Covariation between homeodomain transcription factors and the shape of their DNA binding sites.

ABSTRACT: Protein-DNA recognition is a critical component of gene regulatory processes but the underlying molecular mechanisms are not yet completely understood. Whereas the DNA binding preferences of transcription factors (TFs) are commonly described using nucleotide sequences, the 3D DNA structure is recognized by proteins and is crucial for achieving binding specificity. However, the ability to analyze DNA shape in a high-throughput manner made it only recently feasible to integrate structural information into studies of protein-DNA binding. Here we focused on the homeodomain family of TFs and analyzed the DNA shape of thousands of their DNA binding sites, investigating the covariation between the protein sequence and the sequence and shape of their DNA targets. We found distinct homeodomain regi

SUBMITTER: Dror I 

PROVIDER: S-EPMC3874178 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature