Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE106418 | GEO | 2017/11/02
SECONDARY ACCESSION(S): PRJNA416802
REPOSITORIES: GEO
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Project description:NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify target genes of SOG1, we used wild-type plants harboring the transgene ProSOG1:SOG1-Myc, which expresses the SOG1-Myc fusion gene under the 2-kb SOG1 promoter. It was previously demonstrated that SOG1-Myc can complement the sog1-1 mutation (Yoshiyama et al., 2013). After treatment of plants with 15 µM zeocin for 2 hours, chromatin fragments bound to SOG1-Myc were immunoprecipitated with the anti-Myc antibody, and were subjected to next generation sequencing. We identified 778 SOG1-binding peak summits, which displayed peak values 16-fold higher than those in wild-type plants without the transgene. The genomic regions between 5-kb upstream and downstream of each peak summit included 1514 genes among which we found SMR5, SMR7 and CYCB1;1 that were previously identified as SOG1 target genes (Yi et al., 2014; Weimer et al., 2016). Among 1514 genes identified by ChIP-sequencing, 146 genes were overlapped with the SOG1-regulated genes extracted from the microarray data (GSE106154); therefore, we concluded that the 146 genes are SOG1 ditrect target genes.
2017-11-02 | GSE106415 | GEO
Project description:Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1)-target genes in Arabidopsis
| PRJNA416801 | ENA
Project description:Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis
| PRJNA416802 | ENA
Project description:NAC transcription factor SUPPRESSOR OF GAMMA RESPONSE 1 (SOG1) functions as a master regulator in DNA damage response of Arabidopsis. However, the signaling pathway controlled by SOG1 remains elusive. To identify genes whose expression is regulated by SOG1 in response to double strand breaks, wild-type (WT: Col-0 ecotype) and sog1-1 mutant plants were treated with or without zeocin for 2 h and were subjected to microarray analysis using Arabidopsis custom microarrays (GEO array platform: GPL19830). We found that 432 genes exhibited altered expressions in response to zeocin-induced double strand breaks in the SOG1-dependent manner. In addition, combining them with ChIP-Seq data, we identified 146 genes as SOG1-direct target genes.
2017-11-01 | GSE106154 | GEO
Project description:Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated genes in Arabidopsis
| PRJNA415786 | ENA
Project description:BackgroundHypoxia induced by flooding causes significant losses to crop production almost every year. However, the molecular network of submergence signaling pathway is still poorly understood. According to previous studies, transgenic plants overexpressing the WRKY33 gene showed enhanced resistance to submergence stress. Thus, this transcription factor may regulate a series of target genes in response to submergence. Here, to determine putative downstream targets of WRKY33 at a genome-wide scale in Arabidopsis thaliana, we performed the chromatin immunoprecipitation sequencing (ChIP-seq) using 35S:FLAG-WRKY33 overexpression transgenic lines (WRKY33-OE) after 24 h of submergence treatment.ResultsUsing ChIP-seq data, we identified a total of 104 WRKY33-binding genes under submergence stress (WRKY33BGSs). Most WRKY33BGSs are involved in the oxidation-reduction process, programmed cell death in response to reactive oxygen species, lipid biosynthesis process, and other processes related to stress responses. Moreover, the major motif identified in the WRKY33BGSs promoters is a new cis-element, TCTCTC (named here as "TC box"). This cis-element differs from the previously known W box for WRKY33. Further qPCR experiments verified that genes carrying this motif in their promoters could be regulated by WRKY33 upon submergence treatment.ConclusionsOur study has identified a new putative binding motif of WRKY33 and recovered numerous previously unknown target genes of WRKY33 during submergence stress. The WRKY33 gene positively participates in flooding response probably by transcriptional regulation of the downstream submergence-related target genes via a "TC box".
| S-EPMC8142642 | biostudies-literature
Project description:The Arabidopsis sog1-1 (suppressor of gamma response) mutant was originally isolated as a second-site suppressor of the radiosensitive phenotype of seeds defective in the repair endonuclease XPF. Here, we report that SOG1 encodes a putative transcription factor. This gene is a member of the NAC domain [petunia NAM (no apical meristem) and Arabidopsis ATAF1, 2 and CUC2] family (a family of proteins unique to land plants). Hundreds of genes are normally up-regulated in Arabidopsis within an hour of treatment with ionizing radiation; the induction of these genes requires the damage response protein kinase ATM, but not the related kinase ATR. Here, we find that SOG1 is also required for this transcriptional up-regulation. In contrast, the SOG1-dependent checkpoint response observed in xpf mutant seeds requires ATR, but does not require ATM. Thus, phenotype of the sog1-1 mutant mimics aspects of the phenotypes of both atr and atm mutants in Arabidopsis, suggesting that SOG1 participates in pathways governed by both of these sensor kinases. We propose that, in plants, signals related to genomic stress are processed through a single, central transcription factor, SOG1.
| S-EPMC2722309 | biostudies-literature
Project description:Using PC12 cells as an in vitro model system, we have identified a series of transcripts induced through activation of the leptin receptor. On the basis of kinetic studies, two distinct gene sets could be discerned: signal transducer and activator of transciption-3 (STAT-3), suppressor of cytokine signalling-3 (SOCS-3), MT-II (metallothionein-II), the serine/threonine kinase fibroblast-growth-factor-inducible kinase (Fnk) and modulator recognition factor (MRF-1), which are immediate early response genes, and pancreatitis-associated protein I (PAP I), squalene epoxidase, uridine diphosphate glucuronosyltransferase and annexin VIII, which are late induced target genes. At late time points a strong co-stimulation with beta-nerve growth factor or with the adenylate cyclase activator forskolin was observed. To assess the validity of the PC12-cell model system, we examined the effect of leptin administration on the gene transcription of STAT-3, MT-II, Fnk and PAP I in vivo. Leptin treatment of leptin-deficient ob/ob mice increased the STAT-3, SOCS-3, MT-II and Fnk mRNA, and MT-I protein levels in liver, whereas, in jejunum, expression of PAP I mRNA was down-regulated. Furthermore, administration of leptin to starved wild-type mice enhanced the expression of MT-II and Fnk mRNA in liver, but decreased MT-II and PAP I mRNA expression in jejunum. These findings may help to explain the obese phenotype observed in some colonies of MT-I- and MT-II-null mice and/or the observation that leptin protects against tumour-necrosis-factor toxicity in vivo.
| S-EPMC1221035 | biostudies-other
Project description:BackgroundbZIP 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.ResultsWe 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.ConclusionsBrachypodium bZIP10 is involved in zinc homeostasis, as it relates to oxidative stress.
| S-EPMC5894230 | biostudies-literature
Project description:Arabidopsis SOG1 (suppressor of gamma response 1) is a plant-specific transcription factor that governs the DNA damage response. Here we report that SOG1 is phosphorylated in response to DNA damage, and that this phosphorylation is mediated by the sensor kinase ataxia telangiectasia mutated (ATM). We show that SOG1 phosphorylation is crucial for the response to DNA damage, including transcriptional induction of downstream genes, transient arrest of cell division and programmed cell death. Although the amino-acid sequences of SOG1 and the mammalian tumour suppressor p53 show no similarity, this study demonstrates that ATM-mediated phosphorylation of a transcription factor has a pivotal role in the DNA damage response in both plants and mammals.
| S-EPMC3790055 | biostudies-literature