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Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress.

ABSTRACT: BACKGROUND:bZIP transcription factors play a significant role in many aspects of plant growth and development and also play critical regulatory roles during plant responses to various stresses. Overexpression of the Brachypodium bZIP10 (Bradi1g30140) transcription factor conferred enhanced oxidative stress tolerance and increased viability when plants or cells were exposed to the herbicide paraquat. To gain a better understanding of genes involved in bZIP10 conferred oxidative stress tolerance, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) was performed on BdbZIP10 overexpressing plants in the presence of oxidative stress. RESULTS:We identified a transcription factor binding motif, TGDCGACA, different from most known bZIP TF motifs but with strong homology to the Arabidopsis zinc deficiency response element. Analysis of the immunoprecipitated sequences revealed an enrichment of gene ontology groups with metal ion transmembrane transporter, transferase, catalytic and binding activities. Functional categories including kinases and phosphotransferases, cation/ion transmembrane transporters, transferases (phosphorus-containing and glycosyl groups), and some nucleoside/nucleotide binding activities were also enriched. CONCLUSIONS:Brachypodium bZIP10 is involved in zinc homeostasis, as it relates to oxidative stress.

SUBMITTER: Martin RC

PROVIDER: S-EPMC5894230 | biostudies-literature | 2018 Apr

REPOSITORIES: biostudies-literature

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Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress.

Martin Ruth C RC Vining Kelly K Dombrowski James E JE

BMC plant biology 20180410 1

<h4>Background</h4>bZIP transcription factors play a significant role in many aspects of plant growth and development and also play critical regulatory roles during plant responses to various stresses. Overexpression of the Brachypodium bZIP10 (Bradi1g30140) transcription factor conferred enhanced oxidative stress tolerance and increased viability when plants or cells were exposed to the herbicide paraquat. To gain a better understanding of genes involved in bZIP10 conferred oxidative stress tol ...[more]

PMID: 29636001

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Project description:BackgroundTwo plant-specific transcription factors, NAC and YABBY, are involved in important plant developmental processes. However their molecular mechanisms, especially DNA binding sites and co-regulated genes, are largely unknown during soybean seedling development.ResultsIn order to identify genome-wide binding sites of specific members of the NAC and YABBY transcription factors and co-regulated genes, we performed Chromatin Immunoprecipitation Sequencing (ChIP-Seq) and RNA Sequencing (RNA-Seq) using cotyledons from soybean seedling developmental stages. Our RNA-Seq data revealed that these particular NAC and YABBY transcription factors showed a clear pattern in their expression during soybean seedling development. The highest level of their expression was found in seedling developmental stage 4 when cotyledons undergo a physiological transition from non-photosynthetic storage tissue to a metabolically active photosynthetic tissue. Our ChIP-Seq data identified 72 genes potentially regulated by the NAC and 96 genes by the YABBY transcription factors examined. Our RNA-Seq data revealed highly differentially expressed candidate genes regulated by the NAC transcription factor include lipoxygense, pectin methyl esterase inhibitor, DEAD/DEAH box helicase and homeobox associated proteins. YABBY-regulated genes include AP2 transcription factor, fatty acid desaturase and WRKY transcription factor. Additionally, we have identified DNA binding motifs for the NAC and YABBY transcription factors.ConclusionsGenome-wide determination of binding sites for NAC and YABBY transcription factors and identification of candidate genes regulated by these transcription factors will advance the understanding of complex gene regulatory networks during soybean seedling development. Our data imply that there is transcriptional reprogramming during the functional transition of cotyledons from non-photosynthetic storage tissue to metabolically active photosynthetic tissue.

Project description:Chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-seq) or microarray hybridization (ChIP-chip) has been widely used to determine the genomic occupation of transcription factors (TFs). We have previously developed a probabilistic method, called TIP (Target Identification from Profiles), to identify TF target genes using ChIP-seq/ChIP-chip data. To achieve high specificity, TIP applies a conservative method to estimate significance of target genes, with the trade-off being a relatively low sensitivity of target gene identification compared to other methods. Additionally, TIP's output does not render binding-peak locations or intensity, information highly useful for visualization and general experimental biological use, while the variability of ChIP-seq/ChIP-chip file formats has made input into TIP more difficult than desired.To improve upon these facets, here we present are fined TIP with key extensions. First, it implements a Gaussian mixture model for p-value estimation, increasing target gene identification sensitivity and more accurately capturing the shape of TF binding profile distributions. Second, it enables the incorporation of TF binding-peak data by identifying their locations in significant target gene promoter regions and quantifies their strengths. Finally, for full ease of implementation we have incorporated it into a web server ( http://syslab3.nchu.edu.tw/iTAR/ ) that enables flexibility of input file format, can be used across multiple species and genome assembly versions, and is freely available for public use. The web server additionally performs GO enrichment analysis for the identified target genes to reveal the potential function of the corresponding TF.The iTAR web server provides a user-friendly interface and supports target gene identification in seven species, ranging from yeast to human. To facilitate investigating the quality of ChIP-seq/ChIP-chip data, the web server generates the chart of the characteristic binding profiles and the density plot of normalized regulatory scores. The iTAR web server is a useful tool in identifying TF target genes from ChIP-seq/ChIP-chip data and discovering biological insights.

Dataset Information

Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress.

Publications

Genome-wide (ChIP-seq) identification of target genes regulated by BdbZIP10 during paraquat-induced oxidative stress.

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