Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules

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 analyze...

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Bibliographic Details
Published in:PLoS genetics 2008-02, Vol.4 (2), p.e14-e14
Main Authors: Michael, Todd P, Mockler, Todd C, Breton, Ghislain, McEntee, Connor, Byer, Amanda, Trout, Jonathan D, Hazen, Samuel P, Shen, Rongkun, Priest, Henry D, Sullivan, Christopher M, Givan, Scott A, Yanovsky, Marcelo, Hong, Fangxin, Kay, Steve A, Chory, Joanne
Format: Article
Language:English
Subjects:
Arabidopsis (Thale Cress)
Arabidopsis - genetics
Arabidopsis - physiology
Arabidopsis Proteins - biosynthesis
Arabidopsis Proteins - genetics
Biological clocks
Cell cycle
Circadian rhythm
Circadian Rhythm - genetics
Circadian Rhythm - physiology
Computational Biology
Databases, Genetic
Deoxyribonucleic acid
Developmental Biology
DNA
DNA-Binding Proteins - genetics
Evolutionary Biology
Gene expression
Gene Expression Profiling
Gene Expression Regulation, Plant
Genes, Plant
Genes, Reporter
Genome, Plant
Genomes
Luciferases - genetics
Models, Genetic
Molecular Biology
Oligonucleotide Array Sequence Analysis
Oryza
Oryza - genetics
Oryza - physiology
PBX
Photoperiod
Plant Biology
Plants, Genetically Modified
Populus - genetics
Populus - physiology
Protein synthesis
Species Specificity
Temperature
Transcription Factors - genetics
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Summary: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.
ISSN:1553-7404
1553-7390
1553-7404
DOI:10.1371/journal.pgen.0040014