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

TLDR

Correct daily phasing of transcription confers an adaptive advantage to almost all organisms, including higher plants. The study introduces a hypothesis‑driven network discovery pipeline to identify biologically relevant patterns in genome‑scale data. To demonstrate its utility, the authors analyzed a comprehensive matrix of time‑course nuclear transcriptomes from Arabidopsis thaliana grown under varied thermocycles, photocycles, and circadian conditions. The pipeline revealed that 89 % of Arabidopsis transcripts cycle, with most peaking at specific times that shift with environmental cues, that thermocycles alone drive at least half of transcripts involved in core processes, and that three distinct, evolutionarily conserved transcription modules—including a novel midnight‑specific PBX/TBX/SBX module validated by PBX element activity—underlie this time‑of‑day regulation across Arabidopsis, poplar, and rice.

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.