ChIP-Sequencing of AL5 over-expressing Arabidopsis and its knock out mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE56706 | GEO | 2014/04/12
SECONDARY ACCESSION(S): PRJNA244331
REPOSITORIES: GEO
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Project description:Plant homeodomain (PHD) finger proteins affect growth and development by regulating transcription and reading epigenetic modifications of histones, but their functions in abiotic stress responses remain largely unclear. Here we characterize seven Arabidopsis thaliana Alfin1-like PHD finger proteins (ALs) in the response to abiotic stresses. ALs localize to the nucleus and repress transcription. Except AL6, all the ALs bind to G-box element. Changes of the amino acids at positions 34 and 35 in AL6 cause the loss of G-box binding ability. Expression of the ALs responded differently to osmotic stress, salt, cold and abscisic acid treatments. AL5 was induced by multiple stresses, and AL5-overexpressing plants showed higher tolerance to salt, drought and freezing stress than Col-0. Also, al5 mutants showed reduced stress tolerance. ChIP-Seq assay helps find the direct targets of AL5. Polyclonal antibody of AL5 protein was used to perform ChIP experiment. Two samples were analyzed, AL5 OE sample and its knock out mutant. Data was analyzed as OE sample Vs mutant sample and help find targets of AL5 protein.
2014-04-12 | E-GEOD-56706 | biostudies-arrayexpress
Project description:Plant basic helix-loop-helix (bHLH) transcription factors are involved in physiological and developmental processes, and also play essential roles in abiotic stresses. However, their exact roles in abiotic stress are still need to be elucidated, and most of bHLHs have not been functionally characterized. In the present study, we characterized the functional role of AtbHLH112 in response to abiotic stresses. AtbHLH112 is a nuclear-localized protein, and its nuclear-localization is induced by salt, drought and ABA. Besides binding to E-box motif, AtbHLH112 is found to bind to a novel motif with the sequence M-bM-^@M-^\GG[GT]CC[GT][GA][TA]CM-bM-^@M-^] (GCG-box), and the binding affinity is induced by salt and ABA. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with salt and drought tolerance. AtbHLH112 mediates stress tolerance by upregulating the expression of P5CS genes and decreasing the expression of P5CDH and PRODH genes to increase proline levels, and via enhancing the expression of POD and SOD genes to improve ROS scavenging ability. All data together suggested that AtbHLH112 regulates the expression of genes through binding to GCG-box and E-box to mediate the physiological stress responses, including proline biosynthesis and ROS scavenging pathways to enhance stress tolerance. Differentially expression genes of AtbHLH112-overexpression plants, mutant (SALK_033618C) plants and wild type of Columbia Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.
2014-08-09 | E-GEOD-60260 | biostudies-arrayexpress
Project description:Plant basic helix-loop-helix (bHLH) transcription factors are involved in physiological and developmental processes, and also play essential roles in abiotic stresses. However, their exact roles in abiotic stress are still need to be elucidated, and most of bHLHs have not been functionally characterized. In the present study, we characterized the functional role of AtbHLH112 in response to abiotic stresses. AtbHLH112 is a nuclear-localized protein, and its nuclear-localization is induced by salt, drought and ABA. Besides binding to E-box motif, AtbHLH112 is found to bind to a novel motif with the sequence “GG[GT]CC[GT][GA][TA]C” (GCG-box), and the binding affinity is induced by salt and ABA. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with salt and drought tolerance. AtbHLH112 mediates stress tolerance by upregulating the expression of P5CS genes and decreasing the expression of P5CDH and PRODH genes to increase proline levels, and via enhancing the expression of POD and SOD genes to improve ROS scavenging ability. All data together suggested that AtbHLH112 regulates the expression of genes through binding to GCG-box and E-box to mediate the physiological stress responses, including proline biosynthesis and ROS scavenging pathways to enhance stress tolerance.
2014-08-09 | GSE60260 | GEO
Project description:Plant basic helix-loop-helix (bHLH) proteins play essential roles in physiological and developmental processes and are also involved in abiotic stresses. However, their exact roles in abiotic stress are still not fully understood, and most of them have not been functionally characterised. In the present study, we characterised the functional role of AtbHLH112 in response to abiotic stress. A WRKY gene, AtWRKY66, can regulate the expression of the AtbHLH112 via binding to W-box motifs present in its promoter. AtbHLH112 is a nuclear-localised protein, and its nuclear localisation is increased upon exposure to NaCl, mannitol and ABA. In addition to binding to the G-box motif, AtbHLH112 is found to bind to a novel motif M-bM-^@M-^\GGGCCGGTCM-bM-^@M-^] (named the GCG-box) to regulate gene expression. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with tolerance to salt and drought. AtbHLH112 can confer stress tolerance via enhanced expression of POD and SOD genes to improve ROS scavenging ability and via upregulated expression of P5CS genes and decreased expression of P5CDH and PRODH genes to improve proline levels. Our data suggested that AtbHLH112 regulates the expression of genes via binding to the G-box and the GCG-box to improve stress-related pathways, such as ROS scavenging and proline biosynthesis. Differentially expression genes of AtbHLH112-overexpression plants and mutant (SALK_033618C) plants of Arabidopsis thaliana were measured under salt stressed and normal condition for 3 hours, respectively. Three independent experiments were performed at each treatment using different plants for each experiment.
2013-11-14 | E-GEOD-52326 | biostudies-arrayexpress
Project description:A novel cold-inducible GSK3/Shaggy-like kinase cDNA (TaSK5) was isolated from winter wheat by a macroarray-based differential screening approach. Sequence analysis of TaSK5 revealed high similarity to Arabidopsis subgroup I GSK3/Shaggy-like kinases ASK-alpha, ASK-gamma and ASK-epsilon. Transgenic Arabidopsis plants overexpressing TaSK5 cDNA under the control of CaMV 35S promoter showed enhanced tolerance to salt and drought stresses. In contrast, the tolerance of the transgenic plants to freezing stress was not altered. To identify genes which are differentially regulated in the 35S:TaSK5 over-expressing Arabidopsis plants under non-stress conditions, we compared the genome-wide expression profiles of Col-0 and plants over-expressing TaSK5 using DNA microarrays. Sixty seven genes were found to be expressed at least 2-fold more strongly in 35S:TaSK5 plants than in Col-0, and 17 genes were found to be expressed at least 2-fold more strongly in Col-0 than in 35S:TaSK5 plants. Most of the TaSK5 up-regulated genes were also induced by abiotic stresses, including cold, salt and drought. These results support the involvement of TaSK5 in abiotic stress signal transduction. Keywords: transgenic vs wt Col.-0 comparison
2014-11-02 | GSE59556 | GEO
Project description:Plants will meet various abiotic stresses during their growth and development. One of the important strategies for plants to deal with the stress is involved in metabolic regulation, causing the dramatic changes of metabolite profiles. Metabolomic studies have been intensively conducted to reveal the responses of plants to abiotic stress, but most of them were limited to one or at most two abiotic stresses in a single experiment. In this study, we compared the metabolite profiles of barley seedlings exposed to seven abiotic stresses simultaneously, including drought, salt stress, aluminum (Al), cadmium (Cd), deficiency of nitrogen (N), phosphorus (P) and potassium (K). The results showed that metabolite profiles of barley under these stresses could be classified into three types: osmotic stresses (drought and salt); metal stresses (Al and Cd) and nutrient deficiencies (N, P and K deficiencies). Compared with the control, some metabolites (including polyamines, raffinose and piperonic acid) in plants exposed to all abiotic stresses changed significantly, while some other metabolites showed the specific change only under a certain abiotic stress, such as proline being largely increased by osmotic stress (drought and salinity), the P-containing metabolites being largely decreased under P deficiency, some amino acids (lysine, tyrosine, threonine, ornithine， glutamine and so on) showing the dramatic reduction in the plants exposed to N deficiencies, respectively. The current meta-analysis obtained a comprehensive view on the metabolic responses to various abiotic stress, and improved the understanding of the mechanisms for tolerance of barley to abiotic stress.
2021-01-07 | ST001648 | MetabolomicsWorkbench
Project description:Drought and salinity are two main abiotic-stresses negatively affecting crop growth and productivity worldwide with largely decreasing crop yields. The understanding of plant responses to stresses in physiology, genetics, and molecular biology will be greatly helpful to improve the tolerance of crops to abiotic-stresses through genetic engineering.To identify the genetic loci that control drought and salt tolerance in rice, we performed a large-scale screen for the mutants with altered drought and salt tolerance. A drought and salt tolerance (dst) mutant line was isolated.In this series, we compare the transcriptome of wild-type plant Zhonghua11 and dst mutants under the normal growth conditions. Keywords: genetic modification
2009-07-30 | GSE11175 | GEO
Project description:Plant basic helix-loop-helix (bHLH) proteins play essential roles in physiological and developmental processes and are also involved in abiotic stresses. However, their exact roles in abiotic stress are still not fully understood, and most of them have not been functionally characterised. In the present study, we characterised the functional role of AtbHLH112 in response to abiotic stress. A WRKY gene, AtWRKY66, can regulate the expression of the AtbHLH112 via binding to W-box motifs present in its promoter. AtbHLH112 is a nuclear-localised protein, and its nuclear localisation is increased upon exposure to NaCl, mannitol and ABA. In addition to binding to the G-box motif, AtbHLH112 is found to bind to a novel motif “GGGCCGGTC” (named the GCG-box) to regulate gene expression. Gain- and loss-of-function analyses showed that the transcript level of AtbHLH112 is positively correlated with tolerance to salt and drought. AtbHLH112 can confer stress tolerance via enhanced expression of POD and SOD genes to improve ROS scavenging ability and via upregulated expression of P5CS genes and decreased expression of P5CDH and PRODH genes to improve proline levels. Our data suggested that AtbHLH112 regulates the expression of genes via binding to the G-box and the GCG-box to improve stress-related pathways, such as ROS scavenging and proline biosynthesis.
2013-11-14 | GSE52326 | GEO
Project description:Drought and salinity are two main abiotic-stresses negatively affecting crop growth and productivity worldwide with largely decreasing crop yields. The understanding of plant responses to stresses in physiology, genetics, and molecular biology will be greatly helpful to improve the tolerance of crops to abiotic-stresses through genetic engineering. To identify the genetic loci that control drought and salt tolerance in rice, we performed a large-scale screen for the mutants with altered drought and salt tolerance. A drought and salt tolerance (dst) mutant line was isolated. In this series, we compare the transcriptome of wild-type plant Zhonghua11 and dst mutants under the normal growth conditions. Keywords: genetic modification 6 samples (3 biological replicates for each line) were used in this experiment.
2009-07-29 | E-GEOD-11175 | biostudies-arrayexpress
Project description:Following pathogen infection, plants have developed diverse mechanisms of defense that enhance their immune system for more robust induction of defense responses against recurrent environmental stresses. This induced resistance can be heritable to the progeny, rendering them more tolerant to stressful events. Although within-generational induction of tolerance to abiotic stress is a well-documented phenomenon in virus-infected plants, the transgenerational inheritance of tolerance to abiotic stresses in their progenies has not been explored. Here, we show that infection of Nicotiana benthamiana plants by Potato virus X (PVX) and by a chimeric Plum pox virus (PPV) expressing the P25 protein of PVX (PPV-P25), but not by PPV, conferred tolerance to both salt and osmotic stresses to the progeny, which correlated with the level of virulence of the pathogen. This transgenerational tolerance to abiotic stresses in the progeny was partially sustained even if the plants experience a virus-free generation. Moreover, progenies from a Dicer-like3 mutant, irrespective whether their parents were infected or not, mimicked the enhanced tolerance to abiotic stress observed in progenies of PVX-infected wild-type plants, suggesting the involvement of 24-nt small interfering RNAs in the transgenerational tolerance to abiotic stress induced by virus infection. RNAseq analysis supported the upregulation of genes related to protein folding and response to stress in the progeny of PVX-infected plants. From an environmental point of view, the significance of virus-induced transgenerational tolerance to abiotic stress could be questionable, as its induction was offset by major reproductive costs arising from a detrimental effect on seed production
2022-10-14 | GSE214636 | GEO