Our project investigated how differences in gene expression help plants adapt to different climates. Just as animals adapt to their environment, so do plants, and a significant part of this adaptation involves changing the way their genes are expressed, rather than changing the genes themselves. This is especially important as climate changes, potentially affecting the survival and health of plants.
Using the model plant Arabidopsis thaliana, we studied vast amounts of data on how the plant's genes are expressed in ecotypes adapted to different environments. Our goal was to understand how these changes relate to the climates to which the plants are adapted, discover the genetic changes that drive these adaptations, and determine if we can predict which plants will thrive in new conditions as the climate continues to change.
Interestingly, while studying the natural variation in gene expression among Arabidopsis ecotypes, we made a surprising discovery. Many genetic variations that could explain changes in gene expression were found in an unexpected part of the genome. Instead of being located between genes, as expected, this enrichment occurred within the genes themselves. This serendipitous finding shifted the focus of our project to a fundamental question: Do regions within genes contain important regulatory information that affects gene expression? To answer this question, we developed a synthetic system that allowed us to screen tens of thousands of regulatory sequence combinations. The results showed that plants do use regions within transcribed gene regions to control expression. Furthermore, we found that regulatory sequences function differently depending on whether they are inside or outside these regions, in stark contrast to animal regulatory sequences, which are indifferent to their position.
These findings are likely to have implications for practices of genetic engineering in plants.
