A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation (original) (raw)

1. Amos Tanay1,2,
2. Irit Gat-Viks1, and
3. Ron Shamir
4. School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel

Abstract

The interaction between transcription factors and their DNA binding sites is key to understanding gene regulation. By performing a genome-wide study of the evolutionary dynamics in yeast promoters, we provide a first global view of the network of selection forces in the evolution of transcription factor binding sites. This analysis gives rise to new models for binding site activity, identifies families of related binding sites, and characterizes the functional similarities among them. We discovered rich and highly optimized selective pressures operating inside and around these families. In several cases, this organization reveals that a single transcription factor has multiple functional modes. We demonstrate how such functional heterogeneity is related to the binding site's affinity and how it is exploited in transcription programs.

Footnotes

• [Supplemental material is available online at www.genome.org.\]

• Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.2064404.

• ↵1 These authors contributed equally to this work.

• ↵2 Corresponding author. E-MAIL amos{at}tau.ac.il; FAX 972 3 6405 384.

• • Accepted January 28, 2004.
  • Received October 13, 2003.

• Cold Spring Harbor Laboratory Press

•