Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy

DNA sequence plays an important role in the assembly of nucleosomes, and DNA motifs with high specificity to nucleosomes have been identified. At the same time, important questions such as how the DNA sequence changes DNA wrapping and how the DNA sequence contributes to the interaction between the nucleosomes remain unclear. Here, we addressed these questions by comparing nanoscale properties of nucleosomes assembled on the highest nucleosome positioning sequence, the 601 motif, and essentially random DNA sequences. We used atomic force microscopy to measure the nucleosome positions and the DNA wrapping. The studies showed that nucleosomes assemble on the nonspecific sequence without any preference for position on DNA, but they wrap the same DNA length as DNA of the same length with the 601 sequence. Experiments with longer DNA containing the 601 motif along with nonspecific DNA, capable of forming dinucleosomes, revealed that dinucleosomes assembled on hybrid sequences show a preference for positioning near each other, with one always assembling on the 601 motif. These findings point to the interaction between the nucleosomes and suggest that internucleosomal interactions may play a large role in nucleosome positioning.—Stormberg, T., Stumme-Diers, M., Lyubchenko, Y. L. Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy.