Epigenetics, the intricate regulation of how genes are expressed, involves a variety of complex molecular processes. While we have a solid understanding of how genes can be silenced through the methylation of histones at the H3K27 position, the process of reactivating these silenced genes remains unclear. Recently, researchers explored the epigenetic mechanisms in a model plant organism, revealing a well-conserved group of proteins that play a crucial role in the activation and deactivation of genes, enhancing our understanding of epigenetic processes.
One of the most intriguing findings in biology is that cells possess mechanisms to dynamically adjust gene expression. This capability to either enhance or inhibit the transcription of specific genes without changing the underlying DNA sequences is crucial for all living beings, from simple single-celled organisms to the most intricate plants and animals.
Although our grasp of these so-called epigenetic processes is still evolving, significant advancements have been made, particularly regarding the Polycomb Repressive Complex 2 (PRC2). PRC2 is a protein that, in various plants, attaches to certain DNA sequences known as polycomb response elements (PREs) and tags nearby histones with a chemical mark. This mark, referred to as “trimethylation of H3K27 (H3K27me3),” essentially blocks the conversion of adjacent genes into RNA and ultimately proteins, thereby silencing them. However, scientists have yet to uncover how genes silenced by PRC2 can be reactivated.
A recent study published in eLife conducted by a research team at the Nara Institute of Science and Technology (NAIST) in Japan, led by Nobutoshi Yamaguchi, aimed to address this issue. The team performed extensive experiments on genetically altered Arabidopsis thaliana plants, revealing critical aspects of the intricate epigenetic processes that occur in these and other organisms.
The researchers placed significant emphasis on Set Domain-containing Protein 7 (SDG7), known for its role in regulating protein methylation within the cell’s cytosol. Initial experiments indicated that SDG7 was also present in the cell nucleus, which spurred further investigation.
Through comprehensive analyses of mutant A. thaliana cultures, the researchers identified a new function for SDG7. This protein was found to bind to PREs, competing directly with PRC2. Remarkably, SDG7 can displace PRC2, stopping it from maintaining the H3K27me3 mark. Additionally, SDG7 introduces an active histone mark by methylating H3K36. Once this methylation occurs, the protein duo of SDG8 and Polymerase Associated Factor 1 (PAF1) then spreads this active mark throughout the gene, leading to successful gene activation.
Essentially, the histone sites H3K27 and H3K36 can serve as a “switch,” allowing for the dynamic regulation of gene expression. “This straightforward yet elegant opposing molecular switch between H3K27 and H3K36 methylation is perfectly suited for epigenetic reprogramming during plant development,” explains Yamaguchi. “The observed switching between H3K27 and H3K36 methylation across many flowering plants suggests that the competitive interaction between SDGs and PRC2 at PREs may be common among various plant species involved in developmental regulation.”
This research illuminates the complex epigenetic mechanisms that may underpin countless plant and animal species, potentially leading to significant advancements in agriculture, horticulture, and farming. “We anticipate that our findings will capture the interest of plant biologists and epigeneticists, given the extensive role of epigenetic regulation in gene expression during development and responses to environmental changes,” concludes Yamaguchi.
