Biology – Quantitative Biology – Biomolecules
Scientific paper
2011-11-13
Biophys. J. 101(1), 160-166 (2011)
Biology
Quantitative Biology
Biomolecules
Scientific paper
10.1016/j.bpj.2011.04.037
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.
Lukatsky David B.
Sela Itamar
No associations
LandOfFree
DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA sequence correlations shape nonspecific transcription factor-DNA binding affinity will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-340516