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 cyc

SUBMITTER: Michael TP 

PROVIDER: S-EPMC2222925 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature