GENE EXPRESSION AND REGULATION
Promoters serve a critical role in establishing baseline transcriptional capacity through recruitment of proteins including transcription factors (TFs). Eukaryotic regulatory sequences are comprised of complex arrangements of motifs and elements, while both the primary DNA sequence and secondary DNA structure help to dictate nucleosome architecture1, contributing to regulating gene-expression.
Synthetic biology approaches, using information from genomic datasets to inform the design of sequences, have been used to gain an understanding of CREs in yeast and mammals, revealing important functional properties and enabling the rational design of regulatory elements for biotechnology. The recent availability of similar datasets, including TF Binding Sites – TFBSs, nucleosome occupancy etc., provide resources for similar approaches in plants. Simultaneously, in addition to their traditional roles in agriculture, plants are emerging as commercially-relevant production systems for high-value products, for which suites of non-homologous robust, regulatory elements are highly desirable.
In our laboratory, we are mining these novel datasets to inform the design of libraries of synthetic variants that we can rapidly test to understand how cis-regulatory function is encoded in specific DNA sequences. Rapid testing of the relationship between sequence and function is enabled by transient ratiometric gene expression assays in leaves and protoplasts.