Target Location by DNA-Binding Proteins: Effects of Roadblocks and DNA Looping

TL;DR

This study extends the facilitated diffusion model to crowded cellular environments, showing how DNA-binding proteins and DNA looping influence the efficiency of target location in living cells.

Contribution

It introduces the effects of protein crowding and DNA looping into the facilitated diffusion model, highlighting their roles in target search dynamics within cells.

Findings

Crowding proteins slow down the search process by restricting sliding.

Increasing DNA-binding proteins marginally affects search time due to mutual restriction.

DNA looping provides an alternative, efficient transfer pathway to the target.

Abstract

The model of facilitated diffusion describes how DNA-binding proteins, such as transcription factors (TFs), find their chromosomal targets by combining 3D diffusion through the cytoplasm and 1D sliding along nonspecific DNA sequences. The redundant 1D diffusion near the specific binding site extends the target size and facilitates target location. While this model successfully predicts the kinetics measured in test tubes, it has not been extended to account for the highly crowded environment in living cells. Here, we investigate the effect of other DNA-binding proteins that partially occupy the bacterial chromosome. We show how they would slow down the search process, mainly through restricted sliding near the target. This implies that increasing the overall DNA-binding protein concentration would have a marginal effect in reducing the search time, because any additional proteins would restrict the search process for each other. While the presence of other proteins prevents sliding from the flanking DNA, DNA looping provides an alternative path to transfer from neighboring sites to the target efficiently. We propose that, when looping is faster than the initial search process, the auxiliary binding sites further extend the effective target region and therefore facilitate the target location.