Microarray Meta-Analysis Focused on the Response of Genes Involved in Redox Homeostasis to Diverse Abiotic Stresses in Rice.
ABSTRACT: Plants are exposed to a wide range of abiotic stresses (AS), which often occur in combination. Because physiological investigations typically focus on one stress, our understanding of unspecific stress responses remains limited. The plant redox homeostasis, i.e., the production and removal of reactive oxygen species (ROS), may be involved in many environmental stress conditions. Therefore, this study intended to identify genes, which are activated in diverse AS, focusing on ROS-related pathways. We conducted a meta-analysis (MA) of microarray experiments, focusing on rice. Transcriptome data were mined from public databases and fellow researchers, which represented 36 different experiments and investigated diverse AS, including ozone stress, drought, heat, cold, salinity, and mineral deficiencies/toxicities. To overcome the inherent artifacts of different MA methods, data were processed using Fisher, rOP, REM, and product of rank (GeneSelector), and genes identified by most approaches were considered as shared differentially expressed genes (DEGs). Two MA strategies were adopted: first, datasets were separated into shoot, root, and seedling experiments, and these tissues were analyzed separately to identify shared DEGs. Second, shoot and seedling experiments were classed into oxidative stress (OS), i.e., ozone and hydrogen peroxide treatments directly producing ROS in plant tissue, and other AS, in which ROS production is indirect. In all tissues and stress conditions, genes a priori considered as ROS-related were overrepresented among the DEGs, as they represented 4% of all expressed genes but 7-10% of the DEGs. The combined MA approach was substantially more conservative than individual MA methods and identified 1001 shared DEGs in shoots, 837 shared DEGs in root, and 1172 shared DEGs in seedlings. Within the OS and AS groups, 990 and 1727 shared DEGs were identified, respectively. In total, 311 genes were shared between OS and AS, including many regulatory genes. Combined co-expression analysis identified among those a cluster of 42 genes, many involved in the photosynthetic apparatus and responsive to drought, iron deficiency, arsenic toxicity, and ozone. Our data demonstrate the importance of redox homeostasis in plant stress responses and the power of MA to identify candidate genes underlying unspecific signaling pathways.
Project description:The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B) intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants, including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.]) remain poorly understood. Here, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control), 0.5, and 6 h using RNA-seq analysis. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs) likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS) metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase) rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Our study provides valuable information for deep understanding of UV-B stress defense mechanisms and for the development of resistant soybean genotypes that survive under high-intensity UV-B stress.
Project description:BACKGROUND: Tropospheric ozone, the most abundant air pollutant is detrimental to plant and animal health including humans. In sensitive plant species even a few hours of exposure to this potent oxidant (200-300 nL. L-1) leads to severe oxidative stress that manifests as visible cell death. In resistant plants usually no visible symptoms are observed on exposure to similar ozone concentrations. Naturally occurring variability to acute ozone in plants provides a valuable resource for examining molecular basis of the differences in responses to ozone. From our earlier study in Medicago truncatula, we have identified cultivar Jemalong is ozone sensitive and PI 464815 (JE154) is an ozone-resistant accession. Analyses of transcriptome changes in ozone-sensitive and resistant accession will provide important clues for understanding the molecular changes governing the plant responses to ozone. RESULTS: Acute ozone treatment (300 nL L-1 for six hours) led to a reactive oxygen species (ROS) burst in sensitive Jemalong six hours post-fumigation. In resistant JE154 increase in ROS levels was much reduced compared to Jemalong. Based on the results of ROS profiling, time points for microarray analysis were one hour into the ozone treatment, end of treatment and onset of an ozone-induced ROS burst at 12 hours. Replicated temporal transcriptome analysis in these two accessions using 17 K oligonucleotide arrays revealed more than 2000 genes were differentially expressed. Significantly enriched gene ontologies (GOs) were identified using the Cluster Enrichment analysis program. A striking finding was the alacrity of JE154 in altering its gene expression patterns in response to ozone, in stark contrast to delayed transcriptional response of Jemalong. GOs involved in signaling, hormonal pathways, antioxidants and secondary metabolism were altered in both accessions. However, the repertoire of genes responding in each of these categories was different between the two accessions. Real-time PCR analysis confirmed the differential expression patterns of a subset of these genes. CONCLUSION: This study provided a cogent view of the unique and shared transcriptional responses in an ozone-resistant and sensitive accession that exemplifies the complexity of oxidative signaling in plants. Based on this study, and supporting literature in Arabidopsis we speculate that plants sensitive to acute ozone are impaired in perception of the initial signals generated by the action of this oxidant. This in turn leads to a delayed transcriptional response in the ozone sensitive plants. In resistant plants rapid and sustained activation of several signaling pathways enables the deployment of multiple mechanisms for minimizing the toxicity effect of this reactive molecule.
