regulation of anthocyanin biosynthesis by an antagonistic interaction between H2A.Z and H3K4me3

Involvement of epigenetic factors in flavonoid accumulation during plant cold adaptation

Plant responses to cold stress include either induction of flavonoid biosynthesis as part of defense responses or initially elevated levels of these substances to mitigate sudden temperature fluctuations. The role of chromatin modifying factors and, in general, epigenetic variability in these processes is not entirely clear. In this work, we review the literature to establish the relationship between flavonoids, cold and chromatin modifications. We demonstrate the relationship between cold acclimation and flavonoid accumulation, and then describe the cold adaptation signaling pathways and their relationship with chromatin modifying factors. Particular attention was paid to the cold signaling module OST1-HOS1-ICE1 and the novel function of the E3 ubiquitin protein ligase HOS1 (a protein involved in chromatin modification during cold stress) in flavonoid regulation.

Genome-wide investigation of the PIF gene family in alfalfa (Medicago sativa L.) expression profiles during development and stress

BACKGROUND

Phytochrome-interacting factors (PIFs) plays an important role in plants as hubs for intracellular signaling regulation. The PIF gene family has been identified and characterized in many plants, but alfalfa (Medicago sativa L.), an important perennial high-quality legume forage, has not been reported on the PIF gene family.

RESULTS

In this study, we presented the identification and characterization of five MsPIF genes in alfalfa (Medicago sativa L.). Phylogenetic analysis indicated that PIFs from alfalfa and other four plant species could be divided into three groups supported by similar motif analysis. The collinearity analysis of the MsPIF gene family showed the presence of two gene pairs, and the collinearity analysis with AtPIFs showed three gene pairs, indicating that the evolutionary process of this family is relatively conservative. Analysis of cis-acting elements in promoter regions of MsPIF genes indicated that various elements were related to light, abiotic stress, and plant hormone responsiveness. Gene expression analyses demonstrated that MsPIFs were primarily expressed in the leaves and were induced by various abiotic stresses.

CONCLUSION

This study conducted genome-wide identification, evolution, synteny analysis, and expression analysis of the PIFs in alfalfa. Our study lays a foundation for the study of the biological functions of the PIF gene family and provides a useful reference for improving abiotic stress resistance in alfalfa.

Interaction of ubiquitin-like protein SILENCING DEFECTIVE 2 with LIKE HETEROCHROMATIN PROTEIN 1 is required for regulation of anthocyanin biosynthesis in Arabidopsis thaliana in response to sucrose

The regulatory mechanisms of anthocyanin biosynthesis have been well documented at the transcriptional and translational levels. By contrast, how anthocyanin biosynthesis is epigenetically regulated remains largely unknown. In this study, we employed genetic, molecular biology, and chromatin immunoprecipitation-quantitative polymerase chain reaction assays to identify a regulatory module essential for repressing the expression of genes involved in anthocyanin biosynthesis through chromatin remodeling. We found that SILENCING DEFECTIVE 2 (SDE2), which was previously identified as a negative regulator for sucrose-induced anthocyanin accumulation in Arabidopsis, is cleaved into N-terminal SDE2-UBL and C-terminal SDE2-C fragments at the first diglycine motif, and the cleaved SDE2-C, which can fully complement the sde2 mutant, is localized in the nucleus and physically interacts with LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in vitro and in vivo. Genetic analyses showed that both SDE2 and LHP1 act as negative factors for anthocyanin biosynthesis. Consistently, immunoblot analysis revealed that the level of LHP1-bound histone H3 lysine 27 trimethylation (H3K27me3) significantly decreases in sde2 and lhp1 mutants, compared to wild-type (WT). In addition, we found that sugar can induce expression of SDE2 and LHP1, and enhance the level of the nucleus-localized SDE2-C. Taken together, our data suggest that the SDE2-C-LHP1 module is required for repression of gene expression through H3K27me3 modification during sugar-induced anthocyanin biosynthesis in Arabidopsis thaliana.

For a Colorful Life: Recent Advances in Anthocyanin Biosynthesis during Leaf Senescence

Leaf senescence is the last stage of leaf development, and it is accompanied by a leaf color change. In some species, anthocyanins are accumulated during leaf senescence, which are vital indicators for both ornamental and commercial value. Therefore, it is essential to understand the molecular mechanism of anthocyanin accumulation during leaf senescence, which would provide new insight into autumn coloration and molecular breeding for more colorful plants. Anthocyanin accumulation is a surprisingly complex process, and significant advances have been made in the past decades. In this review, we focused on leaf coloration during senescence. We emphatically discussed several networks linked to genetic, hormonal, environmental, and nutritional factors in regulating anthocyanin accumulation during leaf senescence. This paper aims to provide a regulatory model for leaf coloration and to put forward some prospects for future development.

Chromatin modifications and memory in regulation of stress-related polyphenols: finding new ways to control flavonoid biosynthesis

The influence of epigenetic factors on plant defense responses and the balance between growth and defense is becoming a central area in plant biology. It is believed that the biosynthesis of secondary metabolites can be regulated by epigenetic factors, but this is not associated with the formation of a "memory" to the previous biosynthetic status. This review shows that some epigenetic effects can result in epigenetic memory, which opens up new areas of research in secondary metabolites, in particular flavonoids. Plant-controlled chromatin modifications can lead to the generation of stress memory, a phenomenon through which information regarding past stress cues is retained, resulting in a modified response to recurring stress. How deeply are the mechanisms of chromatin modification and memory generation involved in the control of flavonoid biosynthesis? This article collects available information from the literature and interactome databases to address this issue. Visualization of the interaction of chromatin-modifying proteins with the flavonoid biosynthetic machinery is presented. Chromatin modifiers and "bookmarks" that may be involved in the regulation of flavonoid biosynthesis through memory have been identified. Through different mechanisms of chromatin modification, plants can harmonize flavonoid metabolism with: stress responses, developmental programs, light-dependent processes, flowering, and longevity programs. The available information points to the possibility of developing chromatin-modifying technologies to control flavonoid biosynthesis.

Decoding plant specialized metabolism: new mechanistic insights

Secondary metabolite (SM) production provides biotic and abiotic stress resistance and enables plants to adapt to the environment. Biosynthesis of these metabolites involves a complex interplay between transcription factors (TFs) and regulatory elements, with emerging evidence suggesting an integral role for chromatin dynamics. Here we review key TFs and epigenetic regulators that govern SM biosynthesis in different contexts. We summarize relevant emerging technologies and results from the model species arabidopsis (Arabidopsis thaliana) and outline aspects of regulation that may also function in food, feed, fiber, oil, or industrial crop plants. Finally, we highlight how effective translation of fundamental knowledge from model to non-model species can benefit understanding of SM production in a variety of ecological, agricultural, and pharmaceutical contexts.

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.

Molecular characterization of Red banana and its somaclonal variant: a comprehensive study

The prized Red banana, selected for superior qualities, demands strong genetic uniformity for successful clonal propagation and preservation. Ensuring this uniformity early in the growth of in vitro Red banana plants is essential, as gene mutations and chromosome rearrangements during tissue culture can jeopardize both cloning and germplasm conservation. In this situation, molecular markers play a pivotal role in confirming genetic stability. Thus the study aims to discover a marker that identifies tissue-cultured Red bananas from their virescent variants during initial sub-culturing. A marker linked to anthocyanin has been identified which effectively differentiated Red bananas from virescent variants and it was further validated in various banana cultivars, ornamental Musa species and their interspecific hybrids. The PCR-based marker showed remarkable specificity, discerning Red bananas from virescent variants during tissue culture. It also distinguished green and red offspring, cutting time and resource costs, and shortening the banana breeding cycle.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03868-6.

Role of epigenetic and post-translational modifications in anthocyanin biosynthesis: A review

Anthocyanins are a class of flavonoids having antioxidant and anti-inflammatory properties. They defend plants against various biotic and abiotic stresses and are synthesized by a specific branch of the flavonoid biosynthetic pathway. Different regulatory mechanisms have been found to regulate anthocyanin biosynthesis in plants. These include the MYB-bHLH-WDR (MBW) MBW trimeric complex consisting of bHLH, R2R3 MYB, and WD40 transcription factors. Epigenetic and Post-translational modification (PTMs) of MBW complex and various other transcription factors play important role in both plant developmental processes and modulating plant response to different environmental conditions. Recent studies have broadened our understanding of the role of various epigenetic (methylation and histone modification) and PTMs (phosphorylation, acetylation, ubiquitylation, sumoylation, etc.) mechanisms in regulating anthocyanin biosynthesis in plants. In this review, we are updating various epigenetic and PTMs modifications of various transcription factors which regulate anthocyanin biosynthesis in various plants. In addition to this, we have also briefly discussed in which direction future research on epigenetic and PTMs can be taken so that we can engineer medicinal plants for enhanced secondary metabolite biosynthesis.

Epigenetic regulation of female germline development through ERECTA signaling pathway

Germline development is a key step in sexual reproduction. Sexual plant reproduction begins with the formation of haploid spores by meiosis of megaspore mother cells (MMCs). Although many evidences, directly or indirectly, show that epigenetics plays an important role in MMC specification, how it controls the commitment of the MMC to downstream stages of germline development is still unclear. Electrophoretic mobility shift assay (EMSA), western blot, immunofluorescence, and chromatin immunoprecipitation coupled with quantitative PCR analyses were performed. Genetic interactions between BZR1 transcription factor family and the SWR1-SDG2-ER pathway in the control of female germline development were further studied. The present findings showed in Arabidopsis that two epigenetic factors, the chromatin remodeling complex SWI2/SNF2-RELATED 1 (SWR1) and a writer for H3K4me3 histone modification SET DOMAIN GROUP 2 (SDG2), genetically interact with the ERECTA (ER) receptor kinase signaling pathway and regulate female germline development by restricting the MMC cell fate to a single cell in the ovule primordium and ensure that only that single cell undergoes meiosis and subsequent megaspore degeneration. We also showed that SWR1-SDG2-ER signaling module regulates female germline development by promoting the protein accumulation of BZR1 transcription factor family on the promoters of primary miRNA processing factors, HYPONASTIC LEAVES 1 (HYL1), DICER-LIKE 1 (DCL1), and SERRATE (SE) to activate their expression. Our study elucidated a Gene Regulation Network that provides new insights for understanding how epigenetic factors and receptor kinase signaling pathways function in concert to control female germline development in Arabidopsis.

Epigenetic silencing of callose synthase by VIL1 promotes bud-growth transition in lily bulbs

In plants, restoring intercellular communication is required for cell activity in buds during the growth transition from slow to fast growth after dormancy release. However, the epigenetic regulation of this phenomenon is far from understood. Here we demonstrate that lily VERNALIZATION INSENSITIVE 3-LIKE 1 (LoVIL1) confers growth transition by mediating plasmodesmata opening via epigenetic repression of CALLOSE SYNTHASE 3 (LoCALS3). Moreover, we found that a novel transcription factor, NUCLEAR FACTOR Y, SUBUNIT A7 (LoNFYA7), is capable of recruiting the LoVIL1-Polycomb Repressive Complex 2 (PRC2) and enhancing H3K27me3 at the LoCALS3 locus by recognizing the CCAAT cis-element (Cce) of its promoter. The LoNFYA7-LoVIL1 module serves as a key player in orchestrating the phase transition from slow to fast growth in lily bulbs. These studies also indicate that LoVIL1 is a suitable marker for the bud-growth-transition trait following dormancy release in lily cultivars.

Loss-of-Function Mutation of ACTIN-RELATED PROTEIN 6 (ARP6) Impairs Root Growth in Response to Salinity Stress

H2A.Z-containing nucleosomes have been found to function in various developmental programs in Arabidopsis (e.g., floral transition, warm ambient temperature, and drought stress responses). The SWI2/SNF2-Related 1 Chromatin Remodeling (SWR1) complex is known to control the deposition of H2A.Z, and it has been unraveled that ACTIN-RELATED PROTEIN 6 (ARP6) is one component of this SWR1 complex. Previous studies showed that the arp6 mutant exhibited some distinguished phenotypes such as early flowering, leaf serration, elongated hypocotyl, and reduced seed germination rate in response to osmotic stress. In this study, we aimed to investigate the changes of arp6 mutant when the plants were grown in salt stress condition. The phenotypic observation showed that the arp6 mutant was more sensitive to salt stress than the wild type. Upon salt stress condition, this mutant exhibited attenuated root phenotypes such as shorter primary root length and fewer lateral root numbers. The transcript levels of stress-responsive genes, ABA INSENSITIVE 1 (ABI1) and ABI2, were found to be impaired in the arp6 mutant in comparison with wild-type plants in response to salt stress. In addition, a meta-analysis of published data indicated a number of genes involved in auxin response were induced in arp6 mutant grown in non-stress condition. These imply that the loss of H2A.Z balance (in arp6 mutant) may lead to change stress and auxin responses resulting in alternative root morphogenesis upon both normal and salinity stress conditions.

Advances in biological functions and mechanisms of histone variants in plants

Nucleosome is the basic subunit of chromatin, consisting of approximately 147bp DNA wrapped around a histone octamer, containing two copies of H2A, H2B, H3 and H4. A linker histone H1 can bind nucleosomes through its conserved GH1 domain, which may promote chromatin folding into higher-order structures. Therefore, the complexity of histones act importantly for specifying chromatin and gene activities. Histone variants, encoded by separate genes and characterized by only a few amino acids differences, can affect nucleosome packaging and stability, and then modify the chromatin properties. Serving as carriers of pivotal genetic and epigenetic information, histone variants have profound significance in regulating plant growth and development, response to both biotic and abiotic stresses. At present, the biological functions of histone variants in plant have become a research hotspot. Here, we summarize recent researches on the biological functions, molecular chaperons and regulatory mechanisms of histone variants in plant, and propose some novel research directions for further study of plant histone variants research field. Our study will provide some enlightens for studying and understanding the epigenetic regulation and chromatin specialization mediated by histone variant in plant.

Identification of GA2ox Family Genes and Expression Analysis under Gibberellin Treatment in Pineapple (Ananas comosus (L.) Merr.)

Gibberellin (GAs) plays an important regulatory role in the development and growth of pineapple (Ananas comosus (L.) Merr.). Bioinformatics was used to confirm the differential expression of GA2 gibberellin oxidase gene AcGA2oxs in the pineapple genome, which laid the foundation for exploring its role in pineapple. In this study, 42 GA2ox genes (AcGA2oxs) were identified in the pineapple genome, named from AcGA2ox1 to AcGA2ox42, and divided into four groups according to phylogenetic analysis. We also analyzed the gene structure, conserved motifs and chromosome localization of AcGA2oxs. AcGA2oxs within the same group had similar gene structure and motifs composition. Collinear analysis and cis-element analysis provided the basis for understanding the evolution and function of GA2ox genes in pineapple. In addition, we selected different tissue parts to analyze the expression profile of AcGA2oxs, and the results show that 41 genes were expressed, except for AcGA2ox18. AcGA2ox18 may not be expressed in these sites or may be pseudogenes. qRT-PCR (real-time fluorescence quantitative PCR) was used to detect the relative expression levels of the GA2ox gene family under different concentrations of GA3 treatment, and it was found that AcGA2ox gene expression was upregulated in different degrees under GA3 treatment. These results provide useful information for further study on the evolution and function of the GA2ox family in pineapple.

Anthocyanins distribution, transcriptional regulation, epigenetic and post-translational modification in fruits

Anthocyanins have indispensable functions in plant resistance, human health, and fruit coloring, which arouse people's favorite. It has been reported that anthocyanins are widely found in fruits, and can be affected by numerous factors. In this review, we systematically summarize anthocyanin functions, classifications, distributions, biosynthesis, decoration, transportation, transcriptional regulation, DNA methylation, and post-translational regulation in fruits.

Genome-wide investigation of NLP gene family members in alfalfa (Medicago sativa L.): evolution and expression profiles during development and stress

BACKGROUND

NIN-like protein (NLP) transcription factors (TFs) compose a plant-specific gene family whose members play vital roles in plant physiological processes, especially in the regulation of plant growth and the response to nitrate-nitrogen. However, no systematic identification or analysis of the NLP gene family has been reported in alfalfa. The recently completed whole-genome sequence of alfalfa has allowed us to investigate genome-wide characteristics and expression profiles.

RESULTS

53 MsNLP genes were identified from alfalfa and renamed according to their respective chromosome distributions. Phylogenetic analysis demonstrated that these MsNLPs can be classified into three groups on the basis of their conserved domains. Gene structure and protein motif analyses showed that closely clustered MsNLP genes were relatively conserved within each subgroup. Synteny analysis revealed four fragment duplication events of MsNLPs in alfalfa. The ratios of nonsynonymous (Ka) and synonymous (Ks) substitution rates of gene pairs indicated that the MsNLP genes underwent purifying selection during evolution. Examination of the expression patterns of different tissues revealed specific expression patterns of the MsNLP genes in the leaves, indicating that these genes are involved in plant functional development. Prediction of cis-acting regulatory elements and expression profiles further demonstrated that the MsNLP genes might play important roles in the response to abiotic stress and in phytohormone signal transduction processes.

CONCLUSION

This study represents the first genome-wide characterization of MsNLP in alfalfa. Most MsNLPs are expressed mainly in leaves and respond positively to abiotic stresses and hormonal treatments. These results provide a valuable resource for an improved understanding of the characteristics and biological roles of the MsNLP genes in alfalfa.

Ethylene signals modulate the survival of Arabidopsis leaf explants

BACKGROUND

Leaf explants are major materials in plant tissue cultures. Incubation of detached leaves on phytohormone-containing media, which is an important process for producing calli and regenerating plants, change their cell fate. Although hormone signaling pathways related to cell fate transition have been widely studied, other molecular and physiological events occurring in leaf explants during this process remain largely unexplored.

RESULTS

Here, we identified that ethylene signals modulate expression of pathogen resistance genes and anthocyanin accumulation in leaf explants, affecting their survival during culture. Anthocyanins accumulated in leaf explants, but were not observed near the wound site. Ethylene signaling mutant analysis revealed that ethylene signals are active and block anthocyanin accumulation in the wound site. Moreover, expression of defense-related genes increased, particularly near the wound site, implying that ethylene induces defense responses possibly by blocking pathogenesis via wounding. We also found that anthocyanin accumulation in non-wounded regions is required for drought resistance in leaf explants.

CONCLUSIONS

Our study revealed the key roles of ethylene in the regulation of defense gene expression and anthocyanin biosynthesis in leaf explants. Our results suggest a survival strategy of detached leaves, which can be applied to improve the longevity of explants during tissue culture.

Different photoprotective strategies for white leaves between two co-occurring Actinidia species

At the outer canopy, the white leaves of Actinidia kolomikta can turn pink but they stay white in A. polygama. We hypothesized that the different leaf colors in the two Actinidia species may represent different photoprotection strategies. To test the hypothesis, leaf optical spectra, anatomy, chlorophyll a fluorescence, superoxide (O₂ ˙^- ) concentration, photosystem II photo-susceptibility, and expression of anthocyanin-related genes were investigated. On the adaxial side, light reflectance was the highest for white leaves of A. kolomikta, followed by its pink leaves and white leaves of A. polygama, and the absorptance for white leaves of A. kolomikta was the lowest. Chlorophyll and carotenoid content of white and pink leaves in A. kolomikta were significantly lower than those of A. polygama, while the relative anthocyanin content of pink leaves was the highest. Chloroplasts of palisade cells of white leaves in A. kolomikta were not well developed with a lower maximum quantum efficiency of PSII than the other types of leaves (pink leaves of A. kolomikta and white leaves of A. Polygama at the inner/outer canopy). After high light treatment from the abaxial surface, F_v /F_m decreased to a larger extent for white leaves of A. kolomikta than pink leaf and white leaves of A. polygama, and its non-photochemical quenching was also the lowest. White leaves of A. kolomikta showed higher O₂ ˙^- concentration compared to pink leaves under the same strong irradiance. The expression levels of anthocyanin biosynthetic genes in pink leaves were higher than in white leaves. These results indicate that white leaves of A. kolomikta apply a reflection strategy for photoprotection, while pink leaves resist photoinhibition via anthocyanin accumulation.

Transcription factor GLK1 promotes anthocyanin biosynthesis via an MBW complex-dependent pathway in Arabidopsis thaliana

Anthocyanins are important natural plant pigments and play diverse roles in plant growth and adaptation. Anthocyanins function as screens to protect photosynthetic tissues from photoinhibition. However, the regulatory mechanisms underlying the biosynthesis and spatial accumulation pattern of anthocyanins remain some unresolved issues. Here, we demonstrate that the GARP-type transcription factor GOLDEN2-LIKE 1 (GLK1) functions as a positive factor in anthocyanin accumulation. GLK1 enhances the transcriptional activation activities of MYB75, MYB90, and MYB113 via direct protein-protein interactions to increase the expression of anthocyanin-specific biosynthetic genes. Anthocyanins accumulate in an acropetal manner in Arabidopsis. We also found that the expression pattern of GLK1 overall mimicked the accumulation pattern of anthocyanin from the base of the main stem to the shoot apex. Based on these findings, we established a working model for the role of GLK1 in anthocyanin accumulation and propose that GLK1 mediates the spatial distribution pattern of anthocyanins by affecting the transcriptional activation activities of MYB75, MYB90, and MYB113.

