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An early-morning gene network controlled by phytochromes and cryptochromes regulates photomorphogenesis pathways in Arabidopsis

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  • Martin Balcerowicz
  • Mahair Mahjoub
  • Duy Nguyen
  • Hui Lan
  • Dorothee Stoeckle
  • Susana Conde
  • Katja Jaeger
  • Philip A Wigge
  • Daphne Ezer


Publication details

JournalMolecular plant
DateSubmitted - 30 Dec 2020
DateAccepted/In press - 22 Mar 2021
DateE-pub ahead of print - 23 Mar 2021
DatePublished (current) - 7 Jun 2021
Issue number6
Number of pages14
Pages (from-to)983-996
Early online date23/03/21
Original languageEnglish


Light perception at dawn plays a key role in coordinating multiple molecular processes and in entraining the plant circadian clock. An Arabidopsis mutant lacking the main photoreceptors however still shows clock entrainment, indicating that the integration of light into the morning transcriptome is not well understood. We performed a high-resolution RNA-seq time series experiment, sampling every two-minutes from dawn. In parallel experiments, we perturbed temperature, the circadian clock, photoreceptor signalling and chloroplast-derived light signalling. We used this data to infer a gene network that describes the gene expression dynamics after light stimulus in the morning, and then we validated key edges. By sampling time points at high density, we are able to identify three light- and temperature-sensitive bursts of transcription factor activity, one of which lasts for only about eight minutes. Phytochrome and cryptochrome mutants cause a delay in the transcriptional bursts at dawn, and completely remove a burst of expression in key photomorphogenesis genes (HY5 and BBX family). Our complete network is available online ( Taken together, our results show that phytochrome and cryptochrome signaling is required for fine-tuning the dawn transcriptional response to light, but separate pathways can robustly activate much of the programme in their absence.

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© The Author 2021. This is an author-produced version of the published paper. Uploaded in accordance with the publisher’s self-archiving policy.

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