Relationships between genome methylation, levels of non‐coding RNAs, mRNAs and metabolites in ripening tomato fruit

Abstract

SUMMARY Ripening of tomato fruit is a complex tightly orchestrated developmental process that involves multiple physiological and metabolic changes that render fruit attractive, palatable and nutritious. Ripening requires initiation, activation and coordination of key pathways at the transcriptional and post‐transcriptional levels that lead to ethylene synthesis and downstream ripening events determining quality. We studied wild‐type, Gr and r mutant fruits at the coding and non‐coding transcriptomic, metabolomic and genome methylation levels. Numerous differentially expressed non‐coding RNAs were identified and quantified and potential competing endogenous RNA regulation models were constructed. Multiple changes in gene methylation were linked to the ethylene pathway and ripening processes. A combined analysis of changes in genome methylation, long non‐coding RNAs, circular RNAs, micro‐RNAs and fruit metabolites revealed many differentially expressed genes (DEGs) with differentially methylated regions encoding transcription factors and key enzymes related to ethylene or carotenoid pathways potentially targeted by differentially expressed non‐coding RNAs. These included ACO2 (targeted by MSTRG.59396.1 and miR396b), CTR1 (targeted by MSTRG.43594.1 and miR171b), ERF2 (targeted by MSTRG.183681.1), ERF5 (targeted by miR9470‐3p), PSY1 (targeted by MSTRG.95226.7), ZISO (targeted by 12:66127788|66128276) and NCED (targeted by MSTRG.181568.2). Understanding the functioning of this intricate genetic regulatory network provides new insights into the underlying integration and relationships between the multiple events that collectively determine the ripe phenotype.

Phytochromes B1/B2 Are Major Regulators of Ripening-associated Epigenome Reprogramming in Tomato Fruits

“…The global pro le of methylated cytosines (mCs) in the epigenome of tomato fruits was assessed by whole-genome bisul te sequencing in the IG and BK stages for phyA, phyB1B2 and WT genotypes. In agreement with previous reports 27,28 , regardless of the genotype and fruit stage, the greatest total number of mCs was located in the CHH context, followed by the CG and CHG contexts, while the methylation level was highest in the CG (80%) context followed by the CHG (67%) and CHH (23%) contexts (Supplementary Table 9, Supplementary Fig. 1).…”

“…The link between DNA methylation levels and tomato fruit ripening-associated gene expression has been previously reported 27,28 , but the stimuli and the molecular mechanisms underlying this relationship remained unknown. The integrated analysis of the experimental evidence together with previous gene functional studies in tomato and A. thaliana allowed us to propose that PHYB1B2 is an important triggering factor for chromatin remodelling and, consequently, transcriptional regulation during fruit development.…”

The Regulatory Effect of Light Over Fruit Development and Ripening Is Mediated by Epigenetic Mechanisms

“…and WT genotypes. In agreement with previous reports 27,28 , regardless of the genotype and fruit stage, the greatest total number of mCs was located in the CHH context, followed by the CG and CHG contexts, while the methylation level was highest in the CG (80%) context followed by the CHG (67%) and CHH (23%) contexts (Supplementary Table 9, Supplementary Fig. 1).…”

“…The link between DNA methylation levels and tomato fruit ripening-associated gene expression has been previously reported 27,28 , but the stimuli and the molecular mechanisms allowing one mismatch 56 , approximately 84% of the reads were uniquely mapped (Supplementary Table 1) and were used for statistical analysis.…”

Beyond Ethylene: New Insights Regarding the Role of Alternative Oxidase in the Respiratory Climacteric

“…In contrast to tomato, a climacteric fruit in which demethylation is an important factor in ripening, nonclimacteric orange fruit was recently reported to exhibit global increases in DNA methylation as ripening progresses (Huang and Liu, 2019). In addition to factors known to directly affect methylation, recent evidence suggests that additional factors, including noncoding RNAs, circular RNAs, and microRNAs, may target genes with specific methylation patterns or abundance to elicit changes in expression (Zuo et al, 2020). The breadth of factors that may contribute to alterations in the epigenome is still being elucidated; however, it is possible that methylation status during ripening is tied to fruits' classifications as climacteric or nonclimacteric.…”