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

Chi Nga Chow, Yi Fan Chiang-Hsieh, Chia Hung Chien, Han Qin Zheng, Tzong Yi Lee, Nai Yun Wu, Kuan Chieh Tseng, Ping Fu Hou, Wen Chi Chang

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


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.

Original languageEnglish
Article number85
JournalBMC genomics
Publication statusPublished - 2018 May 9

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics


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