Chromatin Remodeling Complex SWR1 Regulates Root Development by Affecting the Accumulation of Reactive Oxygen Species (ROS)

Reactive oxygen species (ROS), a type of oxygen monoelectronic reduction product, play integral roles in root growth and development. The epigenetic mechanism plays a critical role in gene transcription and expression; however, its regulation of ROS metabolism in root development is still limited. We found that the chromatin remodeling complex SWR1 regulates root length and lateral root formation in Arabidopsis. Our transcriptome results and gene ontology (GO) enrichment analysis showed that the oxidoreductase activity-related genes significantly changed in mutants for the Arabidopsis SWR1 complex components, such as arp6 and pie1, and histone variant H2A.Z triple mutant hta8 hta9 hta11. The three encoding genes in Arabidopsis are the three H2A.Z variants hta8, hta9, and hta11. Histochemical assays revealed that the SWR1 complex affects ROS accumulation in roots. Furthermore, chromatin immunoprecipitation quantitative real-time PCR (ChIP-qPCR) analysis showed that the reduced H2A.Z deposition in oxidoreductase activity-related genes caused ROS to accumulate in arp6, pie1, and hta8 hta9 hta11. H2A.Z deposition-deficient mutants decreased after the trimethylation of lysine 4 on histone H3 (H3K4me3) modifications and RNA polymerase II (Pol II) enrichment, and increased after the trimethylation of lysine 27 on histone H3 (H3K27me3) modifications, which may account for the expression change in oxidoreductase activity-related genes. In summary, our results revealed that the chromatin complex SWR1 regulates ROS accumulation in root development, highlighting the critical role of epigenetic mechanisms.

Contribution of the histone variant H2A.Z to expression of responsive genes in plants

The histone variant H2A.Z plays a critical role in chromatin-based processes such as transcription, replication, and repair in eukaryotes. Although many H2A.Z-associated processes and features are conserved in plants and animals, a distinguishing feature of plant chromatin is the enrichment of H2A.Z in the bodies of genes that exhibit dynamic expression, particularly in response to differentiation and the environment. Recent work sheds new light on the plant machinery that enables dynamic changes in H2A.Z enrichment and identifies additional chromatin-based pathways that contribute to transcriptional properties of H2A.Z-enriched chromatin. In particular, analysis of a variety of responsive loci reveals a repressive role for H2A.Z in expression of responsive genes and identifies roles for SWR1 and INO80 chromatin remodelers in enabling dynamic regulation of H2A.Z levels and transcription. These studies lay the groundwork for understanding how this ancient histone variant is harnessed by plants to enable responsive and dynamic gene expression (Graphical Abstract).

Histone deacetylase CsHDA6 mediates the regulated formation of the anti-insect metabolite α-farnesene in tea (Camellia sinensis)

α-Farnesene accumulated in tea plants following infestations by most insects, and mechanical wounding is the common factor. However, the specific mechanism underlying the wounding-regulated accumulation of α-farnesene in tea plants remains unclear. In this study, we observed that histone deacetylase inhibitor treatment induced the accumulation of α-farnesene. The histone deacetylase CsHDA6 interacted directly with CsMYC2, which was an important transcription factor in the jasmonic acid (JA) pathway, and co-regulated the expression of the key α-farnesene synthesis gene CsAFS. Wounding caused by insect infestation affected CsHDA6 production at the transcript and protein levels, while also inhibited the binding of CsHDA6 to the CsAFS promoter. The resulting increased acetylation of histones H3/H4 in CsAFS enhanced the expression of CsAFS and the accumulation of α-farnesene. In conclusion, our study demonstrated the effect of histone acetylation on the production of tea plant HIPVs and revealed the importance of the CsHDA6-CsMYC2 transcriptional regulatory module.

Involvement of histone deacetylase CsHDA2 in regulating (E)-nerolidol formation in tea (Camellia sinensis) exposed to tea green leafhopper infestation

Herbivore-induced plant volatiles (HIPVs) help the tea plant (Camellia sinensis) adapt to environmental stress, and they are also quality-related components of tea. However, the upstream mechanism regulating the herbivore-induced expression of volatile biosynthesis genes is unclear, especially at the level of epigenetic regulation. In this study, similar to the effects of a tea green leafhopper infestation, treatments with exogenous jasmonic acid (JA) and histone deacetylase inhibitors significantly increased the (E)-nerolidol content in tea and induced the expression of the associated biosynthesis gene CsNES. Furthermore, a key transcription factor related to JA signaling, myelocytomatosis 2 (CsMYC2), interacted with histone deacetylase 2 (CsHDA2) in vitro and in vivo. A tea green leafhopper infestation inhibited CsHDA2 expression and decreased CsHDA2 abundance. Moreover, the tea green leafhopper infestation increased H3 and H4 acetylation levels in the promoter region of CsNES, which in turn upregulated the expression of CsNES and increased the (E)-nerolidol content. In this study, we revealed the effects of histone acetylations on the accumulation of HIPVs, while also confirming that CsHDA2-CsMYC2 is an important transcriptional regulatory module for the accumulation of (E)-nerolidol induced by tea green leafhoppers. The results of this study may be useful for characterizing plant aromatic compounds and the main upstream stress-responsive signaling molecules. Furthermore, the study findings will assist researchers clarify the epigenetic regulation influencing plant secondary metabolism in response to external stress.

Ectopic Overexpression of Pineapple Transcription Factor AcWRKY31 Reduces Drought and Salt Tolerance in Rice and Arabidopsis

Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value, and its growth and development are affected by the external environment. Drought and salt stresses are common adverse conditions that can affect crop quality and yield. WRKY transcription factors (TFs) have been demonstrated to play critical roles in plant stress response, but the function of pineapple WRKY TFs in drought and salt stress tolerance is largely unknown. In this study, a pineapple AcWRKY31 gene was cloned and characterized. AcWRKY31 is a nucleus-localized protein that has transcriptional activation activity. We observed that the panicle length and seed number of AcWRKY31 overexpression transgenic rice plants were significantly reduced compared with that in wild-type plant ZH11. RNA-seq technology was used to identify the differentially expressed genes (DEGs) between wild-type ZH11 and AcWRKY31 overexpression transgenic rice plants. In addition, ectopic overexpression of AcWRKY31 in rice and Arabidopsis resulted in plant oversensitivity to drought and salt stress. qRT-PCR analysis showed that the expression levels of abiotic stress-responsive genes were significantly decreased in the transgenic plants compared with those in the wild-type plants under drought and salt stress conditions. In summary, these results showed that ectopic overexpression of AcWRKY31 reduced drought and salt tolerance in rice and Arabidopsis and provided a candidate gene for crop variety improvement.

Nitrogen deficiency- and sucrose-induced anthocyanin biosynthesis is modulated by HISTONE DEACETYLASE15 in Arabidopsis

Anthocyanin accumulation is a hallmark response to nitrogen (N) deficiency in Arabidopsis. Although the regulation of anthocyanin biosynthesis has been extensively studied, the roles of chromatin modification in this process are largely unknown. In this study we show that anthocyanin accumulation induced by N deficiency is modulated by HISTONE DEACETYLASE15 (HDA15) in Arabidopsis seedlings. The hda15-1 T-DNA insertion mutant accumulated more anthocyanins than the wild-type when the N supply was limited, and this was caused by up-regulation of anthocyanin biosynthetic and regulatory genes in the mutant. The up-regulated genes also had increased levels of histone acetylation in the mutant. The accumulation of anthocyanins induced by sucrose and methyl jasmonate, but not that induced by H2O2 and phosphate starvation, was also greater in the hda15-1 mutant. While sucrose increased histone acetylation in the hda15-1 mutant in genes in a similar manner to that caused by N deficiency, methyl jasmonate only enhanced histone acetylation in the genes involved in anthocyanin biosynthesis. Our results suggest that different stresses act through distinct regulatory modules to activate anthocyanin biosynthesis, and that HDA15-mediated histone modification modulates the expression of anthocyanin biosynthetic and regulatory genes to avoid overaccumulation in response to N deficiency and other stresses.

Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice

Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.

Histone Variants in the Specialization of Plant Chromatin

The basic unit of chromatin, the nucleosome, is an octamer of four core histone proteins (H2A, H2B, H3, and H4) and serves as a fundamental regulatory unit in all DNA-templated processes. The majority of nucleosome assembly occurs during DNA replication when these core histones are produced en masse to accommodate the nascent genome. In addition, there are a number of nonallelic sequence variants of H2A and H3 in particular, known as histone variants, that can be incorporated into nucleosomes in a targeted and replication-independent manner. By virtue of their sequence divergence from the replication-coupled histones, these histone variants can impart unique properties onto the nucleosomes they occupy and thereby influence transcription and epigenetic states, DNA repair, chromosome segregation, and other nuclear processes in ways that profoundly affect plant biology. In this review, we discuss the evolutionary origins of these variants in plants, their known roles in chromatin, and their impacts on plant development and stress responses. We focus on the individual and combined roles of histone variants in transcriptional regulation within euchromatic and heterochromatic genome regions. Finally, we highlight gaps in our understanding of plant variants at the molecular, cellular, and organismal levels, and we propose new directions for study in the field of plant histone variants.

OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice

Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.

Molecular components associated with the regulation of flavonoid biosynthesis

Flavonoids exhibit amazing structural diversity and play different roles in plants. Besides, these compounds have been associated with several health benefits in humans. Several exogenous and endogenous cues, for example, light, temperature, nutrient status, and phytohormones have been reported as modulators of biosynthesis and accumulation of flavonoids. Thus, multiple hormones and stress-related signaling pathways are involved in the regulation of gene expression associated with this pathway. The transcriptional regulators belonging to the MYB and bHLH family transcription factors are well documented as the direct regulators of the structural genes associated with flavonoid biosynthesis. Recent studies also suggest that some of these factors are regulated by molecular components involved in stress and hormone signaling pathways. Adapter proteins for transcriptional activation or repression via recruitment of co-activators and co-repressors, respectively, E2 ubiquitin ligases, miRNA processing complex, and DNA methylation/demethylation factors have been recently discovered in various plants to play key roles in fine-tuning flavonoids synthesis. In the present review, we aim to provide comprehensive information about the role of different factors in the regulation of flavonoid biosynthesis. Besides, we describe the potential upstream regulators involved in the regulation of flavonoid biosynthesis within the context of available information. To sum up, the present review furnishes an updated account of signal transduction pathways modulating the biosynthesis of flavonoids.

Anthocyanins: Traditional Uses, Structural and Functional Variations, Approaches to Increase Yields and Products' Quality, Hepatoprotection, Liver Longevity, and Commercial Products

Anthocyanins are water-soluble, colored compounds of the flavonoid class, abundantly found in the fruits, leaves, roots, and other parts of the plants. The fruit berries are prime sources and exhibit different colors. The anthocyanins utility as traditional medicament for liver protection and cure, and importance as strongest plants-based anti-oxidants have conferred these plants products different biological activities. These activities include anti-inflammation, liver protective, analgesic, and anti-cancers, which have provided the anthocyanins an immense commercial value, and has impelled their chemistry, biological activity, isolation, and quality investigations as prime focus. Methods in extraction and production of anthocyanin-based products have assumed vital economic importance. Different extraction techniques in aquatic solvents mixtures, eutectic solvents, and other chemically reactive extractions including low acid concentrations-based extractions have been developed. The prophylactic and curative therapy roles of the anthocyanins, together with no reported toxicity has offered much-needed impetus and economic benefits to these classes of compounds which are commercially available. Information retrieval from various search engines, including the PubMed®, ScienceDirect®, Scopus®, and Google Scholar®, were used in the review preparation. This imparted an outlook on the anthocyanins occurrence, roles in plants, isolation-extraction, structures, biosynthetic as well as semi- and total-synthetic pathways, product quality and yields enhancements, including uses as part of traditional medicines, and uses in liver disorders, prophylactic and therapeutic applications in liver protection and longevity, liver cancer and hepatocellular carcinoma. The review also highlights the integrated approach to yields maximizations to meet the regular demands of the anthocyanins products, also as part of the extract-rich preparations together with a listing of marketed products available for human consumption as nutraceuticals/food supplements.

Comparative Transcriptome Analysis Revealed Two Alternative Splicing bHLHs Account for Flower Color Alteration in Chrysanthemum

'Jimba' is a white chrysanthemum cultivar, which occasionally and spontaneously produces red flower petals under natural cultivation due to cyanidin-based anthocyanin accumulation. To investigate the underlying mechanism of this process, a comparative transcriptome was analyzed between white and turning red 'Jimba'. The structural and regulatory genes of anthocyanin pathway were significantly up-regulated in turning red 'Jimba'. Among them, two alternative splicings, CmbHLH2 and CmbHLH2.1, showed the most significantly up-regulated in turning red tissue. Transiently over-expressed 35S::CmMYB6-CmbHLH2 strongly induced anthocyanin accumulation in 'Jimba' flower petals, while moderate amount of anthocyanin was detected when over-expressed 35S::CmMYB6-CmbHLH2.1. Both CmbHLH2 and CmbHLH2.1 could interact with CmMYB6 to activate CmDFR promoter according to Yeast two-hybrid and dual-luciferase assay. Moreover, CmMYB6-CmbHLH2 but not CmMYB6-CmbHLH2.1 could activate the CmbHLH2 promoter to provide positive feedback loop regulation. Taken together, it suggested that both CmbHLH2 and CmbHLH2.1 involved in regulation flower color alteration in turning red 'Jimba', and CmbHLH2 played a predominant role in this process.

SDG2 regulates Arabidopsis inflorescence architecture through SWR1-ERECTA signaling pathway

Inflorescence architecture is diverse in flowering plants, and two determinants of inflorescence architecture are the inflorescence meristem and pedicel length. Although the ERECTA (ER) signaling pathway, in coordination with the SWR1 chromatin remodeling complex, regulates inflorescence architecture with subsequent effects on pedicel elongation, the mechanism underlying SWR1-ER signaling pathway regulation of inflorescence architecture remains unclear. This study determined that SDG2 genetically interacts with the SWR1-ER signaling pathways in regulating inflorescence architecture. Transcriptome results showed that auxin might potentially influence inflorescence growth mediated by SDG2 and SWR1-ER pathways. SWR1 and ER signaling are required to enrich H2A.Z histone variant and SDG2 regulated SDG2-mediated H3K4me3 histone modification at auxin-related genes and H2A.Z histone variant enrichment. Our study shows how the regulation of inflorescence architecture is mediated by SDG2 and SWR1-ER, which affects auxin hormone signaling pathways.

