Changing chromatin fiber conformation by nucleosome repositioning.

摘要: Chromatin conformation is dynamic and heterogeneous with respect to nucleosome positions, which can be changed by chromatin remodeling complexes in the cell. These molecular machines hydrolyze ATP translocate or evict nucleosomes, establish loci regularly more irregularly spaced nucleosomes as well nucleosome-depleted regions. The impact of repositioning on three-dimensional structure only poorly understood. Here, we address this issue using a coarse-grained computer model arrays 101 considering several fiber models without linker histones, respectively. We investigated folding chain dependence position central changing length adjacent DNA basepair steps. found our simulations that these translocations had strong effect shape properties fibers: i), Fiber curvature flexibility at center were largely increased long-range contacts between distant promoted. ii), highest destabilization occurred for shifted two basepairs from regular spacing, whereas effects changes ∼10 bp phase helical twist minimal. iii), A fiber stabilize spacing inasmuch favorable stacking interactions are facilitated. This oppose increase energetic costs remodeling. Our computational modeling framework makes it possible describe conformational heterogeneity in terms thus advances theoretical toward better understanding how genome compaction access regulated within