Deconvolving the recognition of DNA shape from sequence

ABSTRACT: Binding of transcription factors to DNA is mediated by the recognition of the chemical signatures of the DNA bases and the three-dimensional shape of the DNA molecule. The direct contribution of DNA shape to DNA-binding specificity has been difficult to assess, as DNA shape is a consequence of its sequence. Here, we teased apart these two modes of recognition in the context of Hox-DNA binding. We made a series of mutations in Hox residues that, in a co-crystal structure, only recognize DNA shape, and tested the effect on DNA binding preferences using SELEX-seq. Analysis of shape features of selected sequences revealed that these residues are both necessary and sufficient for selection of sequences with distinct shape features. We used statistical machine learning to show that the acc

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Harmen Bussemaker 

PROVIDER: E-GEOD-65073 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress