Transcriptome sequencing facilitates reveal molecular mechanisms between GSK2 and WRKY53
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE148099 | GEO | 2023/04/04
REPOSITORIES: GEO
Similar Datasets
Project description:Transcriptome sequencing facilitates reveal molecular mechanisms between GSK2 and WRKY53
| PRJNA623220 | ENA
Project description:Leaf senescence is governed by a complex regulatory network involving dynamic reprogramming of gene expression. Recent evidence indicates that trimethylation of histone H3 at lysine 4 (H3K4me3) alters gene expression during leaf senescence. However, it is largely unknown how histone modification is regulated in an age-dependent manner. We found that JMJ16, an Arabidopsis JmjC-domain containing protein, is a specific H3K4 demethylase that negatively regulates leaf senescence. The histone demethylase activity and the JmjN, JmjC, and FYR domains of JMJ16, but not the zf-C5HC2 domain, are essential for JMJ16 function in the regulation of leaf senescence. Genome-wide analysis revealed a widespread coordinated up-regulation of H3K4me3 and gene expression associated with leaf senescence in the loss-of-function jmj16 mutant compared with the wild type. Genetic analysis indicated that JMJ16 negatively regulates leaf senescence at least partly through repressing the expression of WRKY53 and SAG201, two known positive regulators of leaf senescence. Further analyses demonstrated that JMJ16 associates with WRKY53 and SAG201, and represses precocious expression of WRKY53 and SAG201 in mature leaves by reducing H3K4me3 levels at these loci. Moreover, association of JMJ16 on WRKY53 and SAG201 loci increased at mature stage but decreased at later stage, suggesting that the age-dependent dynamic chromatin association of JMJ16 is required for precise transcriptional activation of SAGs during leaf senescence. Thus, JMJ16 is an important regulator of leaf senescence that demethylates H3K4 at senescence-associated genes in an age-dependent manner.
2019-04-17 | GSE115362 | GEO
Project description:Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian clocks. We derive a mathematical framework where waveforms do reveal hidden biochemical mechanisms of circadian timekeeping. We find that the cost of synthesizing proteins with particular waveforms can be substantially reduced by rhythmic protein half-lives over time, as supported by previous plant and mammalian data, as well as our own seedling experiment. We also find that previously enigmatic, cyclic expression of positive arm components within the mammalian and insect clocks allows both a broad range of peak time differences between protein waveforms and the symmetries of the waveforms about the peak times. Such various peak-time differences may facilitate tissue-specific or developmental stage-specific multicellular processes. Our waveform-guided approach can be extended to various biological oscillators, including cell-cycle and synthetic genetic oscillators.
| S-EPMC6255756 | biostudies-literature
Project description:Sister chromatid separation depends on the activity of separase, which in turn requires the proteolysis of its inhibitor, securin. It has been speculated that securin also supports the activation of separase. In this study, we found that PTTG1 was the major securin isoform expressed in most normal and cancer cell lines. Remarkably, a highly homologous isoform called PTTG2 was unable to interact with separase. Using chimeras between PTTG1 and PTTG2 and other approaches, we pinpointed a single amino acid that accounted for the loss of securin function in PTTG2. Mutation of the homologous position in PTTG1 (H(134)) switched PTTG1 from an inhibitor into an activator of separase. In agreement with this, PTTG1 lacking H(134) was able to trigger premature sister chromatid separation. Conversely, introduction of H(134) into PTTG2 is sufficient to allow it to bind separase. These data demonstrate that while the motif containing H(134) has a strong affinity for separase and is involved in inhibiting it, another domain(s) is involved in activating separase and has a weaker affinity for it. Although PTTG2 lacks securin function, its differences from PTTG1 provide evidence of independent inhibitory and activating functions of PTTG1 on separase.
| S-EPMC3753852 | biostudies-other
Project description:To identify the molecular mechanism of OsCPK21 regulating pollen development, a genome-wide analysis of the gene expression profiles in the rice spikelet of ZH11 and OsCPK21-RNAi transgenic plants during anther development was performed. Hybridization with the microarray and subsequent analysis showed that a total of 5020 genes displayed altered expression (at least 2-fold) under suppressed OsCPK21 expression. Among the altered genes, 1419 were up-regulated, and 3601 were down-regulated.
2018-08-08 | GSE95699 | GEO
Project description:IntroductionClonorchiasis remains a serious global public health problem, causing various hepatobiliary diseases. However, there is still a lack of overall understanding regarding the molecular events triggered by Clonorchis sinensis (C. sinensis) in the liver.MethodsBALB/c mouse models infected with C. sinensis for 5, 10, 15, and 20 weeks were constructed. Liver pathology staining and observation were conducted to evaluate histopathology. The levels of biochemical enzymes, blood routine indices, and cytokines in the blood were determined. Furthermore, alterations in the transcriptome, proteome, and metabolome of mouse livers infected for 5 weeks were analyzed using multi-omics techniques.ResultsThe results of this study indicated that adult C. sinensis can cause hepatosplenomegaly and liver damage, with the most severe symptoms observed at 5 weeks post-infection. However, as the infection persisted, the Th2 immune response increased and symptoms were relieved. Multi-omics analysis of liver infected for 5 weeks identified 191, 402 and 232 differentially expressed genes (DEGs), proteins (DEPs) and metabolites (DEMs), respectively. Both DEGs and DEPs were significantly enriched in liver fibrosis-related pathways such as ECM-receptor interaction and cell adhesion molecules. Key molecules associated with liver fibrosis and inflammation (Cd34, Epcam, S100a6, Fhl2, Itgax, and Retnlg) were up-regulated at both the gene and protein levels. The top three metabolic pathways, namely purine metabolism, arachidonic acid metabolism, and ABC transporters, were associated with liver cirrhosis, fibrosis, and cholestasis, respectively. Furthermore, metabolites that can promote liver inflammation and fibrosis, such as LysoPC(P-16:0/0:0), 20-COOH-leukotriene E4, and 14,15-DiHETrE, were significantly up-regulated.ConclusionOur study revealed that the most severe symptoms in mice infected with C. sinensis occurred at 5 weeks post-infection. Moreover, multi-omics analysis uncovered predominant molecular events related to fibrosis changes in the liver. This study not only enhances our understanding of clonorchiasis progression but also provides valuable insights into the molecular-level interaction mechanism between C. sinensis and its host liver.
| S-EPMC10710275 | biostudies-literature
Project description:We sequenced mRNA from two-week old rice seedlings of jmj704 and wild-type (ZH11) plants to obtain the differntially expressed genes in jmj704 mutant. exzamination the differentially expressed genes between two-week old jmj704 and wild-type (ZH11) rice seedlings.
2015-11-05 | E-GEOD-74670 | biostudies-arrayexpress
Project description:ra09-02_tctp - rnai - Identification of effector genes that act downstream of AtTCTP, using knockout ( tctp-2), RNAi expressing line (35S::RNAi-AtTCTP) and over expressing line (35S::AtTCTP) - transcriptome analysis in leaf of 35S::RNAi-AtTCTP versus wild type Keywords: normal vs rnai mutant comparison
2011-03-17 | GSE19849 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-12-17 | GSE188954 | GEO
Project description:SA0420 is a stable rice (Oryza sativa L.) mutant exhibits multiple traits including a leaf-tip yellowing (YLT), a taro fragrance (or aroma, A), a reduced panicle number (PN), spikelet number (SN), plant height (PH), days to heading (DH), filled grain weight (FGW), and fertility rate (FR), different from those of a local cultivar TNG67. Correlation analysis on F2 progenies of SA0420 and TNG67 revealed that except for aroma which is inheritated independently, phenotypes including YLT, PN, SN, PH, and FGW are tightly associated with each others, indicating a control simultaneously by pleotropic gene. Among those phenotypes, YLT appears the earliest at vegetative stage, therefore may act as a predisposing factor that give rise to other phenotypes. Genetic analysis suggested that YLT is controlled by a single recessive gene. By analyzing the recombinant inbreed lines (RILs) that produce YLT and normal green (G) progenies in a 1:3 ratio, the phenotypes associated with YLT were further confirmed. To investigate the molecular events of leaf-tip yellowing, microarray analyses were performed to compare the gene expression profiles between YLT and G plants of RILs. Clustering of genes according to their involved metabolic pathways revealed that various photosynthesis and carbon fixation gene expressions are lower (~55~75%) in YLT than in G plants, consistent with the observation that photosynthesis rate of SA0420 was only 60% to that of TNG67. Moreover, higher expressions of oxidative phosphorylation-related genes indicated that not only the reduced synthesis rate but also the elevated energy consumptions may synergistically decrease the growth vigor of SA0420. Dissection of the mature leaf revealed that chlorophyll is drastically reduced in the leaf-tip of SA0420 while carotenoids remain stable. This explains the appearance of leaf-tip yellowing and recall an analogy of early senescence. Indeed, many senescence-associated genes (SAG) were found to be up-regulated in SA0420. Keywords: rice (Oryza sativa), yellow and green leaves, molecular functions, signal-microarray, vegetative stage
2008-03-21 | GSE10872 | GEO