High resolution dynamic mapping of histone-DNA interactions in a nucleosome

The nature of the nucleosomal barrier which regulates access to the underlying DNA during many cellular processes is not fully understood. Here we present a detailed map of histone-DNA interactions along the DNA sequence to near basepair accuracy by mechanically unzipping single molecules of DNA, each containing a single nucleosome. This interaction map revealed a distinct ~5 bp periodicity that was enveloped by three broad regions of strong interactions, with the strongest at the dyad and the other two at ~ ±40 bp from the dyad. Unzipping up to the dyad allowed recovery of a canonical nucleosome upon relaxation of the DNA, but unzipping beyond the dyad resulted in removal of histone octamer from its initial DNA sequence. These findings have significant implications for how RNA polymerase and other DNA-based enzymes may gain access to DNA associated with a nucleosome.