Decoding Development of Lateral Roots in Plants Using Recombinase-Based Logic Circuits

There are many open questions about the molecular mechanisms that coordinate the dynamic, multicellular behaviors required for organogenesis. By building synthetic circuits to either record or re-code in vivo signaling networks, synthetic biology brings potential novel inroads into studies of development. Serine integrases mediating site-specific and irreversible DNA recombination allow the implementation of history-dependent logic circuits. By developing an in vivo temporal tracker using recombinases, we will track and decode the cell-lineage gene-expression of signaling events involved in lateral root development in the reference plant Arabidopsis thaliana. To date, we have characterized a number of genetic parts to tune the level of integrase activity. In parallel, we are identifying promoters that are active during early lateral root development via single cell RNA-seq. The techniques developed here should serve as a proof-of-principle that can be extended to studying the development of other organs, as well as to developmental studies in diverse organisms.