Identification of cis- and trans-acting elements in plant promoters under various environments

  • 周 緻雅

Student thesis: Master's Thesis


There are two major research directions to understand the regulation mechanisms of plant stresses responsiveness One is to investigate the functions and metabolic pathways related to stress responsiveness The other is to study the adjustment of transcription when facing to spatial and temporal changes To analysis stress-response genes various microarray-based experiments have been massively preformed to monitor gene expression levels under different stresses and several related databases have been established Unfortunately none of current resources could identify the variation of gene expression profiles and analyze differentially expressed genes (DEGs) and critical stress affected metabolic pathways at the same time On the other hands transcription factors (TFs) play crucial roles in the examination of transcription regulation but still a lot of unknown properties For example among 2296 Arabidopsis TFs most of their corresponding transcription factor binding sites (TFBSs) are unidentified and limit researches focus on dynamic transcriptional regulatory networks depending on different conditions In order to solve the problems mentioned above there are two parts in this study In the first part we comprehensively collected the public microarray expression data including biotic stresses abiotic stresses and hormone treatments and constructed an integrated system for gene expression profiles and metabolic pathways identification EXPath was developed to provide five major analysis functions such as Gene Search Pathway Search DEGs Search Pathways/GO Enrichment Coexpression analysis and the advanced combination analysis between them To resolve the shortage information about transcriptional regulation we set up a novel method for analyzing correlation between trans- and cis- acting elements under various conditions based on expression data of EXPath The heat stress was used as a case to validate our analysis process The results indicated that nine transcription factors were highly specific induced by heat stress and defined as condition specific TFs (CsTFs) Four of nine CsTFs were reported as heat stress transcription factors (HSFs) and could bind on heat shock elements (HSEs) Surprisingly the other five CsTFs had almost not been studied we suggested those CsTFs might highly correlate to plant heat adaption Additionally based on the motif enrichment analysis in promoters of CsTFs coexpressed gene group several 8-mer motifs were significantly been recognized and similar to known HSEs The results demonstrated that the utility and reliability of our methods to discover cis-and trans-acting elements in promoter sequences under different conditions
Date of Award2015 Jul 24
Original languageEnglish
SupervisorWen-Chi Chang (Supervisor)

Cite this