The INO80 chromatin remodeling complex promotes thermomorphogenesis by connecting H2A.Z eviction and active transcription in Arabidopsis

Global warming poses a major threat to plant growth and crop production. In some plants, including Arabidopsis thaliana, elevated temperatures induce a series of morphological and developmental adjustments termed thermomorphogenesis, which facilitates plant cooling under high-temperature conditions. Plant thermal response is suppressed by histone variant H2A.Z. At warm temperatures, H2A.Z is evicted from nucleosomes at thermoresponsive genes, resulting in changes in their expression. However, the mechanisms that regulate H2A.Z eviction and subsequent transcriptional changes are largely unknown. Here, we show that the INO80 chromatin remodeling complex (INO80-C) promotes thermomorphogenesis and activates the expression of thermoresponsive and auxin-related genes. INO80-C associates with PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), a potent regulator of thermomorphogenesis, and mediates temperature-induced H2A.Z eviction at PIF4 targets. Moreover, INO80-C directly interacts with COMPASS-like and transcription elongation factors to promote active histone modification, histone H3 lysine 4 trimethylation, and RNA polymerase II elongation, leading to the thermal induction of transcription. Notably, the transcription elongation factors SPT4 and SPT5 are required for H2A.Z eviction at PIF4 targets, suggesting the cooperation of INO80-C and transcription elongation in H2A.Z removal. Taken together, these results suggest that the (PIF4)-(INO80-C)-(COMPASS-like)-(transcription elongator) module controls plant thermal response, thereby establishing a link between H2A.Z eviction and active transcription.

Anthocyanins: From Mechanisms of Regulation in Plants to Health Benefits in Foods

Anthocyanins represent the major red, purple, and blue pigments in many flowers, fruits, vegetables, and cereals. They are also recognized as important health-promoting components in the human diet with protective effects against many chronic diseases, including cardiovascular diseases, obesity, and cancer. Anthocyanin biosynthesis has been studied extensively, and both biosynthetic and key regulatory genes have been isolated in many plant species. Here, we will provide an overview of recent progress in understanding the anthocyanin biosynthetic pathway in plants, focusing on the transcription factors controlling activation or repression of anthocyanin accumulation in cereals and fruits of different plant species, with special emphasis on the differences in molecular mechanisms between monocot and dicot plants. Recently, new insight into the transcriptional regulation of the anthocyanin biosynthesis, including positive and negative feedback control as well as epigenetic and post-translational regulation of MYB-bHLH-WD40 complexes, has been gained. We will consider how knowledge of regulatory mechanisms has helped to produce anthocyanin-enriched foods through conventional breeding and metabolic engineering. Additionally, we will briefly discuss the biological activities of anthocyanins as components of the human diet and recent findings demonstrating the important health benefits of anthocyanin-rich foods against chronic diseases.

Repressors of anthocyanin biosynthesis

Anthocyanins play a variety of adaptive roles in both vegetative tissues and reproductive organs of plants. The broad functionality of these compounds requires sophisticated regulation of the anthocyanin biosynthesis pathway to allow proper localization, timing, and optimal intensity of pigment deposition. While it is well-established that the committed steps of anthocyanin biosynthesis are activated by a highly conserved MYB-bHLH-WDR (MBW) protein complex in virtually all flowering plants, anthocyanin repression seems to be achieved by a wide variety of protein and small RNA families that function in different tissue types and in response to different developmental, environmental, and hormonal cues. In this review, we survey recent progress in the identification of anthocyanin repressors and the characterization of their molecular mechanisms. We find that these seemingly very different repression modules act through a remarkably similar logic, the so-called 'double-negative logic'. Much of the double-negative regulation of anthocyanin production involves signal-induced degradation or sequestration of the repressors from the MBW protein complex. We discuss the functional and evolutionary advantages of this logic design compared with simple or sequential positive regulation. These advantages provide a plausible explanation as to why plants have evolved so many anthocyanin repressors.

Arabidopsis cryptochrome 1 controls photomorphogenesis through regulation of H2A.Z deposition

Light is a key environmental cue that fundamentally regulates plant growth and development, which is mediated by the multiple photoreceptors including the blue light (BL) photoreceptor cryptochrome 1 (CRY1). The signaling mechanism of Arabidopsis thaliana CRY1 involves direct interactions with CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1)/SUPPRESSOR OF PHYA-105 1 and stabilization of COP1 substrate ELONGATED HYPOCOTYL 5 (HY5). H2A.Z is an evolutionarily conserved histone variant, which plays a critical role in transcriptional regulation through its deposition in chromatin catalyzed by SWR1 complex. Here we show that CRY1 physically interacts with SWC6 and ARP6, the SWR1 complex core subunits that are essential for mediating H2A.Z deposition, in a BL-dependent manner, and that BL-activated CRY1 enhances the interaction of SWC6 with ARP6. Moreover, HY5 physically interacts with SWC6 and ARP6 to direct the recruitment of SWR1 complex to HY5 target loci. Based on previous studies and our findings, we propose that CRY1 promotes H2A.Z deposition to regulate HY5 target gene expression and photomorphogenesis in BL through the enhancement of both SWR1 complex activity and HY5 recruitment of SWR1 complex to HY5 target loci, which is likely mediated by interactions of CRY1 with SWC6 and ARP6, and CRY1 stabilization of HY5, respectively.

Spatiotemporal control of miR398 biogenesis, via chromatin remodeling and kinase signaling, ensures proper ovule development

The coordinated development of sporophytic and gametophytic tissues is essential for proper ovule patterning and fertility. However, the mechanisms regulating their integrated development remain poorly understood. Here, we report that the Swi2/Snf2-Related1 (SWR1) chromatin-remodeling complex acts with the ERECTA receptor kinase-signaling pathway to control female gametophyte and integument growth in Arabidopsis thaliana by inhibiting transcription of the microRNA gene MIR398c in early-stage megagametogenesis. Moreover, pri-miR398c is transcribed in the female gametophyte but is then translocated to and processed in the ovule sporophytic tissues. Together, SWR1 and ERECTA also activate ARGONAUTE10 (AGO10) expression in the chalaza; AGO10 sequesters miR398, thereby ensuring the expression of three AGAMOUS-LIKE (AGL) genes (AGL51, AGL52, and AGL78) in the female gametophyte. In the context of sexual organ morphogenesis, these findings suggest that the spatiotemporal control of miRNA biogenesis, resulting from coordination between chromatin remodeling and cell signaling, is essential for proper ovule development in Arabidopsis.

DNA methylation: from model plants to vegetable crops

As a subgroup of horticultural crops, vegetable food is a kind of indispensable energy source for human beings, providing necessary nutritional components including vitamins, carbohydrates, dietary fiber, and active substances such as carotenoids and flavonoids. The developmental process of vegetable crops is not only regulated by environmental stimulations, but also manipulated by both genetic and epigenetic modifications. Epigenetic modifications are composed by several regulatory mechanisms, including DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs. Among these modifications, DNA methylation functions in multiple biological pathways ranging from fundamental development to environmental stimulations by mediating transcriptomic alterations, resulting in the activation or silencing of target genes. In recent years, intensive studies have revealed that DNA methylation is essential to fruit development and ripening, indicating that the epigenome of fruit crops could be dynamically modified according to the specific requirements in the commercial production. Firstly, this review will present the mechanisms of DNA methylation, and update the understanding on active DNA demethylation in Arabidopsis thaliana. Secondly, this review will summarize the recent progress on the function of DNA methylation in regulating fruit ripening. Moreover, the possible functions of DNA methylation on controlling the expansion of edible organs, senescence of leafy vegetables, and anthocyanin pigmentation in several important vegetable crops will be discussed. Finally, this review will highlight the intractable issues that need to be resolved in the application of epigenome in vegetable crops, and provide perspectives for the potential challenges in the further studies.

MYB transcription factors GmMYBA2 and GmMYBR function in a feedback loop to control pigmentation of seed coat in soybean

Soybean has undergone extensive selection pressures for seed nutrient composition and seed color during domestication, but the major genetic loci controlling seed coat color have not been completely understood, and the transcriptional regulation relationship among the loci remains elusive. Here, two major regulators, GmMYBA2 and GmMYBR, were functionally characterized as an anthocyanin activator and repressor, respectively. Ectopic expression of GmMYBA2 in soybean hairy roots conferred the enhanced accumulation of delphinidin and cyanidin types of anthocyanins in W1t and w1T backgrounds, respectively, through activating anthocyanin biosynthetic genes in the reported loci. The seed coat pigmentation of GmMYBA2-overexpressing transgenic plants in the W1 background mimicked the imperfect black phenotype (W1/w1, i, R, t), suggesting that GmMYBA2 was responsible for the R locus. Molecular and biochemical analysis showed that GmMYBA2 interacted with GmTT8a to directly activate anthocyanin biosynthetic genes. GmMYBA2 and GmMYBR might form a feedback loop to fine-tune seed coat coloration, which was confirmed in transgenic soybeans. Both GmTT8a and GmMYBR that were activated by GmMYBA2 in turn enhanced and obstructed the formation of the GmMYBA2-GmTT8a module, respectively. The results revealed the sophisticated regulatory network underlying the soybean seed coat pigmentation loci and shed light on the understanding of the seed coat coloration and other seed inclusions.

ERECTA signaling regulates plant immune responses via chromatin-mediated promotion of WRKY33 binding to target genes

The signaling pathway mediated by the receptor-like kinase ERECTA (ER) plays important roles in plant immune responses, but the underlying mechanism is unclear. Genetic interactions between ER signaling and the chromatin remodeling complex SWR1 in the control of plant immune responses were studied. Electrophoretic mobility shift assay and yeast one-hybrid analysis were applied to identify ER-WRKY33 downstream components. Chromatin immunoprecipitation analyses were further investigated. In this study, we show that the chromatin remodeling complex SWR1 enhances resistance to the white mold fungus Sclerotinia sclerotiorum in Arabidopsis thaliana via a process mediated by ER signaling. We identify a series of WRKY33 target YODA DOWNSTREAM (YDD) genes and demonstrate that SWR1 and ER signaling are required to enrich H2A.Z histone variant and H3K4me3 histone modification at YDDs and the binding of WRKY33 to YDD promoters upon S. sclerotiorum infection. We also reveal that the binding of WRKY33 to YDD promoters in turn promotes the enrichment of H2A.Z and H3K4me3 at YDD genes, thereby forming a positive regulatory loop to activate YDDs expression. Our study reveals how H2A.Z, H3K4me3 and ER signaling mutually regulate YDDs gene expression upon pathogen infection, highlighting the critical role of chromatin structure in ER-signaling-mediated plant immune responses.

Transgenerational Plasticity in Flower Color Induced by Caterpillars

Variation in flower color due to transgenerational plasticity could stem directly from abiotic or biotic environmental conditions. Finding a link between biotic ecological interactions across generations and plasticity in flower color would indicate that transgenerational effects of ecological interactions, such as herbivory, might be involved in flower color evolution. We conducted controlled experiments across four generations of wild radish (Raphanus sativus, Brassicaceae) plants to explore whether flower color is influenced by herbivory, and to determine whether flower color is associated with transgenerational chromatin modifications. We found transgenerational effects of herbivory on flower color, partly related to chromatin modifications. Given the presence of herbivory in plant populations worldwide, our results are of broad significance and contribute to our understanding of flower color evolution.

H3K4 trimethylation dynamics impact diverse developmental and environmental responses in plants

The H3K4me3 histone mark in plants functions in the regulation of gene expression and transcriptional memory, and influences numerous developmental processes and stress responses. Plants execute developmental programs and respond to changing environmental conditions via adjustments in gene expression, which are modulated in part by chromatin structure dynamics. Histone modifications alter chromatin in precise ways on a global scale, having the potential to influence the expression of numerous genes. Trimethylation of lysine 4 on histone H3 (H3K4me3) is a prominent histone modification that is dogmatically associated with gene activity, but more recently has also been linked to gene repression. As in other eukaryotes, the distribution of H3K4me3 in plant genomes suggests it plays a central role in gene expression regulation, however the underlying mechanisms are not fully understood. Transcript levels of many genes related to flowering, root, and shoot development are affected by dynamic H3K4me3 levels, as are those for a number of stress-responsive and stress memory-related genes. This review examines the current understanding of how H3K4me3 functions in modulating plant responses to developmental and environmental cues.

Contribution of phenylpropanoid metabolism to plant development and plant-environment interactions

Phenylpropanoid metabolism is one of the most important metabolisms in plants, yielding more than 8,000 metabolites contributing to plant development and plant-environment interplay. Phenylpropanoid metabolism materialized during the evolution of early freshwater algae that were initiating terrestrialization and land plants have evolved multiple branches of this pathway, which give rise to metabolites including lignin, flavonoids, lignans, phenylpropanoid esters, hydroxycinnamic acid amides, and sporopollenin. Recent studies have revealed that many factors participate in the regulation of phenylpropanoid metabolism, and modulate phenylpropanoid homeostasis when plants undergo successive developmental processes and are subjected to stressful environments. In this review, we summarize recent progress on elucidating the contribution of phenylpropanoid metabolism to the coordination of plant development and plant-environment interaction, and metabolic flux redirection among diverse metabolic routes. In addition, our review focuses on the regulation of phenylpropanoid metabolism at the transcriptional, post-transcriptional, post-translational, and epigenetic levels, and in response to phytohormones and biotic and abiotic stresses.

OsChz1 acts as a histone chaperone in modulating chromatin organization and genome function in rice

While the yeast Chz1 acts as a specific histone-chaperone for H2A.Z, functions of CHZ-domain proteins in multicellular eukaryotes remain obscure. Here, we report on the functional characterization of OsChz1, a sole CHZ-domain protein identified in rice. OsChz1 interacts with both the canonical H2A-H2B dimer and the variant H2A.Z-H2B dimer. Within crystal structure the C-terminal region of OsChz1 binds H2A-H2B via an acidic region, pointing to a previously unknown recognition mechanism. Knockout of OsChz1 leads to multiple plant developmental defects. At genome-wide level, loss of OsChz1 causes mis-regulations of thousands of genes and broad alterations of nucleosome occupancy as well as reductions of H2A.Z-enrichment. While OsChz1 associates with chromatin regions enriched of repressive histone marks (H3K27me3 and H3K4me2), its loss does not affect the genome landscape of DNA methylation. Taken together, it is emerging that OsChz1 functions as an important H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin for higher eukaryote development.

Function of CHZ-domain proteins in multicellular eukaryotes remains unclear. Here, the authors characterize the sole CHZ-domain protein identified in rice and show that it functions as an H2A/H2A.Z-H2B chaperone in dynamic regulation of chromatin organization and genome function.

The bZIP Transcription Factor GmbZIP15 Negatively Regulates Salt- and Drought-Stress Responses in Soybean

Soybean (Glycine max), as an important oilseed crop, is constantly threatened by abiotic stress, including that caused by salinity and drought. bZIP transcription factors (TFs) are one of the largest TF families and have been shown to be associated with various environmental-stress tolerances among species; however, their function in abiotic-stress response in soybean remains poorly understood. Here, we characterized the roles of soybean transcription factor GmbZIP15 in response to abiotic stresses. The transcript level of GmbZIP15 was suppressed under salt- and drought-stress conditions. Overexpression of GmbZIP15 in soybean resulted in hypersensitivity to abiotic stress compared with wild-type (WT) plants, which was associated with lower transcript levels of stress-responsive genes involved in both abscisic acid (ABA)-dependent and ABA-independent pathways, defective stomatal aperture regulation, and reduced antioxidant enzyme activities. Furthermore, plants expressing a functional repressor form of GmbZIP15 exhibited drought-stress resistance similar to WT. RNA-seq and qRT-PCR analyses revealed that GmbZIP15 positively regulates GmSAHH1 expression and negatively regulates GmWRKY12 and GmABF1 expression in response to abiotic stress. Overall, these data indicate that GmbZIP15 functions as a negative regulator in response to salt and drought stresses.

Genome-wide identification and expression analysis of the ERF transcription factor family in pineapple (Ananas comosus (L.) Merr.)

Pineapple (Ananas comosus (L.) Merr.) is an important tropical fruit with high economic value. The quality and yield of pineapple will be affected by various environmental conditions. Under adverse conditions, plants can produce a complex reaction mechanism to enhance their resistance. It has been reported that the member of ethylene responsive transcription factors (ERFs) plays a crucial role in plant developmental process and stress response. However, the function of these proteins in pineapple remains limited. In this study, a total of 74 ERF genes (AcoERFs) were identified in pineapple genome, named from AcoERF1 to AcoERF74, and divided into 13 groups based on phylogenetic analysis. We also analyzed gene structure, conserved motif and chromosomal location of AcoERFs, and the AcoERFs within the same group possess similar gene structures and motif compositions. Three genes (AcoERF71, AcoERF73 and AcoERF74) were present on unanchored scaffolds, so they could not be conclusively mapped on chromosome. Synteny and cis-elements analysis of ERF genes provided deep insight into the evolution and function of pineapple ERF genes. Furthermore, we analyzed the expression profiling of AcoERF in different tissues and developmental stages, and 22 AcoERF genes were expressed in all examined tissues, in which five genes (AcoERF13, AcoERF16, AcoERF31, AcoERF42, and AcoERF65) had high expression levels. Additionally, nine AcoERF genes were selected for functional verification by qRT-PCR. These results provide useful information for further investigating the evolution and functions of ERF family in pineapple.

Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture

Anthocyanins are antioxidant pigments widely used in drugs and food preparations. Flesh-coloured tubers of the cultivated potato Solanum tuberosum are important sources of different anthocyanins. Due to the high degree of decoration achieved by acylation, anthocyanins from potato are very stable and suitable for the food processing industry. The use of cell culture allows to extract anthocyanins on-demand, avoiding seasonality and consequences associated with land-based-tuber production. However, a well-known limit of cell culture is the metabolic instability and loss of anthocyanin production during successive subcultures. To get a general picture of mechanisms responsible for this instability, we explored both genetic and epigenetic regulation that may affect anthocyanin production in cell culture. We selected two clonally related populations of anthocyanin-producing (purple) and non-producing (white) potato cells. Through targeted molecular investigations, we identified and functionally characterized an R3-MYB, here named StMYBATV. This transcription factor can interact with bHLHs belonging to the MBW (R2R3-MYB, bHLH and WD40) anthocyanin activator complex and, potentially, may interfere with its formation. Genome methylation analysis revealed that, for several genomic loci, anthocyanin-producing cells were more methylated than clonally related white cells. In particular, we localized some methylation events in ribosomal protein-coding genes. Overall, our study explores novel molecular aspects associated with loss of anthocyanins in cell culture systems.

Anthocyanins: A Comprehensive Review of Their Chemical Properties and Health Effects on Cardiovascular and Neurodegenerative Diseases

Anthocyanins are a class of water-soluble flavonoids widely present in fruits and vegetables. Dietary sources of anthocyanins include red and purple berries, grapes, apples, plums, cabbage, or foods containing high levels of natural colorants. Cyanidin, delphinidin, malvidin, peonidin, petunidin, and pelargonidin are the six common anthocyanidins. Following consumption, anthocyanin, absorption occurs along the gastrointestinal tract, the distal lower bowel being the place where most of the absorption and metabolism occurs. In the intestine, anthocyanins first undergo extensive microbial catabolism followed by absorption and human phase II metabolism. This produces hybrid microbial-human metabolites which are absorbed and subsequently increase the bioavailability of anthocyanins. Health benefits of anthocyanins have been widely described, especially in the prevention of diseases associated with oxidative stress, such as cardiovascular and neurodegenerative diseases. Furthermore, recent evidence suggests that health-promoting effects attributed to anthocyanins may also be related to modulation of gut microbiota. In this paper we attempt to provide a comprehensive view of the state-of-the-art literature on anthocyanins, summarizing recent findings on their chemistry, biosynthesis, nutritional value and on their effects on human health.

Skin Color in Apple Fruit (Malus × domestica): Genetic and Epigenetic Insights

Apple skin color is an important trait for organoleptic quality. In fact, it has a major influence on consumer choice. Skin color is, thus, one of the most important criteria taken into account by breeders. For apples, most novel varieties are so-called "mutants" or "sports" that have been identified in clonal populations. Indeed, many "sports" exist that show distinct phenotypic differences compared to the varieties from which they originated. These differences affect a limited number of traits of economic importance, including skin color. Until recently, the detailed genetic or epigenetic changes resulting in heritable phenotypic changes in sports was largely unknown. Recent technological advances and the availability of several high-quality apple genomes now provide the bases to understand the exact nature of the underlying molecular changes that are responsible for the observed phenotypic changes observed in sports. The present review investigates the molecular nature of sports affected in apple skin color giving arguments in favor of the genetic or epigenetic explanatory models.