# A nonequilibrium strategy for fast target search on the genome

## TL;DR

This paper introduces a nonequilibrium mechanism called chromophoresis, enabling proteins to efficiently locate specific DNA targets by active, unidirectional movement along the genome, even in inaccessible regions.

## Contribution

The study proposes and analyzes chromophoresis as a novel nonequilibrium strategy for rapid DNA target search, enhancing binding efficiency in complex genomic regions.

## Key findings

- Chromophoretic proteins can move unidirectionally along DNA.
- They can locally unravel collapsed genomic regions.
- This mechanism improves target search efficiency.

## Abstract

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 colours (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 unidirectional 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 the location of DNA lesions.