Plant PromoterCAD: Data Driven DNA Design

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Robert Sidney Cox III, Koro Nishikata, Yuko Makita, Minami Matsui, Tetsuro Toyoda

RIKEN Yokohama, Japan

We have collected regulatory sequence and gene expression data for Arabidopsis thaliana into a linked data system hosted by, then created a CAD environment for using this data to design synthetically regulated plant promoters. This environment is written in JavaScript and hosted by the companion site There are several advantages of this system. (1) Non-experts can use the CAD environment and linked data to design functional DNA sequences with a fast learning cycle. (2) JavaScript programmers can readily fork and extend functions of the CAD environment with modular ‘GenoApps,’ which perform queries on the data and editing operations on the DNA sequences. Each module searches for different gene properties such as gene expression level in a particular plant tissue or tissues, or phase and amplitude of circadian oscillations. (3) Users can easily upload additional promoter data for use in the CAD environment. Biologists familiar with particular regulatory sequences can easily add them to the design inside the CAD environment. Researchers can upload additional databases of gene expression and regulatory motif data to generate alternate hypothesis designs. (4) Researchers can perform novel analyses on the linked data, and add derivative data for use by the GenoApps. Mashups of cis-regulatory sequence databases (e.g. PPDB, ATTED-II) and gene expression databases (e.g. AtGenExpress, DIURNAL) allow the user to perform advanced queries and modify gene promoter sequences to create synthetic plant promoters for tissue and time specific expression of an introduced gene. Several example promoter designs are being characterized experimentally by Firefly Luciferase expression in Arabidopsis. We will also discuss results from the promoter designs submitted to GenoCon2, the second international rational genomic design contest: