A Molecular Framework for Environment Responsive Chromatin Modification in Plants

To survive in changing environments, plants have to be able to sense their surroundings and modify how they grow and develop. Furthermore, in contrast to animals, plants cannot move and so they have had to evolve different ways in which to quickly and accurately do this. One way in which both animals and plants respond to the environment is through altering their gene expression by modifying specific proteins (histones) in the protein scaffold (chromatin) that supports their DNA. For example, a protein complex called the 'polycomb repressive complex 2' (PRC2) is involved in adding a chemical mark called methylation to histones, which causes genes to be switched off. The PRC2 is found in animals and plants, but interestingly most plants have a larger variety of the different proteins making up the complex, which means they have a broader range of potential combinations. This means that plants have a larger 'tool kit' for controlling the specificity and timing of chromatin methylation.

The PRC2 in plants is involved in a variety of different processes, including the regulation of seed development and germination, and coordinating flowering in spring after winter. In several cases the specific genes that are methylated are known. However, we still know very little about how the PRC2 directly senses the outside world to trigger these changes only when they are needed. We recently showed that a plant PRC2 protein called VERNALIZATION2 (VRN2) is usually very unstable, but can accumulate under certain environmental conditions, including during flooding and exposure to cold temperatures. This suggests that VRN2 might act as a 'sensor' component of the PRC2 in flowering plants that ensures methylation of certain genes is only triggered under the right environmental conditions. However, at present we still do not know much about what happens once VRN2 is stabilised.

Using a range of molecular, biochemistry, genetic and cell biology approaches in Arabidopsis (a plant model organism) we seek to address this gap in our knowledge by answering several timely questions: (1) How do increases and decreases in VRN2 affect the other PRC2 variants and shape the PRC2 landscape? (2) What are the genome-wide targets of stable VRN2-PRC2? (3) How do environment triggered increases in VRN2 translate into plant developmental changes? By answering these questions using diverse experimental approaches across three integrated work packages, we will uncover valuable new knowledge about how plants are able to coordinate chromatin methylation to modify development in response to their environment.

This work will provide a step-change in our understanding of how plants directly translate environmental changes (e.g. the seasons, or stresses such as floods) into chromatin modifications that reprogram gene expression to align growth and development with the prevailing conditions. Crucially, we previously showed that the mechanism controlling VRN2 abundance is widely conserved in flowering plants - including crop species. As such, the fundamental new insights we uncover with this work should have longer term impact, as they will identify new molecular targets that biotechnologists and plant breeders can use to improve agriculturally important traits related to growth and stress-resilience, which is a key aim for ensuring global food security.

The polycomb repressive complex 2 (PRC2) is a conserved enzymatic complex that regulates epigenetic gene repression by methylating histones. In contrast to animals, flowering plants have increased numbers of genes encoding for individual PRC2 subunits. Despite knowledge of PRC2-regulated processes in plants, mechanisms connecting PRC2 activity to the perception of external signals are still relatively unknown. We recently showed that the angiosperm-specific PRC2 subunit VERNALIZATION2 (VRN2) is a proteolytic target of the oxygen-dependent N-degron pathway. This restricts VRN2 to meristems, but permits broader accumulation across tissues in response to environmental inputs such as hypoxia and cold exposure. We propose that VRN2 couples specific PRC2 activities to environment sensing. Here, we will investigate how signal-triggered changes in VRN2 abundance affect global PRC2 dynamics to modulate histone methylation across the genome and influence growth and development. We will test how alterations in VRN2 abundance affects other PRC2 components, PRC2 assembly, and the cellular ratios of different PRC2 variants. We will carry out genome wide ChIP- and RNA-seq analyses to define the global VRN2-responsive epigenome, identifying the breadth of gene targets that are controlled by VRN2-PRC2 in different environmental contexts. Finally, we will use genetic and environment-responsive manipulation of VRN2 stability as a tool to investigate how plants fine-tune the epigenetic control of development, focussing specifically on hypocotyl growth. This work will provide fundamental new insight into a plant-specific mechanism that connects chromatin modification to environmental sensing. Moreover, since regulation of VRN2 through the N-degron pathway is conserved in flowering plants, this work has a strong potential to identify targets that could be manipulated in agronomically relevant crops for improving plant growth and stress resilience, a key target for global food security.