Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana
Abstract Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those oscillations can persist under constant conditions due to regulation by the circadian oscillator. The response of the transcriptome to light regimes is dynam...
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| Format: | Article |
| Language: | English |
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Wiley
2024-08-01
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| Series: | Plant Direct |
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| Online Access: | https://doi.org/10.1002/pld3.70001 |
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| author | Quentin Rivière Virginie Raskin Romário deMelo Stéphanie Boutet Massimiliano Corso Matthieu Defrance Alex A. R. Webb Nathalie Verbruggen Armand D. Anoman |
| author_facet | Quentin Rivière Virginie Raskin Romário deMelo Stéphanie Boutet Massimiliano Corso Matthieu Defrance Alex A. R. Webb Nathalie Verbruggen Armand D. Anoman |
| author_sort | Quentin Rivière |
| collection | DOAJ |
| description | Abstract Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those oscillations can persist under constant conditions due to regulation by the circadian oscillator. The response of the transcriptome to light regimes is dynamic and allows plants to adapt rapidly to changing environmental conditions. We compared the transcriptome of Arabidopsis under LD and constant light (LL) for 3 days and identified different gene co‐expression networks in the two light regimes. Our studies yielded unforeseen insights into circadian regulation. Intuitively, we anticipated that gene clusters regulated by the circadian oscillator would display oscillations under LD cycles. However, we found transcripts encoding components of the flavonoid metabolism pathway that were rhythmic in LL but not in LD. We also discovered that the expressions of many stress‐related genes were significantly increased during the dark period in LD relative to the subjective night in LL, whereas the expression of these genes in the light period was similar. The nocturnal pattern of these stress‐related gene expressions suggested a form of “skotoprotection.” The transcriptomics data were made available in a web application named Cyclath, which we believe will be a useful tool to contribute to a better understanding of the impact of light regimes on plants. |
| format | Article |
| id | doaj-art-6690b57bc5ab4247abc62dd045e28317 |
| institution | Kabale University |
| issn | 2475-4455 |
| language | English |
| publishDate | 2024-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Plant Direct |
| spelling | doaj-art-6690b57bc5ab4247abc62dd045e283172025-02-06T04:40:51ZengWileyPlant Direct2475-44552024-08-0188n/an/a10.1002/pld3.70001Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thalianaQuentin Rivière0Virginie Raskin1Romário deMelo2Stéphanie Boutet3Massimiliano Corso4Matthieu Defrance5Alex A. R. Webb6Nathalie Verbruggen7Armand D. Anoman8Laboratory of Plant Physiology and Molecular Genetics Université Libre de Bruxelles Brussels BelgiumLaboratory of Plant Physiology and Molecular Genetics Université Libre de Bruxelles Brussels BelgiumLaboratory of Plant Physiology and Molecular Genetics Université Libre de Bruxelles Brussels BelgiumUniversité Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin (IJPB) Versailles FranceUniversité Paris‐Saclay, INRAE, AgroParisTech, Institut Jean‐Pierre Bourgin (IJPB) Versailles FranceInteruniversity Institute of Bioinformatics in Brussels Université Libre de Bruxelles Brussels BelgiumDepartment of Plant Sciences University of Cambridge Cambridge UKLaboratory of Plant Physiology and Molecular Genetics Université Libre de Bruxelles Brussels BelgiumLaboratory of Plant Physiology and Molecular Genetics Université Libre de Bruxelles Brussels BelgiumAbstract Light/dark (LD) cycles are responsible for oscillations in gene expression, which modulate several aspects of plant physiology. Those oscillations can persist under constant conditions due to regulation by the circadian oscillator. The response of the transcriptome to light regimes is dynamic and allows plants to adapt rapidly to changing environmental conditions. We compared the transcriptome of Arabidopsis under LD and constant light (LL) for 3 days and identified different gene co‐expression networks in the two light regimes. Our studies yielded unforeseen insights into circadian regulation. Intuitively, we anticipated that gene clusters regulated by the circadian oscillator would display oscillations under LD cycles. However, we found transcripts encoding components of the flavonoid metabolism pathway that were rhythmic in LL but not in LD. We also discovered that the expressions of many stress‐related genes were significantly increased during the dark period in LD relative to the subjective night in LL, whereas the expression of these genes in the light period was similar. The nocturnal pattern of these stress‐related gene expressions suggested a form of “skotoprotection.” The transcriptomics data were made available in a web application named Cyclath, which we believe will be a useful tool to contribute to a better understanding of the impact of light regimes on plants.https://doi.org/10.1002/pld3.70001Arabidopsis thalianacircadian rhythmsco‐expression networksflavonoidslight regimeskotoprotection |
| spellingShingle | Quentin Rivière Virginie Raskin Romário deMelo Stéphanie Boutet Massimiliano Corso Matthieu Defrance Alex A. R. Webb Nathalie Verbruggen Armand D. Anoman Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana Plant Direct Arabidopsis thaliana circadian rhythms co‐expression networks flavonoids light regime skotoprotection |
| title | Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana |
| title_full | Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana |
| title_fullStr | Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana |
| title_full_unstemmed | Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana |
| title_short | Effects of light regimes on circadian gene co‐expression networks in Arabidopsis thaliana |
| title_sort | effects of light regimes on circadian gene co expression networks in arabidopsis thaliana |
| topic | Arabidopsis thaliana circadian rhythms co‐expression networks flavonoids light regime skotoprotection |
| url | https://doi.org/10.1002/pld3.70001 |
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