If you like to start your day with a glass of orange juice, you can thank epigenetics for that. More specifically, you can thank DNA methylation, since it’s been recently shown to play a crucial role in the ripening process of the sweet orange fruit. The collaborative efforts of Jian-Kang Zhu at Purdue University (Indiana, USA) and Zhaobo Lang at the Shanghai Center for Plant Stress Biology (Shanghai, China) have uncovered a juicy link between DNA methylation and gene expression in orange fruit ripening.
Previous work from the Zhu and Lang groups showed that the climacteric (ethylene producing) tomato fruit undergoes global DNA demethylation during ripening. To determine if this trend was true for other fruits, they applied their botanical epigenetic prowess to the ripening process of the non-climacteric sweet orange fruit (Citrus sinensis). Using single-base resolution whole genome bisulfite sequencing (WGBS) they generated genome-wide maps of DNA methylation for 5 different stages of orange fruit ripening and used RNA-seq to generate corresponding transcriptome maps. Here are the freshly squeezed details:
- In contrast to tomatoes, the orange fruit genome undergoes a global increase in DNA methylation during the 120-day ripening process
- Over the same time frame, there is a gradual and corresponding decrease in the transcript levels of demethylase genes
- The global increase in methylation levels is likely due to down-regulation of demethylase genes, rather than increased methylation
- Methylation in the promoter regions of several hundred genes is associated with both positive and negative changes in gene expression, where gene ontology analysis revealed:
- Down-regulation of genes involved in photosynthesis, cell wall maintenance, and development
- Up-regulation of genes involved in abscisic acid signaling (which is important for ripening), and steroid and aromatic metabolism
- Application of a DNA methylation inhibitor to immature orange fruit prevented de-greening (ripening)
This work demonstrates a clear and delicious role for DNA methylation in the ripening of the orange fruit; however, there are additional hormonal and genetic controls in place. How these components work in concert to regulate the ripening process still requires further exploration.