Conservation of epigenetic proteins across plant species

Many epigenetic mechanisms are studied in depth in the model organism Arabidopsis thaliana, but the conservation of these mechanisms and the proteins that mediate these mechanisms is not well known in other plant species, including crops. Our goal is to determine the conservation of protein structure, domain architecture, and amino acids critical to protein regulation of gene expression. By understanding this conservation can epigenetic tools then be developed for crop-specific epigenetic regulation.

Plant biosensors for the development of epigenetic circuits

Creating gene regulatory networks is are ongoing goal in plant synthetic biology. Epigenetic modifications provide useful methodologies for regulating genes with the potential to create synthetic networks in plants without mutating DNA. Our goal is to create novel sensors useful for determining the regulation of genes in plants with easily detectable output signals. This includes the use of protein prediction algorithms combined with genomic approaches to create novel sensors (outputs) that can be attached to epigenetically regulated gene networks in plants for easily detectable and non-toxic outputs. 

Protein accumulation as a novel, plant-specific epigenetic tool

The link between protein dynamics, concentration, and efficient localization to compartments in cells with efficient gene regulation has been demonstrated from humans to plants. From the formation of membraneless compartments (biomolecular condensates) to hyperaccumulation of DNA methylation binding proteins, plants accumulate proteins and macromolecules for gene regulation and to facilitate epigenetic mechanisms. How do plants localize proteins at high concentrations in a regulated manner without aggregation? What specific protein domains, chaperones, or modifications are used in plants that differ from other species? Can these mechanisms be repurposed and leveraged for the development of novel epigenetic tools to localize gene activation or silencing “hubs” at specific loci? This project’s goal is to understand these questions and apply these findings for the creation of novel tools that rely only on plant proteins for targeting of precise epigenetic enzymes dynamically and efficiently for gene regulation.