The DOI matches its Crossref record; 57 of the 57 references it cites were found in a registry or an index.
Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules
Open accessAbstract
Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. In this study, we describe a hypothesis-driven network discovery pipeline that identifies biologically relevant patterns in genome-scale data. To demonstrate its utility, we analyzed a comprehensive matrix of time courses interrogating the nuclear transcriptome of Arabidopsis thaliana plants grown under different thermocycles, photocycles, and circadian conditions. We show that 89% of Arabidopsis transcripts cycle in at least one condition and that most genes have peak expression at a particular time of day, which shifts depending on the environment. Thermocycles alone can drive at least half of all transcripts critical for synchronizing internal processes such as cell cycle and protein synthesis. We identified at least three distinct transcription modules controlling phase-specific expression, including a new midnight specific module, PBX/TBX/SBX. We validated the network discovery pipeline, as well as the midnight specific module, by demonstrating that the PBX element was sufficient to drive diurnal and circadian condition-dependent expression. Moreover, we show that the three transcription modules are conserved across Arabidopsis, poplar, and rice. These results confirm the complex interplay between thermocycles, photocycles, and the circadian clock on the daily transcription program, and provide a comprehensive view of the conserved genomic targets for a transcriptional network key to successful adaptation.
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Self-citationPlant Circadian Clocks Increase Photosynthesis, Growth, Survival, and Competitive Advantage
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Cited by
H2A.Z-containing nucleosomes mediate the thermosensory response in Arabidopsis
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The ELF4–ELF3–LUX complex links the circadian clock to diurnal control of hypocotyl growth
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Self-citationCovington, M. F., Maloof, J. N., Straume, M., Kay, S. A., & Harmer, S. L. (2008) · Genome Biology · doi:10.1186/gb-2008-9-8-r130 · Cited by 747
Self-citationThe Circadian System in Higher Plants
Harmer, S. L. (2009) · Annual Review of Plant Biology · doi:10.1146/annurev.arplant.043008.092054 · Cited by 719
Detecting Rhythms in Time Series with RAIN
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Metadata
- Authors
- Michael, T. P., Mockler, T. C., Breton, G., McEntee, C., Byer, A., Trout, J. D., Hazen, S. P., Shen, R., Priest, H. D., Sullivan, C. M., Givan, S. A., Yanovsky, M., Hong, F., Kay, S. A., & Chory, J.
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2008-02-01
- Volume
- 4
- Issue
- 2
- Pages
- e14
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- OpenAlex
- W2018306071
- Cited by
- 536
- References
- 57
- FWCI
- 51.29
- Type
- journal article
- Language
- en
- Open access
- gold
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- Michael, T. P., Mockler, T. C., Breton, G., McEntee, C., Byer, A., Trout, J. D., Hazen, S. P., Shen, R., Priest, H. D., Sullivan, C. M., Givan, S. A., Yanovsky, M., Hong, F., Kay, S. A., & Chory, J. (2008). Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules. PLoS Genetics. https://doi.org/10.1371/journal.pgen.0040014
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