A Novel Framework for the Identification and Characterization of Putative Negative Cis-Acting Regulatory Elements in Arabidopsis thaliana

Environmental stress leads to the transcriptional reprogramming and adaptation of cell metabolism to new, often non-optimal conditions. Gene expression is induced when specific transcription factor (TF) binds to cis-acting regulatory element (CRE) in the promoter. Although substantial knowledge has been collected over last decades, it is still unclear how CRE combinations control gene expression in plants. Simple presence/absence models or combinatory rules are not sufficient for the prediction of gene expression patterns from the promoter sequence. Thus, we hypothesize that known CREs are influenced by other negative (repressor) motifs (negative CREs, nCREs) in promoters. In the following paper a novel framework for the identification and characterization of nCREs is proposed, based on the expression patterns under multiple stresses. The putative nCREs that might have negative impact on the activity of well-known ABA-responsive element (ABRE) and W-box element were identified. Also, the role of nucleosome localization on the activation of known CREs by corresponding TF was estimated. Our results can improve models of gene expression prediction in response to various stress conditions and lead to better understanding of transcriptional regulation in plants.