Faced with accelerating climate change and rapid population growth, we need crops with higher yields and greater resilience to ensure food security. Crop genome engineering will likely play an important role in meeting future food needs and gene regulatory sequences are promising targets for this engineering. However, we currently lack a sufficient understanding of plant regulatory logic for targeted and predictable engineering of regulatory DNA in crops. To overcome this limitation, I have developed Plant STARR-seq, a massively parallel reporter assay that can measure the species- and condition-specific activity of many different types of cis-regulatory elements. We have successfully applied Plant STARR-seq to characterize enhancers, core promoters, terminators, and insulators. We showed that Plant STARR-seq is sensitive enough to pinpoint regions linked to regulatory activity and define the underlying sequence motifs with single-nucleotide resolution. (...)