Dynamic Changes of DNA Methylation During Wild Strawberry (Fragaria nilgerrensis) Tissue Culture

A Truncated Mutation of TP53 Promotes Chemoresistance in Tongue Squamous Cell Carcinoma

Tongue squamous cell carcinoma (TSCC), a subtype of head and neck squamous cell carcinoma, is characterized by frequent chemoresistance. Genetic mutations commonly observed in TSCC play a critical role in malignant progression; thus, elucidating their functional significance is essential for developing effective treatment strategies. To more accurately investigate the relationship between mutations and chemoresistance, we established low-passage TSCC cells, CTSC-1, obtained from a chemoresistant patient, and CTSC-2, from a treatment-naïve patient. Sanger sequencing revealed a specific TP53 mutation (Q331*) in CTSC-1, leading to the loss of the tetramerization and C-terminal regulatory domains. Notably, CTSC-1 cells harboring TP53-Q331* and CTSC-2 cells with TP53 knockout that have been engineered to ectopically express TP53-Q331* exhibit enhanced chemoresistance and increased cancer stem cell-like properties. Mechanistically, TP53-Q331* upregulates the expression of inhibitor of DNA binding 2 (ID2), which is crucial for maintaining the stemness of TSCC cells. Subsequently, ID2 activates the expression of nucleotide excision repair (NER) pathway-related genes ERCC4 and ERCC8, thereby enhancing the chemoresistance in TSCC. In conclusion, our study demonstrates that the TP53-Q331* mutation enhances TSCC chemoresistance through an ID2-mediated NER pathway, providing a potential prognostic marker and therapeutic target for TSCC chemotherapy resistance.

Genome-wide DNA methylation analysis of sorghum leaves following foreign GA3 exposure under salt stress

Sorghum is an increasingly popular topic of research in elucidating survival and adaptation approaches to augmented salinity. Nonetheless, little is known about the outcome and modulatory networks involved in the gibberellic acid (GA3)-induced salt stress alleviation in sorghum. Here, we identified 50 mg/L GA3 as the optimal concentration for sorghum ('Jitian 3') development under salt stress. Based on genome-wide DNA methylation analysis, CpG sites displayed the most abundant methylation statuses among all stages, with a mean value of 68.2 %, then CHG (57.9 %), and CHH (21.2 %). We identified 18,032 differentially methylated regions (DMRs) in the GA3-exposed groups. In particular, we recognized 5943 DMR genes and 269 DMR-promoter genes. Using conjoint transcriptome and DNA methylation analyses, we identified 337 important methylated-genes, which were involved in "phenylpropanoid biosynthesis", "arginine and proline metabolism" and "tyrosine metabolism". Together, the aforementioned data provides an in-depth understanding of the epigenetic modulation of gene expression during GA3 treatment.

Developmental processes in the Rosaceae through the lens of DNA and RNA methylation

MAIN CONCLUSION

This review discusses the DNA and RNA methylation pathways and their biological roles in Rosaceae developmental processes relevant for breeding and production. The Rosaceae is a plant family of great importance for human nutrition and health. Many traits and developmental processes of the Rosaceae are influenced by epigenetic methylation, functions of which are now being unravelled in several important species of this family. Methylation of DNA at the 5th position of cytosine (5mC) is a well-established epigenetic mark that affects important cellular processes such as gene expression and genome stability and is involved in a wide range of plant biological functions. Further to this, recent technological advances have uncovered other naturally occurring chemical modifications of DNA and RNA as additional layers of regulatory epigenetic information in plants. In this review we give a comprehensive summary of plant 5-methylcytosine DNA methylation mechanisms and review their components identified in species of the Rosaceae family. We detail and discuss the role of 5mC DNA methylation dynamics in Rosaceae developmental processes, including phase transition, bud development, bud dormancy, plant architecture, plant regeneration, fruit development, ripening and senescence. We then review recent advances in understanding the newly identified nucleic acid modifications, N6-adenosine methylation of DNA (6mA) and RNA (m6A) as additional epigenetic mechanisms. We summarise identified components of adenosine methylation pathways in the Rosaceae and discuss the emerging roles of this modification in plant development including recent findings in Rosaceous species. Integrating epigenetic aspects of plant development with plant genetics and physiology is crucial for understanding biological processes in Rosaceous plants.

Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries

Somatic mutations arise and accumulate during tissue culture and vegetative propagation, potentially affecting various traits in horticultural crops, but their characteristics are still unclear. Here, somatic mutations in regenerated woodland strawberry derived from tissue culture of shoot tips under different conditions and 12 cultivated strawberry individuals are analyzed by whole genome sequencing. The mutation frequency of single nucleotide variants is significantly increased with increased hormone levels or prolonged culture time in the range of 3.3 × 10-8-3.0 × 10-6 mutations per site. CG methylation shows a stable reduction (0.71%-8.03%) in regenerated plants, and hypoCG-DMRs are more heritable after sexual reproduction. A high-quality haplotype-resolved genome is assembled for the strawberry cultivar "Beni hoppe." The 12 "Beni hoppe" individuals randomly selected from different locations show 4731-6005 mutations relative to the reference genome, and the mutation frequency varies among the subgenomes. Our study has systematically characterized the genetic and epigenetic variants in regenerated woodland strawberry plants and different individuals of the same strawberry cultivar, providing an accurate assessment of somatic mutations at the genomic scale and nucleotide resolution in plants.

Transcriptomic and Physiological Analyses for the Role of Hormones and Sugar in Axillary Bud Development of Wild Strawberry Stolon

Strawberries are mainly propagated by stolons, which can be divided into monopodial and sympodial types. Monopodial stolons consistently produce ramets at each node following the initial single dormant bud, whereas sympodial stolons develop a dormant bud before each ramet. Sympodial stolon encompasses both dormant buds and ramet buds, making it suitable for studying the formation mechanism of different stolon types. In this study, we utilized sympodial stolons from Fragaria nilgerrensis as materials and explored the mechanisms underlying sympodial stolon development through transcriptomic and phytohormonal analyses. The transcriptome results unveiled that auxin, cytokinin, and sugars likely act as main regulators. Endogenous hormone analysis revealed that the inactivation of auxin could influence bud dormancy. Exogenous cytokinin application primarily induced dormant buds to develop into secondary stolons, with the proportion of ramet formation being very low, less than 10%. Furthermore, weighted gene co-expression network analysis identified key genes involved in ramet formation, including auxin transport and response genes, the cytokinin activation gene LOG1, and glucose transport genes SWEET1 and SFP2. Consistently, in vitro cultivation experiments confirmed that glucose enhances the transition of dormant buds into ramets within two days. Collectively, cytokinin and glucose act as dormant breakers, with cytokinin mainly driving secondary stolon formation and glucose promoting ramet generation. This study improved our understanding of stolon patterning and bud development in the sympodial stolon of strawberries.

Epigenomic and transcriptomic persistence of heat stress memory in strawberry (Fragaria vesca)

BACKGROUND

In plants, epigenetic stress memory has so far been found to be largely transient. Here, we wanted to assess the heritability of heat stress-induced epigenetic and transcriptomic changes following woodland strawberry (Fragaria vesca) reproduction. Strawberry is an ideal model to study epigenetic inheritance because it presents two modes of reproduction: sexual (self-pollinated plants) and asexual (clonally propagated plants named daughter plants). Taking advantage of this model, we investigated whether heat stress-induced DNA methylation changes can be transmitted via asexual reproduction.

RESULTS

Our genome-wide study provides evidence for stress memory acquisition and maintenance in F. vesca. We found that specific DNA methylation marks or epimutations are stably transmitted over at least three asexual generations. Some of the epimutations were associated with transcriptional changes after heat stress.

CONCLUSION

Our findings show that the strawberry methylome and transcriptome respond with a high level of flexibility to heat stress. Notably, independent plants acquired the same epimutations and those were inherited by their asexual progenies. Overall, the asexual progenies can retain some information in the genome of past stresses encountered by their progenitors. This molecular memory, also documented at the transcriptional level, might be involved in functional plasticity and stress adaptation. Finally, these findings may contribute to novel breeding approaches for climate-ready plants.

