Gene regulatory grids (GRGs) encompass the space of all the possible transcription factor (TF)-target gene interactions that regulate gene expression, with gene regulatory networks (GRNs) representing a temporal and spatial manifestation of a portion of the GRG, essential for the specification of gene expression. Thus, understanding GRG architecture provides a valuable tool to explain how genes are expressed in an organism, an important aspect of synthetic biology and essential toward the development of the "in silico" cell. Progress has been made in some unicellular model systems (eg, yeast), but significant challenges remain in more complex multicellular organisms such as plants. Key to understanding the organization of GRGs is therefore identifying the genes that TFs bind to, and control. The application of sensitive and high-throughput methods to investigate genome-wide TF-target gene interactions is providing a wealth of information that can be linked to important agronomic traits. We describe here the methods and resources that have been developed to investigate the architecture of plant GRGs and GRNs. We also provide information regarding where to obtain clones or other resources necessary for synthetic biology or metabolic engineering.