Abstract
Plants are exposed to a variety of environmental conditions, and their ability to respond to environmental variation depends on the proper regulation of gene expression in an organ-, tissue-, and cell type-specific manner. Although our knowledge of how stress responses are regulated is accumulating, a genome-wide model of how plant transcription factors (TFs) and cis-regulatory elements control spatially specific stress response has yet to emerge. Using Arabidopsis (Arabidopsis thaliana) as a model, we identified a set of 1,894 putative cis-regulatory elements (pCREs) that are associated with high-salinity (salt) up-regulated genes in the root or the shoot. We used these pCREs to develop computational models that can better predict salt up-regulated genes in the root and shoot compared with models based on known TF binding motifs. In addition, we incorporated TF binding sites identified via large-scale in vitro assays, chromatin accessibility, evolutionary conservation, and pCRE combinatorial relationships in machine learning models and found that only consideration of pCRE combinations led to better performance in salt up-regulation prediction in the root and shoot. Our results suggest that the plant organ transcriptional response to high salinity is regulated by a core set of pCREs and provide a genome-wide view of the cis-regulatory code of plant spatial transcriptional responses to environmental stress.