Phased gap-free genome assembly of octoploid cultivated strawberry illustrates the genetic and epigenetic divergence among subgenomes

The genetic and epigenetic mechanisms underlying the coexistence and coordination of the four diverged subgenomes (ABCD) in octoploid strawberries (Fragaria × ananassa) remains poorly understood. In this study, we have assembled a haplotype-phased gap-free octoploid genome for the strawberry, which allowed us to uncover the sequence, structure, and epigenetic divergences among the subgenomes. The diploid progenitors of the octoploid strawberry, apart from subgenome A (Fragaria vesca), have been a subject of public controversy. Phylogenomic analyses revealed a close relationship between diploid species Fragaria iinumae and subgenomes B, C, and D. Subgenome A, closely related to F. vesca, retains the highest number of genes, exhibits the lowest content of transposable elements (TEs), experiences the strongest purifying selection, shows the lowest DNA methylation levels, and displays the highest expression level compared to the other three subgenomes. Transcriptome and DNA methylome analyses revealed that subgenome A-biased genes were enriched in fruit development biological processes. In contrast, although subgenomes B, C, and D contain equivalent amounts of repetitive sequences, they exhibit diverged methylation levels, particularly for TEs located near genes. Taken together, our findings provide valuable insights into the evolutionary patterns of subgenome structure, divergence and epigenetic dynamics in octoploid strawberries, which could be utilized in strawberry genetics and breeding research.

Integrated transcriptome and methylome analyses reveal the molecular regulation of drought stress in wild strawberry (Fragaria nilgerrensis)

BACKGROUND

Fragaria nilgerrensis, which is a diploid wild strawberry with excellent drought-resistance, would provide useful candidate genes for improving drought resistance of cultivated strawberry. So far, its molecular regulatory networks involved in drought stress are unclear. We therefore investigated the drought response regulatory networks of F. nilgerrensis based on the integrated analysis of DNA methylation, transcriptome and physiological traits during four time points under drought stress.  RESULTS: The most differentially expressed genes and the physiological changes were found at 8 days (T8) compared with 0 day (T0, control). Methylome analysis revealed slight dynamic changes in genome-wide mC levels under drought conditions, while the most hypomethylated and hypermethylated regions were identified at T4 and T8. Association analysis of the methylome and transcriptome revealed that unexpressed genes exhibited expected hypermethylation levels in mCHG and mCHH contexts, and highly expressed genes exhibited corresponding hypomethylation levels in the gene body, but mCG contexts showed the opposite trend. Then, 835 differentially methylated and expressed genes were identified and grouped into four clustering patterns to characterize their functions. The genes with either negative or positive correlation between methylation and gene expression were mainly associated with kinases, Reactive Oxygen Species (ROS) synthesis, scavenging, and the abscisic acid (ABA) signal pathway. Consistently, weighted gene co-expression network analysis (WGCNA) revealed Hub genes including NCED, CYP707A2, PP2Cs and others that play important roles in the ABA signaling pathway.

CONCLUSION

F. nilgerrensis drought is dominated by ABA-dependent pathways, possibly accompanied by ABA-independent crosstalk. DNA methylation may affect gene expression, but their correlation was more subtle and multiple types of association exist. Maintaining the balance between ROS regeneration and scavenging is an important factor in drought resistance in F. nilgerrensis. These results deepen our understanding of drought resistance and its application in breeding in strawberry plants.

Phenotypic variation and epigenetic insight into tissue culture berry crops

Berry crops, a nutrient powerhouse for antioxidant properties, have long been enjoyed as a health-promoting delicious food. Significant progress has been achieved for the propagation of berry crops using tissue culture techniques. Although bioreactor micropropagation has been developed as a cost-effective propagation technology for berry crops, genetic stability can be a problem for commercial micropropagation that can be monitored at morphological, biochemical, and molecular levels. Somaclonal variations, both genetic and epigenetic, in tissue culture regenerants are influenced by different factors, such as donor genotype, explant type and origin, chimeral tissues, culture media type, concentration and combination of plant growth regulators, and culture conditions and period. Tissue culture regenerants in berry crops show increased vegetative growth, rhizome production, and berry yield, containing higher antioxidant activity in fruits and leaves that might be due to epigenetic variation. The present review provides an in-depth study on various aspects of phenotypic variation in micropropagated berry plants and the epigenetic effects on these variations along with the role of DNA methylation, to fill the existing gap in literature.