A High-Resolution Map of Regulatory DNA in Arabidopsis thaliana

As sessile organisms, plants are intricately linked to their environment and respond acutely to light and temperature cues. These responses involve gene expression changes that are caused by the interaction of trans-acting regulatory factors with a combination of gene-proximal and distal cis-regulatory sites.

Despite the critical importance of plants for ecosystem stability and human survival, plant regulatory DNA landscapes, including those of the extensively-studied model plant Arabidopsis thaliana, remain largely unknown. For example, of the 1500 A. thaliana transcription factors, only a handful are functionally characterized with well-described gene targets and/or binding motifs.

Using high-resolution DNaseI-seq, we mapped the regulatory DNA landscape of whole A. thaliana seedlings, specific cell types, and selected organs. We further interrogated the dynamic changes of the A. thaliana regulatory DNA landscape in response to light and temperature cues. We identified hundreds of thousands of protein ‘footprints’, where bound DNA is protected from DNaseI cleavage. Within footprints we identified over 150 novel motifs. These novel motifs behave similarly to known motifs with regard to nucleotide diversity and conservation. Finally, we used footprint information together with high-quality motif data for over ~250 transcription factors to build the first system-level empirical regulatory networks and demonstrate their extensive re-wiring in response to light and temperature cues. We also report evidence that genetic variation within footprints is associated with previously reported phenotypic variation across wild A. thaliana strains.