Grant: Canada Research Chairs

In eukaryotic genome, the function of a large portion of noncoding DNA remains unknown, but we know that it is integral to cell function and transcriptional regulation. Gene expression is regulated by the concerted action of multiple factors including cis-regulatory elements, transposable elements and noncoding RNAs, each of which experience distinct selection pressures and consequently evolve at a different rate. The characterization of the functional elements and of their evolution, especially in plant genomes, represents a major challenge that needs to be explored since most genetic variants associated with important and complex traits fall outside the coding-protein genes, and often in cis-regulatory elements. As Canada Research Chair in evolutionary genomics of noncoding DNA, Pre. Zoé Joly-Lopez aims to better understand the function and evolution of noncoding DNA elements, with an emphasis on cis-regulatory elements. Plants are optimal model systems for this research: as sessile organisms, they are subject to potentially strong selective pressures in their environments, leading to changes that range from gene regulatory interactions to genome duplication. Combining cutting-edge functional genomics techniques with evolutionary models from comparative and population genetics, as well as environmental stress assays and genome editing techniques, Pre. Joly-Lopez and her research group will investigate regulatory elements arising from three evolutionary contexts. • First, discovering novel enhancers, which often evolve within species, in the context of resilience to abiotic stress in rice (Oryza sativa) varieties. • Second, tracking the evolution of regulatory regions in the context of a recent polyploid in the Brassicas species. • Third, studying the emergence of cis-regulatory elements in rice that are derived from transposable elements, which are DNA sequences that populate most eukaryotic genomes by moving from one location to another and are viewed as important drivers of evolution and gene regulation. Pre. Joly-Lopez’s research offers insight into functionally important types of noncoding elements in economically relevant plant species. This could directly guide efforts in both traditional and synthetic plant breeding for important traits such as stress resilience.