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Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation

Kirk J-M. MacKinnon, Benjamin J. Cole, Chang Yu, Joshua H. Coomey, Nolan T. Hartwick, Marie-Stanislas Remigereau, Tomás Duffy, Todd P. Michael, Steve A. Kay, Samuel P. Hazen
doi: https://doi.org/10.1101/762021
Kirk J-M. MacKinnon
1Biology Department, University of Massachusetts, Amherst, MA, USA
2Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
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Benjamin J. Cole
3DOE Joint Genome Institute, Walnut Creek, CA, USA
4Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Chang Yu
1Biology Department, University of Massachusetts, Amherst, MA, USA
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Joshua H. Coomey
1Biology Department, University of Massachusetts, Amherst, MA, USA
5Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
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Nolan T. Hartwick
6J. Craig Venter Institute, La Jolla, CA, USA
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Marie-Stanislas Remigereau
4Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Tomás Duffy
4Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Todd P. Michael
6J. Craig Venter Institute, La Jolla, CA, USA
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Steve A. Kay
4Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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Samuel P. Hazen
1Biology Department, University of Massachusetts, Amherst, MA, USA
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  • For correspondence: hazensam@umass.edu
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SUMMARY

  • Plants are continuously exposed to diurnal fluctuations in light and temperature, and spontaneous changes in their physical or biotic environment. The circadian clock coordinates regulation of gene expression with a 24-hour period, enabling the anticipation of these events.

  • We used RNA sequencing to characterize the Brachypodium distachyon transcriptome under light and temperature cycles, as well as under constant conditions.

  • Approximately 3% of the transcriptome was regulated by the circadian clock, a smaller proportion reported in most other species. For most transcripts that were rhythmic under all conditions, including many known clock genes, the period of gene expression lengthened from 24 to 27 h in the absence of external cues. To functionally characterize the cyclic transcriptome in B. distachyon, we used Gene Ontology enrichment analysis, and found several terms significantly associated with peak expression at particular times of the day. Furthermore we identified sequence motifs enriched in the promoters of similarly-phased genes, some potentially associated with transcription factors.

  • When considering the overlap in rhythmic gene expression and specific pathway behavior, thermocycles was the prevailing cue that controlled diurnal gene regulation. Taken together, our characterization of the rhythmic B. distachyon transcriptome represents a foundational resource with implications in other grass species.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 21, 2019.
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Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation
Kirk J-M. MacKinnon, Benjamin J. Cole, Chang Yu, Joshua H. Coomey, Nolan T. Hartwick, Marie-Stanislas Remigereau, Tomás Duffy, Todd P. Michael, Steve A. Kay, Samuel P. Hazen
bioRxiv 762021; doi: https://doi.org/10.1101/762021
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Changes in ambient temperature are the prevailing cue in determining Brachypodium distachyon diurnal gene regulation
Kirk J-M. MacKinnon, Benjamin J. Cole, Chang Yu, Joshua H. Coomey, Nolan T. Hartwick, Marie-Stanislas Remigereau, Tomás Duffy, Todd P. Michael, Steve A. Kay, Samuel P. Hazen
bioRxiv 762021; doi: https://doi.org/10.1101/762021

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