Transcription factors and other DNA binding proteins employ two different DNA readout mechanisms to recognize their genomic target sites. Direct readout or �base readout� refers to hydrogen bonds and hydrophobic contacts between amino acid side chains and functional groups of the bases. These contacts are sequence-specific only when formed in the major groove whereas direct contacts in the minor groove cannot distinguish A/T and T/A base pairs, or G/C and C/G base pairs, because of degeneracy in the pattern of functional groups. We previously identified variations of electrostatic potential upon changes in minor groove topography as the source of protein-DNA binding specificity. Modifications in DNA structure alter the dielectric boundary with the surrounding solvent. These variations deform field lines resulting in enhanced negative electrostatic potential in regions of narrow minor groove, a process also known as �electrostatic focusing�. This observation explains biophysically why arginine and other basic residues often recognize regions of narrow minor groove. This form of indirect readout, known as �shape readout�, requires knowledge of three-dimensional DNA structure. To be able to derive DNA structural features for whole-genome data, we developed a high-throughput method for prediction of DNA shape and validated the predictions based on X-ray and NMR structures, and hydroxyl radical cleavage data. We now expanded this approach to high-throughput prediction of electrostatic potential where we mine data from Poisson-Boltzmann calculations on naked DNA molecules. Defining minor groove electrostatic potential as a function of pentamer sequence, we can add electrostatics as an additional feature in statistical machine learning approaches for quantitative prediction of DNA binding specificities of transcription factors. Integrating biophysical data in the analysis of high-throughput sequencing data enables, for the first time, the use of electrostatic potential in genome analysis with the potential to reveal yet unknown mechanisms of gene regulation.

High-throughput prediction of minor groove electrostatic potential in studies of protein-DNA recognition

248th National Meeting (2014)

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