Project description:Identification of TBF1-dependent and SA, elf18-responsive genes in Arabidopsis 24 samples total, 2 treatments with corresponding mock, wild type samples served as control, 3 biological replicates
Project description:0.5 mM SA plus 0.02% Silwet or 0.02% Silwet (control) was sprayed on leaves of 3.5 week old Arabidopsis plants. Samples were harvested at 0 (prior to treatment) , 3, 6, 12, and 24 hours post treatment. A subset of these samples were processed.
Project description:Profiling of binding sites for hundreds of A. thaliana transcription factors genome-wide revealed an unexpected enrichment of conserved TF binding sites (TFBSs) in coding sequence (CDS) for specific TF families, yet little association with cell type-specific gene expression. To differentiate between possible explanations for this, gene expression was profiled using bulk RNA-seq in response to hormone-induced stress. Abscisic Acid (ABA) treatment time-course data revealed that TFs known to activate transcription in response to ABA were significantly up-regulated, and most target genes of these TFs were upregulated as well - with the exception being target genes with TFBSs exclusively in coding sequence, which showed no significant expression change. Salicylic acid (SA) treatment further confirmed that target genes of known SA-responsive activators were induced only when TFBSs were found outside the coding region. However a key SA-responsive repressor (ABR1) showed strong repression of genes with CDS binding sites, suggesting a mechanism for rapid antagonistic response. Moreover, integration with chromatin accessibility data from the same tissues revealed strong links between constitutive TFBS accessibility and stress-induced target gene expression, suggesting that rapid, tissue-wide regulatory responses might preferentially operate through constitutively accessible sites primarily located close to transcription start sites.
Project description:0.5 mM SA plus 0.02% Silwet or 0.02% Silwet (control) was sprayed on leaves of 3.5 week old Arabidopsis plants. Samples were harvested at 0 (prior to treatment) , 3, 6, 12, and 24 hours post treatment. A subset of these samples were processed. Arabidopsis plants grown in parallel under standardized conditions were treated with SA + Silwet or Silwet alone (control). Only mature leaves of the same developmental age were harvested using leaves from 2-4 plants, totalling ~0.2 grams per sample. Plants were not resampled. In our hands, experimental replicates are highly reproducible. This was an exploratory experiment to look for candidate genes impacted by exogenous SA treatment. We were only able to process a subset of samples and chose to process key time points, sacrificing replicates at each time point.
Project description:The Arabidopsis Pathoarray 464_001 (GPL3638) was used to compare response of Col-0, pad4-1 (Zhou et al., 1998; Jirage et al., 1999) and sid2-2 (Wildermuth et al., 2001) to Pseudomonas syringae pv. tomato DC3000 hrcC mutant. SA production is drastically reduced in sid2 mutants. PAD4 is required for SA-mediated responses. The results suggested that the SA increase triggered by MAMPs is one major component in the MAMPs-triggered signaling mechanism. Keywords: Responses of Arabidopsis to Pseudomonas syringae pv. tomato DC3000 hrcC mutant
Project description:Salicylic acid (SA) has long been implicated in plant responses to oxidative stress. A direct assessment of SA effects in planta has been difficult, as SA-overproducing Arabidopsis mutants are compromised in growth or other developmental processes. We now report that transgenic Populus expressing a bacterial bifunctional SA synthase accumulated two to three orders of magnitude more total SA than wild type without affecting growth. Microarray experiments were performed to gauge the transcriptional responses of young source leaves to SA manipulation and/or heat stress. Differentially expressed genes due to SA perturbation or temperature treatment were identified. Co-expression network analysis was performed to identify key driver genes in SA-modulated response.
Project description:Single cell analysis of tumor infiltrating CD8 T cells in wild-type (WT) and Ifnar1-SA (SA) mice identifies differentially expressed genes and signaling pathways.
Project description:Plant hormones involved in environmental stresses, namely abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), have been shown to interact with each other in a complex manner. To address the network of the hormone interactions, we have investigated the changes in expression under multiple hormone treatments, ABA+SA and ABA+JA. We chose cultured cells to remove the difference in the response to hormones among developmental cells or tissues. The cells were treated for 3hr and 24hr to see the rapid or transient response and steady-state response. The obtained data indicate that ABA and SA affect antagonistically, but these hormones affected many genes collaboratively. Indeed, according to the microarray data, there are many genes that responded only to ABA+SA. In addition, the ABA+SA responsive genes also responded to ABA+JA. These data suggest that hormone crosstalk is more complicated than expected and that more systematic analysis is required to untangle the hormone crosstalk network. To investigate the hormonal interactions, Arabidopsis T87 cultured cells were exposed to ABA, SA, or JA alone, or two hormones simultaneously, ABA+SA or ABA+JA, for 3hr and 24 hr. Comparing the data among those treatments, the relationships among these hormones were deduced.