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A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Oryza sativa Indica Group

PROVIDER: GSE271626 | GEO | 2025/09/03

REPOSITORIES: GEO

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A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [RNA-seq]

Project description:We performed RNA-seq experiments on two KO lines of OsWRKY53. WE also perfomred, wounding, OsPep2 and PSK treatment of KO1 line of WRKY53 followed by RNA-seq analysis. We performed OsPep2 treatment of KO2 lines.

2025-09-02 | GSE271625 | GEO

A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [ChIP-seq]

Project description:OsWRKY53 responded to both wounding and wound-derived peptide, OsPep2 treatment. We have performed ChIP-seq experiments to determine the contribution of OsWRKY53 to both wounding as well as OsPep2 treatment.

2025-09-02 | GSE271624 | GEO

A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception

Project description:A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception

| PRJNA1132519 | ENA

A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [RNA-seq]

Project description:A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [RNA-seq]

| PRJNA1132521 | ENA

A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [ChIP-seq]

Project description:A wound-responsive transcription factor, OsWRKY53 dictates downstream wound responses upon OsPep2 perception [ChIP-seq]

| PRJNA1132522 | ENA

The transcription factor titration effect dictates level of gene expression.

Project description:Models of transcription are often built around a picture of RNA polymerase and transcription factors (TFs) acting on a single copy of a promoter. However, most TFs are shared between multiple genes with varying binding affinities. Beyond that, genes often exist at high copy number-in multiple identical copies on the chromosome or on plasmids or viral vectors with copy numbers in the hundreds. Using a thermodynamic model, we characterize the interplay between TF copy number and the demand for that TF. We demonstrate the parameter-free predictive power of this model as a function of the copy number of the TF and the number and affinities of the available specific binding sites; such predictive control is important for the understanding of transcription and the desire to quantitatively design the output of genetic circuits. Finally, we use these experiments to dynamically measure plasmid copy number through the cell cycle.

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Early IFNβ secretion determines variable downstream IL-12p70 responses upon TLR4 activation.

Project description:The interleukin-12 (IL-12) family comprises the only heterodimeric cytokines mediating diverse functional effects. We previously reported a striking bimodal IL-12p70 response to lipopolysaccharide (LPS) stimulation in healthy donors. Herein, we demonstrate that interferon β (IFNβ) is a major upstream determinant of IL-12p70 production, which is also associated with numbers and activation of circulating monocytes. Integrative modeling of proteomic, genetic, epigenomic, and cellular data confirms IFNβ as key for LPS-induced IL-12p70 and allowed us to compare the relative effects of each of these parameters on variable cytokine responses. Clinical relevance of our findings is supported by reduced IFNβ-IL-12p70 responses in patients hospitalized with acute severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or chronically infected with hepatitis C (HCV). Importantly, these responses are resolved after viral clearance. Our systems immunology approach defines a better understanding of IL-12p70 and IFNβ in healthy and infected persons, providing insights into how common genetic and epigenetic variation may impact immune responses to bacterial infection.

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Epithelial Expression of Human ABO Blood Group Genes Is Dependent upon a Downstream Regulatory Element Functioning through an Epithelial Cell-specific Transcription Factor, Elf5.

Project description:The human ABO blood group system is of great importance in blood transfusion and organ transplantation. The ABO system is composed of complex carbohydrate structures that are biosynthesized by A- and B-transferases encoded by the ABO gene. However, the mechanisms regulating ABO gene expression in epithelial cells remain obscure. On the basis of DNase I-hypersensitive sites in and around ABO in epithelial cells, we prepared reporter plasmid constructs including these sites. Subsequent luciferase assays and histone modifications indicated a novel positive regulatory element, designated the +22.6-kb site, downstream from ABO, and this was shown to enhance ABO promoter activity in an epithelial cell-specific manner. Expression of ABO and B-antigen was reduced in gastric cancer KATOIII cells by biallelic deletion of the +22.6-kb site using the CRISPR/Cas9 system. Electrophoretic mobility shift assay and chromatin immunoprecipitation assay demonstrated that the site bound to an epithelial cell-specific transcription factor, Elf5. Mutation of the Ets binding motifs to abrogate binding of this factor reduced the regulatory activity of the +22.6-kb site. Furthermore, ELF5 knockdown with shRNA reduced both endogenous transcription from ABO and B-antigen expression in KATOIII cells. Thus, Elf5 appeared to be involved in the enhancer potential of the +22.6-kb site. These results support the contention that ABO expression is dependent upon a downstream positive regulatory element functioning through a tissue-restricted transcription factor, Elf5, in epithelial cells.

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The HSV-1 ICP22 protein selectively impairs histone repositioning upon Pol II transcription downstream of genes.

Project description:Herpes simplex virus 1 (HSV-1) infection and stress responses disrupt transcription termination by RNA Polymerase II (Pol II). In HSV-1 infection, but not upon salt or heat stress, this is accompanied by a dramatic increase in chromatin accessibility downstream of genes. Here, we show that the HSV-1 immediate-early protein ICP22 is both necessary and sufficient to induce downstream open chromatin regions (dOCRs) when transcription termination is disrupted by the viral ICP27 protein. This is accompanied by a marked ICP22-dependent loss of histones downstream of affected genes consistent with impaired histone repositioning in the wake of Pol II. Efficient knock-down of the ICP22-interacting histone chaperone FACT is not sufficient to induce dOCRs in ΔICP22 infection but increases dOCR induction in wild-type HSV-1 infection. Interestingly, this is accompanied by a marked increase in chromatin accessibility within gene bodies. We propose a model in which allosteric changes in Pol II composition downstream of genes and ICP22-mediated interference with FACT activity explain the differential impairment of histone repositioning downstream of genes in the wake of Pol II in HSV-1 infection.

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STIFDB2: an updated version of plant stress-responsive transcription factor database with additional stress signals, stress-responsive transcription factor binding sites and stress-responsive genes in Arabidopsis and rice.

Project description:Understanding the principles of abiotic and biotic stress responses, tolerance and adaptation remains important in plant physiology research to develop better varieties of crop plants. Better understanding of plant stress response mechanisms and application of knowledge derived from integrated experimental and bioinformatics approaches are gaining importance. Earlier, we showed that compiling a database of stress-responsive transcription factors and their corresponding target binding sites in the form of Hidden Markov models at promoter, untranslated and upstream regions of stress-up-regulated genes from expression analysis can help in elucidating various aspects of the stress response in Arabidopsis. In addition to the extensive content in the first version, STIFDB2 is now updated with 15 stress signals, 31 transcription factors and 5,984 stress-responsive genes from three species (Arabidopsis thaliana, Oryza sativa subsp. japonica and Oryza sativa subsp. indica). We have employed an integrated biocuration and genomic data mining approach to characterize the data set of transcription factors and consensus binding sites from literature mining and stress-responsive genes from the Gene Expression Omnibus. STIFDB2 currently has 38,798 associations of stress signals, stress-responsive genes and transcription factor binding sites predicted using the Stress-responsive Transcription Factor (STIF) algorithm, along with various functional annotation data. As a unique plant stress regulatory genomics data platform, STIFDB2 can be utilized for targeted as well as high-throughput experimental and computational studies to unravel principles of the stress regulome in dicots and gramineae. STIFDB2 is available from the URL: http://caps.ncbs.res.in/stifdb2.

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