ArticleGenome biology2024
Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 40 citations in OpenAlex.
- The telomere-to-telomere gap-free reference genome and DNA methylome unveil epigenetic regulation of proanthocyanidin biosynthesis during apricot fruit development.The Plant journal : for cell and molecular biology · 2026Article
- DNA hypomethylation enables the transcriptional repressor SlSPL-CNR to control fruit flavor ester biosynthesis.Nature communications · 2026Article
- DNA methylation around transcription start sites is not globally associated with transcription in the grain of natural and synthetic hexaploid wheat.BMC plant biology · 2026Article
- Metabolic response strategies of spring wheat under osmotic stress.Frontiers in plant science · 2026Article
- Research progress on sucrose accumulation characteristics and their molecular regulatory networks in the fruits of fruit trees.Frontiers in plant science · 2026Review
- Integrated genomic and DNA methylome analyses reveal epigenetic regulation of stevia glycoside biosynthesis inHorticulture research · 2025Article
- Plant Growth-Promoting Rhizobacteria and Bacterial Biocontrol Agents in Tomato Disease Management: Mechanisms, Applications, and Omics Perspectives.Global challenges (Hoboken, NJ) · 2025Review
- Malate metabolism in horticultural crops: mechanistic insights and agricultural practices for quality improvement.Molecular horticulture · 2025Review
- Spatiotemporal methylome remodeling during fiber differentiation in Gossypium hirsutum.BMC genomics · 2025Article
- Epigenetic regulation modulates seasonal temperature-dependent growth of soybean in southern China.Plant biotechnology journal · 2025Article
- Alternative splicing occurs in auxin-mediated trade-off between fruit development and quality in tomato.BMC plant biology · 2025Article
- Occurrence of White Flesh Color and Refreshing Flavor FollowingJournal of agricultural and food chemistry · 2025Article
- Gap-free genome assemblies of two Pyrus bretschneideri cultivars and GWAS analyses identify a CCCH zinc finger protein as a key regulator of stone cell formation in pear fruit.Plant communications · 2025Article
- Identification ofGenes · 2025Article
- Light-mediated activation ofFrontiers in plant science · 2025Article
- Novel Targets for Fruit Conservation Strategies Revealed by Omics Studies: A Systematic Review and Meta-Analysis.International journal of food science · 2025Review
- Transcription factor PbrERF114 is involved in the regulation of ethylene synthesis during pear fruit ripening.Molecular horticulture · 2024Article
- Article
- Multi-omics provide insights into the regulation of DNA methylation in pear fruit metabolism.Genome biology · 2024Article
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundExtensive research has been conducted on fruit development in crops, but the metabolic regulatory networks underlying perennial fruit trees remain poorly understood. To address this knowledge gap, we conduct a comprehensive analysis of the metabolome, proteome, transcriptome, DNA methylome, and small RNAome profiles of pear fruit flesh at 11 developing stages, spanning from fruitlet to ripening. Here, we systematically investigate the metabolic landscape and regulatory network involved.
resultsWe generate an association database consisting of 439 metabolites and 14,399 genes to elucidate the gene regulatory network of pear flesh metabolism. Interestingly, we detect increased DNA methylation in the promoters of most genes within the database during pear flesh development. Application of a DNA methylation inhibitor to the developing fruit represses chlorophyll degradation in the pericarp and promotes xanthophyll, β-carotene, and abscisic acid (ABA) accumulation in the flesh. We find the gradual increase in ABA production during pear flesh development is correlated with the expression of several carotenoid pathway genes and multiple transcription factors. Of these transcription factors, the zinc finger protein PbZFP1 is identified as a positive mediator of ABA biosynthesis in pear flesh. Most ABA pathway genes and transcription factors are modified by DNA methylation in the promoters, although some are induced by the DNA methylation inhibitor. These results suggest that DNA methylation inhibits ABA accumulation, which may delay fruit ripening.
conclusionOur findings provide insights into epigenetic regulation of metabolic regulatory networks during pear flesh development, particularly with regard to DNA methylation.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.