Topological Polymorphism of Two-Start Nucleosome Fibers: A Stereochemical Analysis

Abstract

The spatial organization of nucleosomes in 30-nm fibers remains unknown in detail. To address this issue, we analyzed all stereochemically possible configurations of two-start nucleosome fibers with short DNA linkers L = 13 - 37 bp (nucleosome repeat length NRL = 160 - 184 bp). Four superhelical parameters – inclination of nucleosomes, twist, rise and diameter – uniquely describe a uniform symmetric fiber. The energy of a fiber is defined as the sum of four terms: elastic energy of the linker DNA, steric repulsion, electrostatics and a phenomenological (H4 tail - acidic patch) interaction between two stacked nucleosomes. By optimizing the fiber energy with respect to the superhelical parameters, we found two types of topological transition in fibers (associated with the change in inclination angle): one caused by an abrupt 360° change in the linker DNA twisting, and another caused by over-crossing of the linkers. (The first transition is characterized by change in the DNA linking number, ΔLk = 1, and the second one by ΔLk = 2.) To the best of our knowledge, this topological polymorphism of the two-start fibers was not reported in the computations published earlier. Importantly, the optimal configurations of the fibers with linkers L = 10n and 10n+5 bp are topologically different. Our results are consistent with experimental observations, such as the inclination 60-70° (the angle between the nucleosomal disks and the fiber axis), helical rise, diameter and left-handedness of the fibers. In addition, we make several testable predictions, among them existence of different degree of DNA supercoiling in the fibers with L = 10n and 10n+5 bp, different stiffness of the two types of fibers, and a correlation between the local NRL and the level of transcription in different parts of the yeast genome.