Simulating the evolution of transcription factors and their binding sites
Transcription factors govern the regulation of genes by binding to specific locations in the promoter region of genes, enhancing or repressing their transcription by the RNA-polymerase holoenzyme. The mechanisms by which transcription factors recognize their cognate binding sites in DNA remain obscure and many questions about the evolution of these genetic elements remain unaddressed. Here we propose the use of UMBC parallel computing facilities to simulate the evolution of virtual transcription factors operating on synthetic genomes in order to analyze the evolutionary constraints operating on transcription factors and their binding sites. A combination of experimental data and combinatorial approaches to simulate evolutionary processes can shed light on the nature and evolution of transcription factor-finding motifs like the one depicted in this picture.