Understanding the Dinucleosome Structural Dynamics at All Atom Resolution

By regulating the chromatin compaction and accessibility to specific regions, a cell can tune many biological processes and even decide its fate. A myriad of factors such as chromatin remodelers, post-translational modifications and the microenvironment are known to govern chromatin accessibility. Investigation of nucleosomal structural dynamics serves as a peephole to the bigger picture of genome accessibility regulation and allows us to gain insight into how various epigenetic and non-epigenetic factors are intricately involved. In this study, we have investigated the structural dynamics of a dinucleosome (147 bp mononucleosomes connected by 15 bp linker) using MD simulation at atomic resolution. We observed that, in the absence of histone tails, the distance between NCP particles fluctuates in the range of 11 nm to 17 nm. The addition of histone tails remarkably reduces this fluctuation that is further promoted by increasing salt concentration. In any conditions we studied, we did not observe any crucial structural changes like bent or kink formation in the linker DNA. Instead, we observed considerable variation in the DNA conformation near the entry or exit site of nucleosomes, letting nucleosomes move away from or towards each other. In the presentation, we discuss the possible relevance of these observations with biological processes.量子生命科学会第２回大