Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Chow CN

PROVIDER: S-EPMC5954277 | biostudies-literature | 2018 May

REPOSITORIES: biostudies-literature

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

Chow Chi-Nga CN Chiang-Hsieh Yi-Fan YF Chien Chia-Hung CH Zheng Han-Qin HQ Lee Tzong-Yi TY Wu Nai-Yun NY Tseng Kuan-Chieh KC Hou Ping-Fu PF Chang Wen-Chi WC

BMC genomics 20180509 Suppl 2

<h4>Background</h4>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.<h4>Results</h4>Here, we developed a series of bioinformatics analysis methods to infer transcriptional regulation by using numerous gene expression data from abiotic stresses and hormone ...[more]

PMID: 29764390

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Dataset Information

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

Publications

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

Similar Datasets

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