Understanding the role of chromatin modifying complexes in the abiotic stress response mechanisms of cereal plants

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Plants are constantly exposed to environmental stresses (e.g. low temperature) to which they must adapt. These stresses regulate the expression of overlapping suites of genes involved in stress response mechanisms. Our long-term goal is to understand the chromatin mechanisms that control agronomically important traits such as abiotic stress tolerance in cereals. We hypothesize that in addition to the role of transcriptional elements, the dynamic tuning of chromatin upon perception of stress is a major regulatory mechanism necessary for adaptation.  To achieve this goal, we will build on knowledge and momentum generated by our first NSERC Discovery grant. During the 2015-2020 funding period we will focus on 3 new objectives: 1) Determine the cold acclimation parameters of spring, facultative and winter Brachypodium accessions for optimal freezing tolerance development. We have established that the 7 accessions commonly used have either facultative or winter habits. However, more than 180 diploid accessions are now available, offering us the opportunity to uncover accessions with true spring (sensitive) and winter (tolerant) habits. This will allow us to perform functional comparative analyses; 2) Characterize the role of BdADA2 in low temperature chromatin dynamics. SAGA-targeted genes are known to be regulated by stress and we have shown in planta that an important component of this complex - ADA2 - interacts with CBF1. We have generated Brachypodium transgenic lines that overexpress ADA2. These lines have increased acetylation at the H3 lysines targeted by GCN5, as well as reduced expression of some COR genes. These lines will be used to provide evidence that the interaction between CBF1 and ADA2 potentially represents an integration node between the transcriptional and chromatin regulatory responses of cold hardening; 3) Characterize the role of DNA methylation during cold hardening in Brachypodium. DNA methylation is believe to play a predominant role in the cold acclimation response of cereals. We have generated Brachypodium knockdown and overexpression lines for several key genes of this pathway: DRM2, CMT3 and AGO4. We will expose these lines to low temperatures to reveal the importance of DNA methylation during cold acclimation, which will precise the role of these modifiers in monocots. This unique project aiming at understanding chromatin control of stress tolerance in cereals will have a major impact on epigenetic research on other taxonomic groups given the universal logic to the molecular circuitry involved. In addition, our research will lead to the development of strategies for the improvement of important traits in crops by harnessing specific chromatin modifiers for genetic and epigenetic editing strategies. In line with the increasing need for HQP in epigenetics, this project will train 3 PhD, 2 MSc and several undergraduate students.