Abstract
The structure and function of chromatin can be regulated through positioning patterns of nucleosomes. DNA-based processes are regulated via nucleosomes. Therefore, it is significant to determine nucleosome positions in DNA-based processes. A deformation energy model was proposed to predict nucleosome positions in our previous study. A free web server based on the model (http://lin-group.cn/server/deform-nu/) was firstly established to estimate the occupancy and rotational positioning of nucleosomes in the study. Then, the performance of the model was verified by several examples. The results indicated that nucleosome positioning relied on the physical properties of DNA, such as deformation energy.
Highlights
A nucleosome is a histone-DNA complex, in which the histone octamer is wrapped with a ∼147-bp DNA (Kornberg and Lorch, 1999; Richmond and Davey, 2003)
We found that bending energy could be used to predict the free energy in nucleosome reconstitution and revealed various patterns of bending energy profile corresponding to different organized chromatin structures, including well-positioned nucleosomes, linker regions, and fuzzy nucleosomes (Liu et al, 2018)
The nucleosome stability was positively correlated with the strength of the bending anisotropy of DNA segment, and directionality and accessibility of nucleosome sliding might be regulated via various patterns of DNA bending energy profile (Liu et al, 2018)
Summary
A nucleosome is a histone-DNA complex, in which the histone octamer is wrapped with a ∼147-bp DNA (Kornberg and Lorch, 1999; Richmond and Davey, 2003). We proposed a deformation energy model and successfully predicted occupancy and rotational positioning of nucleosomes with the model (Liu et al, 2016).
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