Network Discovery Pipeline Elucidates Conserved Time-of-Day–Specific cis-Regulatory Modules

Abstract

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.

Organ specificity in the plant circadian system is explained by different light inputs to the shoot and root clocks

“…qPCR reactions were performed with Brilliant III SYBR Green QPCR Master Mix (Agilent) on a Mx3000P (Agilent Technologies Ltd, Stockport, UK) or a StepOnePlus (Fisher Scientific‐UK Ltd, Loughborough, UK) real‐time PCR system. IRON SULFUR CLUSTER ASSEMBLY PROTEIN 1 ( ISU1 , At4G22220) was used as the reference gene as its expression has been shown not to cycle over a range of conditions (Michael et al ., 2008). All primer sequences are given in Table S1.…”

NO FLOWERING IN SHORT DAY (NFL) is a bHLH transcription factor that promotes flowering specifically under short-day in Arabidopsis

“…The expression pattern of NFL was monitored during diurnal growth conditions using publicly available data (http://diurnal. mocklerlab.org/) (Michael et al, 2008). NFL expression is regulated under diurnal conditions with a peak at 12-16 h after dawn under SD conditions (Fig.…”

Abiotic stress and the plant circadian clock

“…56,57 This analysis suggested that such an extensive control was achieved by dispersed promoter sequences throughout the plant genome that provide a particular time frame of expression. 56,57 These authors also found that at least in one of the conditions tested, more than 10,000 genes were under circadian control, while more than 16,000 were…”