Free energy profile of nucleosomal DNA sliding

Kanaeda, Naoko; Ishida, Hisashi; Kono, Hidetoshi

The nucleosome, consisting of a histone octomer with DNA wrapped around it, is the basic repeating unit of the eukaryotic chromosome structure. Because the DNA is wrapped around the histone core, it is difficult for proteins that regulate transcription, DNA replication, repair and recombination to access the nucleosomal DNA. Nucleosomes have been known to dynamically change their positions in accordance with cell states. ATP-hydrolyzing chromatin remodelers are considered to loosen the form of the DNA and relocate the DNA inside the nucleosome in order to expose cis-elements to which regulatory proteins bind. We believe that the free energy profile of nucleosomal DNA sliding can provide some important clues to help understand the mechanism of changes in nucleosome positioning.