Project description:Oxidative stress (OS), a common intracellular phenomenon induced by excess reactive oxygen species (ROS) generation, has been shown to be associated with mammalian ovarian follicular development blockage and granulosa cell (GC) impairment. However, the mechanism involved in these effects remains unknown, and the effect of OS on the transcriptome profiles in porcine GCs has not been fully characterized. In this study, we found that hydrogen peroxide-mediated oxidative stress induced porcine GC apoptosis and impaired cell viability. Moreover, RNA-seq analysis showed that oxidative stress induced dramatic changes in gene expression in porcine GCs. A total of 2025 differentially expressed genes (DEGs) were identified, including 1940 DEmRNAs and 55 DEmiRNAs. Functional annotation showed that the DEGs were mainly associated with cell states and function regulation. In addition, multiple hub genes (FOXO1, SOD2, BMP2, DICER1, BCL2L11, FZD4, ssc-miR-424, and ssc-miR-27b) were identified by constructing protein-protein interaction and DEmiRNA-DEmRNA regulatory networks. Furthermore, a gene-pathway-function coregulatory network was established and demonstrated that these hub genes were enriched in FoxO, TGF-?, Wnt, PIK3-Akt, MAPK, and cAMP signaling pathways, which play important roles in regulating cell apoptosis, cell proliferation, stress responses, and hormone secretion. The current research provides a comprehensive perspective of the effects of oxidative stress on porcine GCs and also identifies potential therapeutic targets for oxidative stress-induced female infertility.
Project description:Hashimoto's thyroiditis (HT) is present in the background of around 30% of papillary thyroid carcinomas (PTCs). The genetic predisposition effect of this autoimmune condition is not thoroughly understood. We analyzed the microarray expression profiles of 13 HT, eight PTCs with (w/) coexisting HT, six PTCs without (w/o) coexisting HT, six micro PTCs (mPTCs), and three normal thyroid (TN) samples. Based on a false discovery rate (FDR)-adjusted p-value ? 0.05 and a fold change (FC) > 2, four comparison groups were defined, which were HT vs. TN; PTC w/ HT vs. TN; PTC w/o HT vs. TN; and mPTC vs. TN. A Venn diagram displayed 15 different intersecting and non-intersecting differentially expressed gene (DEG) sets, of which a set of 71 DEGs, shared between the two comparison groups HT vs. TN ? PTC w/ HT vs. TN, harbored the relatively largest number of genes related to immune and inflammatory functions; oxidative stress and reactive oxygen species (ROS); DNA damage and DNA repair; cell cycle; and apoptosis. The majority of the 71 DEGs were upregulated and the most upregulated DEGs included a number of immunoglobulin kappa variable genes, and other immune-related genes, e.g., CD86 molecule (CD86), interleukin 2 receptor gamma (IL2RG), and interferon, alpha-inducible protein 6 (IFI6). Upregulated genes preferentially associated with other gene ontologies (GO) were, e.g., STAT1, MMP9, TOP2A, and BRCA2. Biofunctional analysis revealed pathways related to immunogenic functions. Further data analysis focused on the set of non-intersecting 358 DEGs derived from the comparison group of HT vs. TN, and on the set of 950 DEGs from the intersection of all four comparison groups. In conclusion, this study indicates that, besides immune/inflammation-related genes, also genes associated with oxidative stress, ROS, DNA damage, DNA repair, cell cycle, and apoptosis are comparably more deregulated in a data set shared between HT and PTC w/ HT. These findings are compatible with the conception of a genetic sequence where chronic inflammatory response is accompanied by deregulation of genes and biofunctions associated with oncogenic transformation. The generated data set may serve as a source for identifying candidate genes and biomarkers that are practical for clinical application.
Project description:Eriocheir sinensis, an extremely invasive alien crab species, has important economic value in China. It encounters different salinities during its life cycle, and at the megalopal stage it faces a turning point regarding the salinity in its environment. We applied RNA sequencing to E. sinensis megalopae before (MB) and after (MA) desalination, resulting in the discovery of 21,042 unigenes and 908 differentially expressed genes (DEGs, 4.32% of the unigenes). The DEGs primarily belonged to the Gene Ontology groups "Energy metabolism," "Oxidoreductase activity," "Translation," "Transport," "Metabolism," and "Stress response." In total, 33 DEGs related to transport processes were found, including 12 proton pump genes, three ATP-binding cassettes (ABCs), 13 solute carrier (SLC) family members, two sweet sugar transporter (ST) family members and three other substance transporters. Mitochondrial genes as well as genes involved in the tricarboxylic acid cycle, glycolytic pathway, or ?-oxidation pathway, which can generate energy in the form of ATP, were typically up-regulated in MA. 11 unigenes related to amino acid metabolism and a large number of genes related to protein synthesis were differentially expressed in MB and MA, indicating that E. sinensis possibly adjusts its concentration of free amino acid osmolytes for hyper-osmoregulation. Additionally, 33 salinity and oxidative stress induced genes were found to be differentially expressed, such as the LEA2, HSPs, GST and coagulation factor genes. Notably, LEA2 is an extremely hydrophilic protein that responds to desiccation and reported for the first time in crabs. Therefore, we suppose that when the environment is hypo-osmotic, the megalopae might compensate for ion loss via hyper-osmoregulation by consuming more energy, accompanied by a series of stress induced adaptions. This study provides the first genome-wide transcriptome analysis of E. sinensis megalopae for studying its osmoregulation and stress adaption mechanisms.
Project description:Objective:To evaluate the association between upregulated differentially expressed genes (DEGs) and the outcomes of patients with hepatocellular carcinoma (HCC). Methods:Using Gene Expression Omnibus (GEO) datasets including GSE45436, GSE55092, GSE60502, GSE84402, and GSE17548, we detected upregulated DEGs in tumors. KEGG, GO, and Reactome enrichment analysis of the DEGs was conducted to clarify their function. The impact of the upregulated DEGs on patients' survival was analyzed based on TCGA profile. Results:161 shared upregulated DEGs were identified among GSE45436, GSE55092, GSE60502, and GSE84402 profiles. Cell cycle was the shared pathway/biological process in the gene sets investigation among databases of KEGG, GO, and Reactome. After being validated in GSE17548, 13 genes including BUB1B, CCNA2, CCNB1, CCNE2, CDC20, CDC6, CDC7, CDK1, CDK4, CDKN2A, CHEK1, MAD2L1, and MCM3 in cell cycle pathway were shared in the three databases for enrichment. The expression of BUB1B, CCNB1, CDC7, CDC20, and MCM3 was upregulated in HCC tissues when compared with adjacent normal tissues in 6.67%, 7.5%, 8.06%, 5.56%, and 9.72% of HCC patients, respectively. Overexpression of BUB1B, CCNB1, CDC7, CDC20, and MCM3 in HCC tissues accounted for poorer overall survival (OS) and disease-free survival (DFS) in HCC patients (all log rank P < 0.05). BUB1B, CCNB1, CDC7, CDC20, and MCM3 were all overexpressed in HCC patients with neoplasm histologic grade G3-4 compared to those with G1-2 (all P < 0.05). BUB1B, CCNB1, and CDC20 were significantly upregulated in HCC patients with vascular invasion (all P < 0.05). Additionally, levels of BUB1B, CCNB1, CDC7, and CDC20 were significantly higher in HCC patients deceased, recurred, or progressed (all P < 0.05). Conclusion:Correlated with advanced histologic grade and/or vascular invasion, upregulation of BUB1B, CCNB1, CDC7, CDC20, and MCM3 in HCC tissues predicted worse OS and DFS in HCC patients. These genes could be novel therapeutic targets for HCC treatment.
Project description:Plant regeneration via somatic embryogenesis (SE) is the key step for genetic improvement of cotton (Gossypium hirsutum L.) through genetic engineering mediated by Agrobacteria, but the molecular mechanisms underlying SE in cotton is still unclear. Here, RNA-Sequencing was used to analyze the genes expressed during SE and their expression dynamics using RNAs isolated from non-embryogenic callus (NEC), embryogenic callus (EC) and somatic embryos (SEs). A total of 101, 670 unigenes were de novo assembled. The genes differentially expressed (DEGs) amongst NEC, EC and SEs were identified, annotated and classified. More DEGs were found between SEs and EC than between EC and NEC. A significant number of DEGs were related to hormone homeostasis, stress and ROS responses, and metabolism of polyamines. To confirm the expression dynamics of selected DEGs involved in various pathways, experiments were set up to investigate the effects of hormones (Indole-3-butytric acid, IBA; Kinetin, KT), polyamines, H2O2 and stresses on SE. Our results showed that exogenous application of IBA and KT positively regulated the development of EC and SEs, and that polyamines and H2O2 promoted the conversion of EC into SEs. Furthermore, we found that low and moderate stress is beneficial for proliferation of EC and SEs formation. Together, our global analysis of transcriptomic dynamics reveals that hormone homeostasis, polyamines, and stress response synergistically regulating SE in cotton.
