Delineation of condition specific Cis - and Trans -acting elements in plant promoters under various Endo- and exogenous stimuli

Background Transcription factors (TFs) play essential roles during plant development and response to environmental stresses. However, the relationships among transcription factors, cis -acting elements and target gene expression under endo- and exogenous stimuli have not been systematically characterized. Results Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormones treatments. After filtering the expression profiles of TF-encoding genes, 291 condition specific transcription factors (CsTFs) were obtained. Differentially expressed genes were then classified into various co-expressed gene groups based on each CsTFs. In the case studies of heat stress and ABA treatment, several known and novel cis -acting elements were identified following our bioinformatics approach. Significantly, a palindromic sequence of heat-responsive elements is recognized, and also obtained from a 3D protein structure of heat-shock protein-DNA complex. Notably, overrepresented 3- and 4-mer motifs in an enriched 8-mer motif could be a core cis -element for a CsTF. In addition, the results suggest DNA binding preferences of the same CsTFs are different according to various conditions. Conclusions The overall results illustrate this study may be useful in identifying condition specific cis - and trans - regulatory elements and facilitate our understanding of the relationships among TFs, cis- acting elements and target gene expression.