Using Epigenomic Tools to Define the Regulatory Structure of Plant Genomes

Compared to animal genomes, the cis-regulatory structure of plant genomes remains poorly defined. It is currently unclear how many enhancer elements exist in plant genomes, where these elements lie in relation to their target promoters, and how many elements are typically used to regulate each gene. To address these issues, we have employed ATAC-seq in four different plant species (Arabidopsis, Medicago, Tomato, and Rice) to delineate open chromatin regions and transcription factor binding sites across each genome. Despite major variations in genome size and evolutionary divergence, we find that the distribution of open chromatin sites is highly similar across species. The majority of these regions lie within 4kb upstream of a transcription start site (TSS) in all four species. Nearly 70% of genes in Arabidopsis, Medicago, and Rice have a single putative enhancer region upstream of the TSS, while a similar percentage of Tomato genes have 2-5 such elements. We have also used ATAC-seq profiling of specific cell types in Arabidopsis to address the differential utilization of regulatory elements during cell differentiation. We find that while closely related cell types often have qualitatively indistinguishable open chromatin profiles, deeper sequencing reveals major differences in transcription factor binding within these regions. This suggests that individual regulatory elements can be occupied by different regulators in different cell types, and that shallow sequencing of ATAC libraries is likely to miss important regulatory events. In this talk I will discuss the key findings of this work and future goals for deciphering transcriptional control in plants.