ArticleBMC genomics2018
Delineation of condition specific Cis- and Trans-acting elements in plant promoters under various Endo- and exogenous stimuli.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 33 citations in OpenAlex.
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- ZmHsp18 screened from the ZmHsp20 gene family confers thermotolerance in maize.BMC plant biology · 2024Article
- Genome-Wide Identification, Expression and Evolution Analysis of m6A Writers, Readers and Erasers inPlants (Basel, Switzerland) · 2023Article
- Genome-Wide Identification and Analysis of the Plant Cysteine Oxidase (PCO) Gene Family inInternational journal of molecular sciences · 2023Article
- Genome-Wide Analyses of Thaumatin-like Protein Family Genes Reveal the Involvement in the Response to Low-Temperature Stress inInternational journal of molecular sciences · 2023Article
- Global Identification and Characterization of C2 Domain-Containing Proteins Associated with Abiotic Stress Response in Rice (International journal of molecular sciences · 2022Article
- Molecular evolutionary analysis of theFrontiers in plant science · 2022Article
- Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes inFrontiers in plant science · 2021Article
- Genome-Wide Analysis of the DUF4228 Family in Soybean and Functional Identification ofFrontiers in plant science · 2021Article
- Male Sterility in Maize after Transient Heat Stress during the Tetrad Stage of Pollen Development.Plant physiology · 2019Article
Corrections and comments
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Authors and funding
9 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscription 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.
resultsHere, 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.
conclusionsThe 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.
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