The establishment of cell type-specific transcription programs during development is brought about through the coordinated action of transcription factors, cis-regulatory DNA elements, and chromatin components including histone variants, chromatin remodeling enzymes, and post-translational modifications of the histones themselves. However, we are only beginning to understand how these factors act and interact to establish the transcriptional output of a genome. In this talk I will discuss my laboratory’s efforts to understand the role of the enigmatic histone variant H2A.Z as both a transcriptional activator and repressor during development in the model plant Arabidopsis thaliana. In addition, I will describe our recent advances in defining the networks of cis-regulatory elements and transcription factors that drive plant cell fate specification. Collectively, this work is bringing us closer to a mechanistic understanding how a single genome can be used to generate the multitude of diverse cellular phenotypes found in both plants and animals.