TY - JOUR
T1 - Nonequilibrium Strategy for Fast Target Search on the Genome
AU - Michieletto, Davide
AU - Cagnetta, Francesco
AU - Marenduzzo, Davide
PY - 2020/5/15
Y1 - 2020/5/15
N2 - Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on “chromophoresis,” the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colors (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled—a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform undirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and “dive” deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for DNA repair.
AB - Vital biological processes such as genome repair require fast and efficient binding of selected proteins to specific target sites on DNA. Here we propose an active target search mechanism based on “chromophoresis,” the dynamics of DNA-binding proteins up or down gradients in the density of epigenetic marks, or colors (biochemical tags on the genome). We focus on a set of proteins that deposit marks from which they are repelled—a case which is only encountered away from thermodynamic equilibrium. For suitable ranges of kinetic parameter values, chromophoretic proteins can perform undirectional motion and are optimally redistributed along the genome. Importantly, they can also locally unravel a region of the genome which is collapsed due to self-interactions and “dive” deep into its core, for a striking enhancement of the efficiency of target search on such an inaccessible substrate. We discuss the potential relevance of chromophoresis for DNA repair.
UR - http://www.scopus.com/inward/record.url?scp=85085737056&partnerID=8YFLogxK
U2 - 10.1103/PhysRevLett.124.198101
DO - 10.1103/PhysRevLett.124.198101
M3 - Article
SN - 0031-9007
VL - 124
JO - Physical Review Letters
JF - Physical Review Letters
IS - 19
M1 - 198101
ER -