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

Academic Article
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Overview

authors

  • Michael, T. P.
  • Mockler, T. C.
  • Breton, G.
  • McEntee, C.
  • Byer, A.
  • Trout, J. D.
  • Hazen, S. P.
  • Shen, R.
  • Priest, H. D.
  • Sullivan, C. M.
  • Givan, S. A.
  • Yanofsky, M.
  • Hong, F.
  • Kay, Steve A.
  • Chory, Joanne

publication date

  • February 2008

journal

  • PLoS Genetics  Journal

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.

subject areas

  • Arabidopsis
  • Arabidopsis Proteins
  • Circadian Rhythm
  • DNA-Binding Proteins
  • Databases, Genetic
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genes, Plant
  • Genes, Reporter
  • Genome, Plant
  • Luciferases
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis
  • Oryza
  • Photoperiod
  • Plants, Genetically Modified
  • Populus
  • Species Specificity
  • Temperature
  • Transcription Factors
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Identity

PubMed Central ID

  • PMC2222925

International Standard Serial Number (ISSN)

  • 1553-7390

Digital Object Identifier (DOI)

  • 10.1371/journal.pgen.0040014

PubMed ID

  • 18248097
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Additional Document Info

start page

  • e14

volume

  • 4

issue

  • 2

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