Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit

Zuo, Jinhua; Wang, Yunxiang; Zhu, Beiwei; Luo, Yunbo; Wang, Qing; Gao, Lipu

doi:10.3390/genes9050266

Cited by 20 publications

(15 citation statements)

References 54 publications

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“…As reviewed (Kyndt et al , 2013), the ET pathway plays different spatio‐temporal roles at different stages of the nematode infection process, including activation of jasmonic‐acid‐dependent defence responses. Intriguingly, research on fruit ripening has revealed a similar link between DNA hypomethylation and ET, with, for example, active hypomethylation at the induction of tomato ripening and hypermethylation during maturation of sweet oranges (Lang et al , 2017; Yin et al , 2017; Zuo et al , 2018; Huang et al , 2019). Whether temporal patterns in DNA methylation also occur during induction or maturation of nematode feeding sites remains to be investigated.…”

Section: Discussionmentioning

confidence: 97%

Genome‐wide DNA hypomethylation shapes nematode pattern‐triggered immunity in plants

et al. 2020

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Summary A role for DNA hypomethylation has recently been suggested in the interaction between bacteria and plants; it is unclear whether this phenomenon reflects a conserved response. Treatment of plants of monocot rice and dicot tomato with nematode‐associated molecular patterns from different nematode species or bacterial pathogen‐associated molecular pattern flg22 revealed global DNA hypomethylation. A similar hypomethylation response was observed during early gall induction by Meloidogyne graminicola in rice. Evidence for the causal impact of hypomethylation on immunity was revealed by a significantly reduced plant susceptibility upon treatment with DNA methylation inhibitor 5‐azacytidine. Whole‐genome bisulphite sequencing of young galls revealed massive hypomethylation in the CHH context, while not for CG or CHG nucleotide contexts. Further, CHH hypomethylated regions were predominantly associated with gene promoter regions, which was not correlated with activated gene expression at the same time point but, rather, was correlated with a delayed transcriptional gene activation. Finally, the relevance of CHH hypomethylation in plant defence was confirmed in rice mutants of the RNA‐directed DNA methylation pathway and DECREASED DNA METHYLATION 1. We demonstrated that DNA hypomethylation is associated with reduced susceptibility in rice towards root‐parasitic nematodes and is likely to be part of the basal pattern‐triggered immunity response in plants.

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Section: Discussionmentioning

confidence: 97%

Genome‐wide DNA hypomethylation shapes nematode pattern‐triggered immunity in plants

et al. 2020

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“…It is known that the ethylene biosynthesis pathway involving SAM [75][76][77] contributes to DNA methylation [78]. At low SAM concentration, the expression of genes involved in DNA repair and lipid and glucose metabolism is altered [79].…”

Section: Discussionmentioning

confidence: 99%

Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture

Bednarek

Żebrowski

Orłowska

2020

IJMS

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Tissue culture is an essential tool for the regeneration of uniform plant material. However, tissue culture conditions can be a source of abiotic stress for plants, leading to changes in the DNA sequence and methylation patterns. Despite the growing evidence on biochemical processes affected by abiotic stresses, how these altered biochemical processes affect DNA sequence and methylation patterns remains largely unknown. In this study, the methylation-sensitive Amplified Fragment Length Polymorphism (metAFLP) approach was used to investigate de novo methylation, demethylation, and sequence variation in barley regenerants derived by anther culture. Additionally, we used Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy to identify the spectral features of regenerants, which were then analyzed by mediation analysis. The infrared spectrum ranges (710–690 and 1010–940 cm−1) identified as significant in the mediation analysis were most likely related to β-glucans, cellulose, and S-adenosyl-L-methionine (SAM). Additionally, the identified compounds participated as predictors in moderated mediation analysis, explaining the role of demethylation of CHG sites (CHG_DMV) in in vitro tissue culture-induced sequence variation, depending on the duration of tissue culture. The data demonstrate that ATR-FTIR spectroscopy is a useful tool for studying the biochemical compounds that may affect DNA methylation patterns and sequence variation, if combined with quantitative characteristics determined using metAFLP molecular markers and mediation analysis. The role of β-glucans, cellulose, and SAM in DNA methylation, and in cell wall, mitochondria, and signaling, are discussed to highlight the putative cellular mechanisms involved in sequence variation.

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“…ACC may be a precursor of enzymatic and non-enzymatic copper-stimulated ethylene production [ 47 ]. Interestingly, demethylation in the CG context impact on the expression of several genes involved in the ethylene synthesis and signaling pathway [ 48 ], indicating a putative regulatory role of DNA methylation [ 49 ]. Moreover, copper also participates in a broad range of biochemical pathways that cross with DNA methylation [ 50 ].…”

Section: Introductionmentioning

confidence: 99%

CG Demethylation Leads to Sequence Mutations in an Anther Culture of Barley Due to the Presence of Cu, Ag Ions in the Medium and Culture Time

Bednarek

Orłowska

2020

IJMS

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During plant tissue cultures the changes affecting regenerants have a broad range of genetic and epigenetic implications. These changes can be seen at the DNA methylation and sequence variation levels. In light of the latest studies, DNA methylation change plays an essential role in determining doubled haploid (DH) regenerants. The present study focuses on exploring the relationship between DNA methylation in CG and CHG contexts, and sequence variation, mediated by microelements (CuSO4 and AgNO3) supplemented during barley anther incubation on induction medium. To estimate such a relationship, a mediation analysis was used based on the results previously obtained through metAFLP method. Here, an interaction was observed between DNA demethylation in the context of CG and the time of culture. It was also noted that the reduction in DNA methylation was associated with a total decrease in the amount of Cu and Ag ions in the induction medium. Moreover, the total increase in Cu and Ag ions increased sequence variation. The importance of the time of tissue culture in the light of the observed changes resulted from the grouping of regenerants obtained after incubation on the induction medium for 28 days. The present study demonstrated that under a relatively short time of tissue culture (28 days), the multiplication of the Cu2+ and Ag+ ion concentrations (‘Cu*Ag’) acts as a mediator of demethylation in CG context. Change (increase) in the demethylation in CG sequence results in the decrease of ‘Cu*Ag’, and that change induces sequence variation equal to the value of the indirect effect. Thus, Cu and Ag ions mediate sequence variation. It seems that the observed changes at the level of methylation and DNA sequence may accompany the transition from direct to indirect embryogenesis

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Comparative Analysis of DNA Methylation Reveals Specific Regulations on Ethylene Pathway in Tomato Fruit

Cited by 20 publications

References 54 publications

Genome‐wide DNA hypomethylation shapes nematode pattern‐triggered immunity in plants

Genome‐wide DNA hypomethylation shapes nematode pattern‐triggered immunity in plants

Exploring the Biochemical Origin of DNA Sequence Variation in Barley Plants Regenerated via in Vitro Anther Culture

CG Demethylation Leads to Sequence Mutations in an Anther Culture of Barley Due to the Presence of Cu, Ag Ions in the Medium and Culture Time

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