Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure

The organization of DNA into chromatin is important in the regulation of tr anscription, by influencing the access of transcription factors to their DN A binding sites. Nuclear factor 1 (NF-1) is a transcription factor which bi nds to DNA constitutively and which interacts with its cognate DNA site wit h high affinity. However, this affinity is drastically reduced, similar to 100- to 300-fold, when the binding site is organized into a nucleosome. Her e we demonstrate that the introduction of stretches of adenines of length 5 nt (A-tracts) on both sides of the NF-1 binding site has a distinct effect on NF-1 binding to a nucleosomal, but not to a free, NF-1 binding site, Th e position of the A-tracts, relative to the rotational phase of a synthetic DNA bending sequence, the TG-motif, decides whether the NF-1 affinity incr eases or decreases. The NF-1 binding affinity is seven times stronger when the flanking A-tracts are positioned out-of-phase with the TG-motif than it is when the A-tracts are positioned in-phase with the TG-motif, We demonst rate that this effect correlates with differences in DNA curvature and appa rent histone octamer affinity. We conclude that DNA curvature influences th e local histone-DNA contacts and hence the accessibility of the NF-1 site i n a nucleosome context.