• Research

Recoding Regulation

Creating genetic and epigenetic variation in non-coding regulatory sequences of plant genes.

Project summary.

Start date: April 2019

End date: 2022




Promoters serve a critical role in establishing baseline transcriptional capacity through the recruitment of proteins, including transcription factors.

Previously, a paucity of data for cis-regulatory elements in plants meant that it was challenging to determine which sequence elements in plant promoter sequences contributed to transcriptional function. We identified functional elements and established a quantitative experimental system to investigate transcriptional function, investigating how identity, density and position contribute to regulatory function. We have used this system to identify permissive architectures for minimal synthetic plant promoters, enabling the computational design of a suite of synthetic promoters.

We are currently using genome engineering tools and developing synthetic regulatory elements to engineer complex traits in plants by disrupting and rewiring gene regulatory networks that coordinate the growth of plants in response to changes in their environment. 


Genetic variations within coding sequences have been heavily exploited for crop improvement. However, quantitative, complex traits that respond to changes in the environment are the result of genetic and epigenetic variation in the non-coding regulatory sequences of multiple genes.

Analyses of transcriptional networks have enabled the identification of suites of genes that coordinate network responses, shaping complex phenotypes. For example, a plant's environmental nitrogen status is coordinated by multiple factors interacting in combination. Such advances have coincided with the development of molecular tools for targeted genome engineering.

In this project, we are applying our expertise in understanding gene regulatory sequences and genome engineering to engineer a complex trait. We are developing genome engineering technologies for inducing multiplexed mutations in coding and non-coding genic regions as well as epimutations in non-coding regions. We are applying these tools to create mutations in the genes that coordinate large-scale transcriptional responses to environmental nitrogen availability.


Rational design of minimal synthetic promoters for plants.

Cai YM, Kallam K, Tidd H, Gendarini G, Salzman A, Patron NJ. 

Nucleic Acids Res. 2020 Dec 2;48(21):11845-11856. doi: 10.1093/nar/gkaa682.


Siobhan Brady

UC Davis

David Segal

UC Davis

Impact statement.

This project is intended to develop new tools and approaches for engineering crops that are resilient to stress.