title: 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: the fibers with linkers L = 10nand 10n+ 5 bp have DNA linking numbers per nucleosome ΔLk≈ -1.5 and -1.0, respectively. In other words, the level of DNA supercoiling is directly related to the length of the inter-nucleosome linker in the chromatin fiber (and therefore, to NRL). We hypothesize that this topological polymorphism of chromatin fibers may play a role in the process of transcription, which is known to generate different levels of DNA supercoiling upstream and downstream from RNA polymerase. A genome-wide analysis of the NRL distribution in active and silent yeast genes yielded results consistent with this assumption.
authors.affiliation: Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA.
authors.forename: Davood
authors.initials: D
authors.lastname: Norouzi
authors.affiliation: Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA.
authors.forename: Ataur
authors.initials: A
authors.lastname: Katebi
authors.affiliation: Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, 85 Lomb Memorial Drive, Rochester, NY 14623, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Cui
authors.affiliation: Laboratory of Cell Biology, National Cancer Institute, NIH Bethesda, MD 20892, USA.
authors.forename: Victor B
authors.initials: VB
authors.lastname: Zhurkin
keywords: DNA linking number; DNA topology; chromatin fiber; nucleosome repeat length; regulation of transcription