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Heterochronic evolution reveals modular timing changes in budding yeast transcriptomes.

Daniel F Simola1, Chantal Francis, Paul D Sniegowski

  • 1Department of Biology, University of Pennsylvania, 433 S, University Ave, Philadelphia, PA 19104, USA. simola@mail.med.upenn.edu

Genome Biology
|October 26, 2010
PubMed
Summary
This summary is machine-generated.

Gene expression timing evolves more than levels, driven by modular changes in regulation. This suggests a dynamic, event-timeline architecture underlies complex gene regulation evolution.

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Area of Science:

  • Evolutionary biology
  • Genomics
  • Systems biology

Background:

  • Gene expression is dynamic, with regulatory evolution altering timing more than mean levels.
  • Co-regulated gene modules can shift expression timing during evolutionary divergence.

Purpose of the Study:

  • Investigate transcriptome evolution in budding yeast's cell-division cycle.
  • Determine the extent of expression timing divergence and its regulatory architecture.

Main Methods:

  • Utilized a custom microarray platform for 6,263 genes across 18 timepoints.
  • Analyzed cell-division cycle dynamics in nine S. cerevisiae and one S. paradoxus strain.

Main Results:

  • Significant divergence in expression dynamics observed across transcriptome scales.
  • Timing evolution better explained 82% of gene expression changes compared to level evolution.
  • Identified seven dynamically-autonomous modules with coherent evolutionary timing changes.

Conclusions:

  • Transcriptome evolution favors changes in expression timing (heterochrony) over levels (heterometry).
  • Modular changes in timing control, mediated by module-specific transcription factors, drive evolution.
  • Hypothesize a genome-wide regulatory architecture of semi-autonomous event timelines for combinatorial timing control.