Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription.

ABSTRACT: The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To tackle this problem, we analyzed all stereochemically possible configurations of two-start chromatin fibers with DNA linkers L = 10-70 bp (nucleosome repeat length NRL = 157-217 bp). In our model, the energy of a fiber is a sum of the elastic energy of the linker DNA, steric repulsion, electrostatics, and the H4 tail-acidic patch interaction between two stacked nucleosomes. We found two families of energetically feasible conformations of the fibers-one observed earlier, and the other novel. The fibers from the two families are characterized by different DNA linking numbers-that is, they are topologically different. Remarkably, the optimal geometry of a fiber and its topology depend on the linker length: t

SUBMITTER: Norouzi D 

PROVIDER: S-EPMC5271602 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature