DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry

Recently,increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening.However,the role of DNA methylation in regulating specific traits,such as flavor,remains unclear.Here,we report a role of DNA methylation in affecting furanone biosynthesis in strawberry.Strawberry quinone oxidoreductase(FaQR)is a key enzyme in furanone biosynthesis.There are four FaQR homologs in strawberry cultivar‘Yuexin’,and one of them,FaQR3,contributes∼50%of FaQR transcripts,indicating a major role of FaQR3 in furanone biosynthesis.Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor,we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation,suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression,and responded to different temperatures consistently.In addition,transient expression of a gene in the RNA-directed DNA methylation(RdDM)pathway,FaAGO4,and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway.Transient RNA interference(RNAi)of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation.These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.

Single-cell RNA sequencing reveals spatial heterogeneity and immune evasion of circulating tumor cells

Circulating tumor cells(CTCs),recognized as intermediaries between primary and distant lesions,are key to understanding the mechanisms of cancer metastasis.Because the dissemination of tumor cells in the circulatory system is a spatially and temporally dynamic process,CTCs can logically be assumed to be a population of cells displaying both spatial and temporal heterogeneity^(1).Prior studies have revealed substantial temporal heterogeneity in CTC phenotypes during anti-cancer treatments^(2,3).However,current knowledge of CTCs is derived mostly from peripheral venous blood;thus,only a snapshot of the entire circulatory process has been determined,and much more remains to be understood.

Comparative analysis of fruit firmness and genes associated with cell wall metabolisms in three cultivated strawberries during ripening and postharvest

Cultivated strawberry(Fragaria×ananassa),a world-famous fruit,is subjected to rapid softening during ripening,resulting in a shorter shelf life and severe economic losses during storage and transportation.However,there is limited understanding of the molecular mechanism underlying differences in fruit firmness during ripening and postharvest among cultivated strawberries.Here,we explored this molecular mechanism by comparing three cultivated strawberries via firmness measurement,transcriptome analysis,quantitative real-time polymerase chain reaction,and correlation analysis,and revealed FaEXP7,FaPG2,FaPLA,and Faβ-Gal4 as potential softening activators expressed before harvest to determine fruit with more softened texture and shorter shelf life,and that extremely high expression levels of FaCEL1-1 and FaCEL1-3 during ripening might be accelerators to intensify this situation.Additionally,both the enzyme activities of FaCEL and the expression pattern of FaCEL1-3 showed a significantly negative correlation with fruit firmness after harvest,suggesting that FaCEL1-3 might play a key role in promoting strawberry fruit softening not only during ripening but also postharvest.These results showed that the difference in fruit firmness and shelf life among cultivated strawberries was controlled by the temporal expression pattern of a legion of cell wall-associated genes during ripening and postharvest.

scDPN for High-throughput Single-cell CNV Detection to Uncover Clonal Evolution During HCC Recurrence

Single-cell genomics provides substantial resources for dissecting cellular heterogeneity and cancer evolution.Unfortunately,classical DNA amplification-based methods have low throughput and introduce coverage bias during sample preamplification.We developed a single-cell DNA library preparation method without preamplification in nanolitre scale(scDPN)to address these issues.The method achieved a throughput of up to 1800 cells per run for copy number variation(CNV)detection.Also,our approach demonstrated a lower level of amplification bias and noise than the multiple displacement amplification(MDA)method and showed high sensitivity and accuracy for cell line and tumor tissue evaluation.We used this approach to profile the tumor clones in paired primary and relapsed tumor samples of hepatocellular carcinoma(HCC).We identified three clonal subpopulations with a multitude of aneuploid alterations across the genome.Furthermore,we observed that a minor clone of the primary tumor containing additional alterations in chromosomes 1q,10q,and 14q developed into the dominant clone in the recurrent tumor,indicating clonal selection during recurrence in HCC.Overall,this approach provides a comprehensive and scalable solution to understand genome heterogeneity and evolution.