Project description:Salt stress is one of the most crucial factors impacting plant growth, development and reproduction. However, information regarding differences in tissue-specific gene expression patterns, which may improve a plant's tolerance to salt stress, is limited. Here, we investigated the gene expression patterns in tissues of Populus euphratica Oliv. seedlings using RNA sequencing (RNA-Seq) technology. A total of 109.3 million, 125bp paired-end clean reads were generated, and 6428, 4797, 2335 and 3358 differentially expressed genes (DEGs) were identified in leaf, phloem, xylem and root tissues, respectively. While the tissue-specific DEGs under salt stress had diverse functions, "membrane transporter activity" was the most significant leaf function, whereas "oxidation-reduction process" was the most significant function in root tissue. Further analysis of the tissue-specific DEGs showed that the expression patterns or functions of gene families, such as SOS, NHX, GolS, GPX, APX, RBOHF and CBL, were diverse, suggesting that calcium signaling, reactive oxygen species (ROS) and salt overly sensitive (SOS) pathways are all involved in ionic homeostasis in tissues from P. euphratica seedlings. The DEGs, for example the up-regulated antioxidant genes, contribute to ROS-scavenging induced by salt stress but result in decreased Na? concentrations in root vasculature cells and in xylem sap, while the down-regulated rbohF leads to the reverse results. These results suggest that the divergence of DEGs expression patterns contribute to maintenance of ionic and ROS homeostasis in tissues and improve plant salinity tolerance. We comprehensively analyzed the response of P. euphratica seedlings to salt stress and provide helpful genetic resources for studying plant-abiotic stress interactions.
Project description:The formation of Reactive oxygen species (ROS) has been detected in all cellular departments and even in apoplastic space of plants. As multifaceted molecule, ROS are known to accumulate in response to various stresses, and ROS burst accompanied with transcriptomic reprogramming leading to defense response or programmed cell death. Acute ozone exposure has been used as a noninvasive tool to study ROS burst induced defense response and cell death for a long time. Moreover the variation of ozone sensitivity in different Arabidopsis accessions highlights the flexibility of complex genetic architecture to adapt to specific stresses. In this study, we combine classic Quantitative Trait Loci (QTL) mapping and RNA-seq to identify the cause QTLs and potential gene candidates in response to ozone. RNA sequencing was performed on both control and ozone treated 3 weeks old accessions C24 (ozone tolerant), Te (ozone sensitive) and on a RIL line CT101 (a hypersensitive line of RIL population from reciprocal cross between C24 and Te), in triplicate. We identified 69 potential genes candidates inside the QTL regions and about 200 potential genes outside QTL region in response to ozone by comparing control to treatment within same genotype or comparing control between genotypes. Transcriptome profiling of ozone response using two arabidopsis accessions C24 and Te with different ozone sensitivity
Project description:Litchi is an important subtropical fruit tree that requires an appropriately low temperature to trigger floral initiation. Our previous studies have shown that reactive oxygen species (ROS) are involved in litchi flowering. To identify oxidative stress-induced flowering related genes in leaves, 'Nuomici' potted trees were grown at medium low-temperature conditions (18/13 °C for day/night, medium-temperature). The trees were treated with the ROS generator methyl viologen dichloride hydrate (MV) as the MV-generated ROS treatment (MM, medium-temperature plus MV) and water as the control treatment (M, medium-temperature plus water). Sixteen RNA-sequencing libraries were constructed, and each library generated more than 5,000,000 clean reads. A total of 517 differentially expressed genes (DEGs) were obtained. Among those DEGs, plant hormone biosynthesis and signal transduction genes, ROS-specific transcription factors, such as AP2/ERF and WRKY genes, stress response genes, and flowering-related genes FLOWERING LOCUS T1 (FT1) and FLOWERING LOCUS T2 (FT2) were significantly enriched. Then, as a confirmatory experiment, the potted trees were uniformly sprayed with MV, N,N'-dimethylthiourea (DMTU, ROS scavenger) plus MV, and water at medium-temperature. The results showed that the MV-generated ROS promoted flowering and changed related gene expression, but these effects were repressed by DMTU treatment. The results of our studies indicate that ROS could promote flowering and partly bypass chilling for litchi flowering.