At the center of the mechanism is a histone demethylase enzyme called lysine-specific demethylase 1-like 1 (LDL1), which according to Professor Matsunaga has a lot of real-world applications.
Various stresses cause instabilities or errors in an organism's genome, resulting to damages or "breaks" in the sequences. These breaks are repaired autonomously by a process called homologous recombination (HR). HR is then essential for maintaining a genome's stability. The chromatin structure needs to be modified for HR to occur smoothly. Professor Matsunaga's previously discovered protein called RAD54 was found to be involved in chromatin remodeling in Arabidopsis, helping genomic stability and response to DNA damage. However, recruitment of RAD54 at the site of HR and the proper dissociation of RAD54 from the site are important for it to be effective.
The scientists identified and shortlisted proteins that interact with RAD54 and regulate its dynamics with chromatin during HR-based DNA damage repair in Arabidopsis. They then identified, for the first time, that the histone demethylase LDL1 interacts with RAD54 at DNA damage sites. They found that RAD54 specifically interacts with the methylated 4th lysine amino acid on one of the four core histones in the chromatin, H3 (H3K4me2). The scientists then found that LDL1 suppresses this interaction by demethylating H3K4me2. They concluded that LDL1 removes excess of RAD54 from DNA damage sites via the demethylation of H3K4me2 and thus promotes HR repair in Arabidopsis. Thus, LDL1 ensures proper dissociation of RAD54 from the HR repair site in the DNA.
Professor Matsunaga explains the most important part of their research. "Plants can be treated with LDL1 to artificially control epigenetic modification so that they become more tolerant to stresses such as infections, environmental stresses and mechanical stress. This will be useful in creating resistant varieties of crops with improved growth and longevity and better characteristics, thus contributing to global food security."
For more details, read the media release from the Tokyo University of Science.