The C/EBP family of proteins distorts DNA upon binding but does not introduce a large directed bend

Abstract

The DNA-bending properties of several C/EBP family proteins, bound to two different sites, have been determined using circular permutation and phasing analyses. All the proteins examined by circular permutation analysis induced a significant distortion in the DNA (40-66 degrees), and this distortion was of the same magnitude at both C/EBP sites. However, phasing analysis revealed that the size of the directed bend induced in the DNA by C/EBP proteins was only 1-4 degrees. Both the magnitude and orientation of the directed bend were affected by the specific sequence of the DNA-binding site. All proteins induced a directed bend of similar magnitude and orientation (toward the minor groove) when bound to the C/EBP site derived from the IgH enhancer, but the induced bend was smaller when the protein was bound to the C/EBP site derived from the VH1 promoter. The study also included a heterodimer between Ig/EBP and ATF4. Similar to C/EBP protein homodimers, this heterodimer induces a small directed bend of 4 degrees oriented toward the minor groove when bound to the enhancer-derived C/EBP site.