Sequence-dependent nucleosome sliding in rotation-coupled and uncoupled modes revealed by molecular simulations.

ABSTRACT: While nucleosome positioning on eukaryotic genome play important roles for genetic regulation, molecular mechanisms of nucleosome positioning and sliding along DNA are not well understood. Here we investigated thermally-activated spontaneous nucleosome sliding mechanisms developing and applying a coarse-grained molecular simulation method that incorporates both long-range electrostatic and short-range hydrogen-bond interactions between histone octamer and DNA. The simulations revealed two distinct sliding modes depending on the nucleosomal DNA sequence. A uniform DNA sequence showed frequent sliding with one base pair step in a rotation-coupled manner, akin to screw-like motions. On the contrary, a strong positioning sequence, the so-called 601 sequence, exhibits rare, abrupt transitions o

SUBMITTER: Niina T 

PROVIDER: S-EPMC5728581 | biostudies-literature | 2017 Dec

REPOSITORIES: biostudies-literature