Defining gene regulatory mechanisms in plant growth and development
The main goal of my research is to understand how plant genomes are programmed to have a specific transcriptional output through the interplay of regulatory DNA elements, transcription factors, and chromatin components. In this talk I will discuss our recent work to define the general regulatory features of plant genomes and to understand how these features are differentially utilized to produce specialized cell types during development.
The transcriptional regulatory structure of plant genomes has remained poorly defined relative to that of animals. For example, it is unclear how many cis-regulatory elements exist in plant genomes, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis, Medicago, Tomato, and Rice) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. Collectively, this work shows that cis-regulatory elements in plant genomes are generally fewer in number per gene and are much closer to the genes they regulate than those of animal genomes. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-target gene networks are generally conserved over evolutionary timescales. Comparative ATAC-seq profiling of the two Arabidopsis root epidermal cell types, the root hair and non-hair, revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding within these differentially accessible chromatin regions identified a TF regulatory network unique to the hair cell, which appears to link hair cell fate specification to nutrient availability. This work has revealed common gene regulatory principles among species and shed light on the mechanisms that produce cell type-specific transcriptomes during development.