Figure 3.

The minimal promoter approach for synthetic promoter creation.

DNA arrays are synthesized and ligated with a minimal or core promoter to generate SPLs. The synthetic promoters are recombined with a reporter gene such as GFP to generate reporter MSPs. The middle panel shows MSPs in which cis-regulatory elements (CREs) originate from bacteria or yeast. The reporter module is composed of a synthetic promoter, a reporter gene, and a terminator; the synthetic promoter contains cis elements bound by synthetic activators or repressors to conditionally control downstream gene expression. The modules are transiently expressed in plants or protoplasts. After analyzing expression profiles of the reporter gene and DNA sequences of the promoters, promoter datasets are created and used by machine learning (ML) for expression profile prediction. ML models predict promoter sequences and corresponding expression strengths in silico. New synthetic promoters are validated and undergo further iterative rounds if needed. CNN, ANN, DeepMind, and iPro-GAN are deep learning methods.