Expanding the repertoire of DNA shape features for genome-scale studies of transcription factor binding.

ABSTRACT: Uncovering the mechanisms that affect the binding specificity of transcription factors (TFs) is critical for understanding the principles of gene regulation. Although sequence-based models have been used successfully to predict TF binding specificities, we found that including DNA shape information in these models improved their accuracy and interpretability. Previously, we developed a method for modeling DNA binding specificities based on DNA shape features extracted from Monte Carlo (MC) simulations. Prediction accuracies of our models, however, have not yet been compared to accuracies of models incorporating DNA shape information extracted from X-ray crystallography (XRC) data or Molecular Dynamics (MD) simulations. Here, we integrated DNA shape information extracted from MC or MD simul

SUBMITTER: Li J 

PROVIDER: S-EPMC5728407 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature