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

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

来源：BMC Genomics, 2018, 19(S2): 85.

DOI：10.1186/s12864-018-4469-4

• Abiotic stress
• Cis-acting elements
• Co-expression
• Hormone
• Microarray
• Transcription factors

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 transregulatory elements and facilitate our understanding of the relationships among TFs, cis-acting elements and target gene expression.

• 出版日期2018-5-9
• 单位香港中文大学（深圳）