Rewiring the regulome: Evolution of plant cis-regulatory elements

Robust gene regulatory architectures are critical for proper development, response to environmental cues, and adaptation in plants. Owing to technical limitations imposed by the cell wall, the understanding of gene regulation in plants has lagged behind that of other organisms. However, innovation in molecular profiling techniques now make identifying active regulatory sequences across diverse cellular, developmental, and environmental contexts in a wide range of plant species routine. Despite these advances, most studies of plant regulatory elements have focused on regulatory dynamism within a single individual organism. As a result, the functional implications and mechanistic rules governing gene regulatory evolution remain less understood. With rates of genetic diversity in plants often far greater than metazoan species, plant models are uniquely positioned to address outstanding questions in regulatory evolution. Here, we review recent advances in the fundamental principles underlying gene regulatory evolution and the consequences towards molecular, cellular, and organismal phenotypes in plants.