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Abstract The circadian clock helps organisms to anticipate and coordinate gene regulatory responses to changes in environmental stimuli. Under stresses, both time of day and the circadian clock closely control the magnitude of plant responses. The identification of clock-regulated genes is, therefore, important when studying the influence of environmental factors. Here, we present CAST-R (Circadian And heat STress-Responsive), a “Shiny” application that allows users to identify and visualize circadian and heat stress-responsive genes in plants. More specifically, users can generate and export profiles and heatmaps representing transcript abundance of a single or of multiple Arabidopsis (Arabidopsis thaliana) genes over a 24-h time course, in response to heat stress and during recovery following the stress. The application also takes advantage of published Arabidopsis chromatin immunoprecipitation-sequencing datasets to visualize the connections between clock proteins and their targets in an interactive network. In addition, CAST-R offers the possibility to perform phase (i.e. timing of expression) enrichment analyses for rhythmic datasets from any species, within and beyond plants. This functionality combines statistical analyses and graphical representations to identify significantly over- and underrepresented phases within a subset of genes. Lastly, profiles of transcript abundance can be visualized from multiple circadian datasets generated in Arabidopsis, Brassica rapa, barley (Hordeum vulgare), and rice (Oryza sativa). In summary, CAST-R is a user-friendly interface that allows the rapid identification of circadian and stress-responsive genes through multiple modules of visualization. We anticipate that this tool will make it easier for users to obtain temporal and dynamic information on genes of interest that links plant responses to environmental signals.
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Clock-Controlled and Cold-Induced CYCLING DOF FACTOR6 Alters Growth and Development in Arabidopsis
The circadian clock represents a critical regulatory network, which allows plants to anticipate environmental changes as inputs and promote plant survival by regulating various physiological outputs. Here, we examine the function of the clock-regulated transcription factor, CYCLING DOF FACTOR 6 (CDF6), during cold stress in Arabidopsis thaliana . We found that the clock gates CDF6 transcript accumulation in the vasculature during cold stress. CDF6 mis-expression results in an altered flowering phenotype during both ambient and cold stress. A genome-wide transcriptome analysis links CDF6 to genes associated with flowering and seed germination during cold and ambient temperatures, respectively. Analysis of key floral regulators indicates that CDF6 alters flowering during cold stress by repressing photoperiodic flowering components, FLOWERING LOCUS T ( FT ), CONSTANS ( CO ), and BROTHER OF FT (BFT) . Gene ontology enrichment further suggests that CDF6 regulates circadian and developmental-associated genes. These results provide insights into how the clock-controlled CDF6 modulates plant development during moderate cold stress.
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- Award ID(s):
- 1942949
- PAR ID:
- 10386333
- Date Published:
- Journal Name:
- Frontiers in Plant Science
- Volume:
- 13
- ISSN:
- 1664-462X
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3389/fpls.2022.919676
