Plants are subjected to a variety of environmental stress, and their ability to respond to stress depends, in a large part, on the proper regulation of gene activities including transcription. Earlier studies show that the regulation of stress transcriptional response has a significant spatial component, namely, each organ, tissue, and cell type may respond to a stress by differentially regulating different sets of genes. Although our knowledge is accumulating on how specific transcription factors (TFs) and their associated cis-regulatory elements (CREs) are involved in stress responses, a genome wide model of what plant TFs and CREs are key to the spatial stress response regulation has yet to emerge. In this study, a set of 1,894 putative CREs (pCREs) were identified that are associated with salt stress up-regulated genes in the root and shoot of Arabidopsis thaliana. These pCREs led to models that can better predict salt up-regulated genes in root and shoot compared to models based on known TF binding motifs. The full pCRE set could be broken into root, shoot and general subsets that are enriched amongst root, shoot, or both root and shoot salt up-regulated genes, respectively. We also identified pCRE subsets that are enriched amongst genes induced by salt in root cell-types. Most importantly, combinations of the pCRE subsets allowed predictions of genes up-regulated by high salinity in root, shoot, as well as various root cell types. In addition, consideration of pCRE combinatorial rules further improved salt upregulation prediction. Our results suggest that the organ and cell-type transcriptional response to high salinity is regulated by a core set of pCREs that need to be considered in combinations, and provides a genome-wide view on the cis-regulation of spatial transcriptional responses to stress.
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