Seminar “How do proteins search for their targets on a folded chromosome?”
Date
Tuesday, 2nd October of 2018
Time
12:00 am
Place
University of Barcelona
Faculty of Physics Building
Room 3.20, 3rd floor
Speaker
Dr Ruggero Cortini, Centre for Genomic Regulation (Spain)
Abstract
Organisms regulate the expression of their genes by, among other mechanisms, expression of proteins called transcription factors. These proteins can bind at specific DNA sequences (binding motif) called promoters and initiate the transcription of the genes.
Why do we find transcription factors at many sites that do not contain their corresponding binding motif? And conversely, why are many DNA sequences that contain a binding motif not bound by the transcription factor?
I try to shed light on these questions by looking at the role that the three-dimensional structure of the chromosomes might play in shaping the process of transcription factor search in the genome. To do so, I set up molecular dynamics simulations of particles (tracers) that explore the structure of a folded polymer. The results of the simulations show that knowing how the polymer is folded in three dimensions it is possible to extract information about which site of the polymer is more or less visited by the tracers. The results have important implications for understanding experimental data of transcription factors binding on genomes.
