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

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 applied the pipeline to 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 tested 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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