RT Journal
A1 Tanay, Amos
A1 Gat-Viks, Irit
A1 Shamir, Ron
T1 A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation
JF Genome Research 
JO Genome Research 
YR 2004 
FD May 01 
VO 14 
IS 5 
SP 829 
OP 834 
DO 10.1101/gr.2064404 
UL http://genome.cshlp.org/content/14/5/829.abstract 
AB 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.