Tomato (Solanum lycopersicum) holds a significant position among horticultural crops, renowned for its rich iron content and vitamin abundance. Iron (Fe) is an essential micro-element for plants, and its deficiency not only hampers tomato growth, development, and fruit quality but also carries health implications for animals and humans, contributing to nutritional disorders worldwide.
While researchers have made significant strides in unraveling the transcriptional and post-transcriptional mechanisms governing plant responses to Fe deficiency, the contribution of epigenetic modifications, particularly DNA methylation, has remained a subject of limited exploration. In a recent study, the intricate interplay between DNA methylation and RNA transcriptome responses to both short-term (12 hours) and long-term (72 hours) Fe deficiency in tomato roots was investigated.
The research combined methylome analysis with a genetic approach, shedding light on the dynamic epigenetic DNA methylation patterns in the CG context within the bHLH39 promoter, which play a pivotal role in its transcriptional regulation, thus influencing the Fe deficiency-induced responses in tomato.
To explore the significance of DNA methylation, the researchers employed 5-azacytidine (Aza), a DNA methylase inhibitor. Their findings indicated that exogenous application of Aza significantly suppressed the induction of root ferric chelate reductase (FCR) activity, hindered the development of root morphology induced by Fe deficiency, and attenuated the transcript levels of three core genes (IRT1;1, FRO1, and bHLH39), underscoring the essential role of DNA methylation in regulating Fe deficiency responses.
Subsequently, the study revealed dynamic changes in DNA methylation and gene expression over time, particularly in the CG and CHG contexts. These changes coincided with increased transcript levels of Fe deficiency-induced genes. Notably, while there was no clear correlation between alterations in DNA methylation levels and changes in transcript levels for most affected genes, core Fe deficiency-induced genes like bHLH39 exhibited associations between gene expression and DNA methylation changes, especially under long-term treatment.
Furthermore, an intriguing observation was the prevalence of hypermethylation over hypomethylation at CG sites in the bHLH39 promoter, closely linked to the upregulation of bHLH39 expression in response to long-term Fe deficiency treatment. The study further corroborated the positive relationship between promoter CG methylation and gene transcription by analyzing MET1-RNA interference lines, which displayed lower CG methylation at the bHLH39 promoter, reduced bHLH39 expression, and more pronounced chlorosis compared to wild-type seedlings.
In conclusion, this research has illuminated the dynamics of both DNA methylation and the transcriptome, offering crucial insights into the mechanisms governing Fe deficiency-induced responses in tomato roots. Particularly, it underscores the positive influence of DNA methylation in the CG context on gene expression, exemplified by the regulation of bHLH39, a key player in Fe deficiency responses. These findings not only advance our comprehension of regulatory mechanisms during Fe deficiency in plants but also provide valuable theoretical and technical foundations for enhancing crop quality and resilience.