The long-term goal of research in the Wilkins lab is to understand the regulatory networks that govern the response of cereal crops and forest trees to environmental change. Gene regulatory networks coordinate the timing and rate of gene expression genome-wide in response to environmental and developmental cues. The lab uses a variety of high-throughput molecular biology techniques, including RNA-seq, ATAC-seq, transcription factor binding assays, and genetic manipulations, to investigate multi-scale mechanisms of gene regulation, transcription factor activity and network inference for bulk tissue and for individual cell types.
Gene regulatory networks are at the interface between environmental perception and environmental response in all living things. My research uses the tools of systems biology to study and manipulate gene regulatory networks in cereal crops in order to improve their response to climate change-associated environmental stressors.
We study how plants perceive the environment and how they use this information to formulate adaptive responses to environmental stress. We use the tools of systems biology to study and to reprogram gene regulatory networks, the interactions between transcription factors and regulatory sequences encoded in DNA, as they are the interface of environmental perception and response. Our research focuses on three interconnected themes:
Regulatory diversity across ecotypically divergent crop varieties: Cereal crops have been selected by producers and breeders to grow in a wide range of environments. As a consequence, these varieties have acquired markedly different responses to environmental stresses. These differences provide invaluable guidance for rationale crop design.
Cell type specific regulatory networks: Different cell types within a tissue play different functional roles and have distinct gene regulatory networks. By studying these tissue-specific regulatory networks, we can target genome editing to have maximal impact on stress response and minimal impact on other agronomic traits.
Regulatory networks in agricultural settings: One of the challenges of engineering agricultural crops with improved environmental stress tolerance is translating experimental advances from the lab into the complex and fluctuating environments found in the field. Studying gene regulation in the field is the essential next step for crop improvement.