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

MacKinnon, Kirk J‐M.; Cole, Benjamin J.; Yu, Chang; Coomey, Joshua H.; Hartwick, Nolan T.; Remigereau, Marie‐Stanislas; Duffy, Tomás; Michael, Todd P.; Kay, Steve A.; Hazen, Samuel P.

doi:10.1111/nph.16507

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

Journal Article · Wed Apr 01 00:00:00 EDT 2020 · New Phytologist

DOI:https://doi.org/10.1111/nph.16507· OSTI ID:1650702

MacKinnon, Kirk J‐M. ^[1]; ^[2]; ^[3]; ^[4]; Hartwick, Nolan T. ^[5]; Remigereau, Marie‐Stanislas ^[6]; ^[6]; ^[5]; ^[6]; ^[3]

Biology Department University of Massachusetts Amherst MA 01003 USA, Molecular and Cellular Biology Graduate Program University of Massachusetts Amherst MA 01003 USA
DOE Joint Genome Institute Walnut Creek CA 94598 USA, Department of Neurology Keck School of Medicine University of Southern California Los Angeles CA 90033 USA
Biology Department University of Massachusetts Amherst MA 01003 USA
Biology Department University of Massachusetts Amherst MA 01003 USA, Plant Biology Graduate Program University of Massachusetts Amherst MA 01003 USA
J. Craig Venter Institute La Jolla CA 92037 USA
Department of Neurology Keck School of Medicine University of Southern California Los Angeles CA 90033 USA

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 h 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 than 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.

View Accepted Manuscript (Publisher)

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0006621

OSTI ID:: 1650702

Alternate ID(s):: OSTI ID: 1801700

Journal Information:: New Phytologist, Journal Name: New Phytologist Journal Issue: 6 Vol. 227; ISSN 0028-646X

Publisher:: Wiley-BlackwellCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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Circadian and Light Regulated Expression of CBFs and their Upstream Signalling Genes in Barley Gierczik, Krisztián; Novák, Aliz; Ahres, Mohamed International Journal of Molecular Sciences, Vol. 18, Issue 8 https://doi.org/10.3390/ijms18081828	journal	August 2017
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