DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity

TL;DR

This paper predicts that specific DNA sequence correlations, such as homo-oligonucleotide tracts, enhance non-specific transcription factor binding affinity, influencing gene regulation and search efficiency.

Contribution

It analytically demonstrates that DNA sequence correlations universally control non-specific TF-DNA binding affinity, supported by genomic analysis.

Findings

DNA regions with strong homo-oligonucleotide correlations have higher TF occupancy.

Sequence correlations act as localization potentials for TF diffusion.

The effect limits the size of TF-DNA binding motifs.

Abstract

Transcription factors (TFs) are regulatory proteins that bind DNA in promoter regions of the genome and either promote or repress gene expression. Here we predict analytically that enhanced homo-oligonucleotide sequence correlations, such as poly(dA:dT) and poly(dC:dG) tracts, statistically enhance non-specific TF-DNA binding affinity. This prediction is generic and qualitatively independent of microscopic parameters of the model. We show that non-specific TF binding affinity is universally controlled by the strength and symmetry of DNA sequence correlations. We perform correlation analysis of the yeast genome and show that DNA regions highly occupied by TFs exhibit stronger homo-oligonucleotide sequence correlations, and thus higher propensity for non-specific binding, as compared with poorly occupied regions. We suggest that this effect plays the role of an effective localization potential enhancing the quasi-one-dimensional diffusion of TFs in the vicinity of DNA, speeding up the stochastic search process for specific TF binding sites. The predicted effect also imposes an upper bound on the size of TF-DNA binding motifs.