Next Generation Sequencing Facilitates Quantitative Analysis of WT and cry1cry2 mutant and cis1-1 mutant in dark and Blue light Transcriptomes
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE196648 | GEO | 2022/10/31
REPOSITORIES: GEO
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Project description:Total RNA was extracted from samples including dark-grown WT and tir1 afb123, blue light-grown WT and cry1 cry2 seedlings in continuous conditions for 4.5 days and subjected to high throughput sequencing. Light and auxin co-regulate a variety of developmental processes. This study reveals the molecular basis for light and auxin crosstalk by analyzing gene expression profile under control of both signals. mRNA from dark-grown WT, BL-grown WT, BL-grown BL photoreceptors, and dark-grown auxin receptors was sequenced to analyze the genes regulated by CRY-mediated BL signaling and TIR1/AFBs-mediated auxin signaling.
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Project description:Light is a crucial exogenous signal sensed by cryptochrome (CRY) blue light receptors to modulate growth and the circadian clock in plants and animals. However, how CRYs interpret light quantity to regulate growth in plants remains poorly understood. Furthermore, CRY2 protein levels and activity are tightly regulated in light to fine-tune hypocotyl growth; however, details of the mechanisms that explain precise control of CRY2 levels are not fully understood. We show that in Arabidopsis, UBP12 and UBP13 deubiquitinases physically interact with CRY2 in light. UBP12/13 negatively regulates CRY2 by promoting its ubiquitination and turnover to modulate hypocotyl growth. Growth and development were explicitly affected in blue light when UBP12/13 were disrupted or overexpressed, indicating their role alongside CRY2. UBP12/13 also interacted with and stabilized COP1, which is partially required for CRY2 turnover. Our combined genetic and molecular data support a mechanistic model in which UBP12/13 interact with CRY2 and COP1, leading to the stabilization of COP1. Stabilized COP1 then promotes the ubiquitination and degradation of CRY2 under blue light. Despite decades of studies on deubiquitinases, the knowledge of how their activity is regulated is limited. Our study provides insight into how exogenous signals and ligands, along with their receptors, regulate deubiquitinase activity by protein-protein interaction. Collectively, our results provide a framework of cryptochromes and deubiquitinases to detect and interpret light signals to control plant growth at the most appropriate time.
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Project description:Purpose: The goal of this study was to characterize the transcript levels of genes in Drosophila photoreceptor neurons in response to blue light. Using transcriptome profiling of isolated photoreceptor nuclei, we analyzed the changes in gene expression that occur in response to 3h of blue light exposure at 1 or 6 days post-eclosion. We identified sets of genes with both up-regulated and down-regulated expression in response to blue light at either age.
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Project description:We identified 737 differentially expressed genes, including 430 upregulated genes and 307 downregulated genes, by calculating the gene FPKM in each sample and conducting differential gene analysis. Gene ontology analysis and KEGG pathway enrichment analysis suggested that blue light influenced visual perception, sensory perception of light stimulus, phototransduction, and JAK-STAT signaling pathways. Differential lncRNA, circRNA and miRNA analysis suggested that blue light exposure affected pathways for retinal cone cell development and phototransduction, among others.
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Project description:A tuberization inhibitor has long been postulated, but not yet found. We found that blue light inhibits tuberization in Norland, a day-neutral variety of Solanum tuberosum L. Tissue-cultured plants formed tubers within 8 weeks under continuous darkness, and white, red, or far-red light. Preliminary experiments indicated that a one- or two-day exposure to blue light after 3-4 weeks of dark treatment will inhibit tuber formation in ‘Norland’ plants. Using this system and expression profiling, we may be able to identify candidate tuberization inhibitors. 'Norland' plants (subcultured from existing cultures and grown for two weeks under continuous 100 umol/m2-s white fluorescent light) were placed in tuber-inducing media containing 6% sucrose, vitamins, MS salts, and kinetin (2.5 mg/L). Tubes containing plants were wrapped in two layers of aluminum foil. After 3 weeks and 2 days, half of the tubes were exposed to 6-7 umol/m2-s blue light. The other half of the tubes were left in darkness (controls). After 2 days, all plants were harvested and frozen in liquid nitrogen. Plants exposed to blue light were harvested under blue light. Control plants were harvested under < 2 umol/m2-s light conditions. All plant transfers were done at 1700 (5 PM) to avoid possible complications due to circadian effects. Experiments were performed four times, from subculture to harvest. RNA was extracted from stem and leaf tissue of plants using the Qiagen RNeasy Plant Mini kit. Extracted RNA was then converted to dsDNA using the Invitrogen protocol and reagents for double stranded cDNA synthesis. The resulting dsDNA was in vitro transcribed into amplified RNA using the Ambion procedure and reagents for in vitro transcription. cDNA was purified using Qiagen MinElute columns and protocol. Amplified RNA was purified using Ambion columns or Qiagen RNeasy columns and the Ambion protocol, and quantified using RiboGreen dye fluorometry. Keywords: Direct comparison
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Project description:Purpose: In an effort to better understand the mechanism of blue light inhibition in Staphylococcus aureus, a whole transcriptome analysis of S. aureus isolate BUSA2288 was performed using RNA-seq to analyze the differential gene expression in response to blue light exposure. Methods: RNA was extracted from S. aureus cultures pooled from 24 one ml well samples illuminated with a dose of 250 J/cm2 of 465 nm blue light, and from control cultures grown in the dark. Complementary DNA (cDNA) were generated from the RNA samples and then sequenced using the Illumina MiSeq Next Generation Sequencer. The combined results of 2 independent experiments were analyzed using the Pairwise Analysis tools in GeneSifter®. The genes were normalized by Mapped Reads using EdgeR statistics including a Benjamini and Hochberg false discovery rate correction. Quality was set at a minimum number of 10 reads and a p value of 0.05. The lower threshold for change was 5 fold. Results: Transcriptomic comparisons using a cutoff of 5 fold identified a total of 28 down-regulated genes and 6 up-regulated genes in the samples that were exposed to blue light. All but 6 of the differentially regulated genes fall into 8 functional categories: amino acid biosynthesis, cell envelope components, cellular processes, central intermediary metabolism, energy metabolism, protein synthesis, regulatory function, and transport and binding proteins. Five genes encode conserved proteins of unknown function. Conclusions: Blue light has been shown to be bactericidal against S. aureus and is a potential alternative therapy for antibiotic resistant organisms. The mechanism for the inactivation of bacteria is hypothesized to involve ROS. We have found evidence that supports this hypothesis that involves multiple pathways including essential metabolic pathways and known virulence pathways.
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