A unified approach for quantifying and interpreting DNA shape readout by transcription factors.

ABSTRACT: Transcription factors (TFs) interpret DNA sequence by probing the chemical and structural properties of the nucleotide polymer. DNA shape is thought to enable a parsimonious representation of dependencies between nucleotide positions. Here, we propose a unified mathematical representation of the DNA sequence dependence of shape and TF binding, respectively, which simplifies and enhances analysis of shape readout. First, we demonstrate that linear models based on mononucleotide features alone account for 60-70% of the variance in minor groove width, roll, helix twist, and propeller twist. This explains why simple scoring matrices that ignore all dependencies between nucleotide positions can partially account for DNA shape readout by a TF Adding dinucleotide features as sequence-to-shape pre

SUBMITTER: Rube HT 

PROVIDER: S-EPMC5822049 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature