Understanding and engineering the logic behind plant decisions
The formation of every multicellular organism starts with an individual cell dividing to give rise to a group of cells that will differentiate into many unique cell types. While these cell types differ in appearance and function, every cell contains an identical genome. The genome contains the exact instructions for every cell type needed; however, it’s essential that individual cells only access the information required for their specific cell type. Each cell decides which parts of the genome to read and which to ignore. Our lab explores the logic behind how plant cells choose what genetic information to read in response to environmental or developmental signals.
The findings and technology developed through our research will increase the understanding of the fundamental rules behind transcriptional regulation and guide the breeding programs of agriculturally relevant plants.
The role of DNA methylation in transcriptional memory
Complementary to the genome, which is stable and identical throughout an organism, is the epigenome which fluctuates and changes between cell types. The epigenetic landscape made up of the absence or presence of epigenetic marks, such as DNA methylation, helps establish the expression of specific genes in specific cells in response to developmental or environmental signals. In plants, the absence or presence of DNA methylation can guide the activation or repression of genes in a mitotically and meiotically heritable way, allowing the maintenance of alterations in DNA methylation to be maintained through cell division or even over generations. DNA-methylated loci are dynamic in the amount of DNA methylation and transcriptional consequences, making the underlying mechanism connecting DNA methylation and transcriptional control challenging to uncover. By understanding this mark and the requirements for silencing, we can better understand cells decide which genes to silence and which to activate to control their development and environmental response.
Here we are focusing on using a synthetic biology approach to extend our understanding of how plants use DNA methylation to interpret and remember developmental and environmental signals. We aim to develop a library of methylation-sensitive promoter modules to help us understand how methylation controls gene expression and how we can design new synthetic systems to be methylation sensitive.
Integrating epigenetic memory into synthetic systems
In addition to understanding epigenetic memory in plants, it is also important that this information informs the development of the next generation of crop species. From a synthetic biology perspective, DNA methylation offers a mechanism for stably maintaining new information delivered by a compound or condition within synthetic systems.
The ability to cause the expression of specific genes in specific cells under specific conditions requires flexible synthetic systems that can take in and store information. Current synthetic systems for manipulating traits are often limited by their reliance on the constitutive
expression of pathway components, leading to unwanted exogenous expression and phenotypes. While the inclusion of inducible promoters takes a step closer to systems that can receive information in the form of specific compounds or conditions, this induction is only active for the duration of the stimulus and is not stored.
Instead we aim to develop tools and systems that give the plant new ways to interpret and react to its surroundings through the optimization and development of new targeted epimutagenesis tools and the assembly of control systems to regulate the expression of extensive multigene pathways.