Peeling and Sliding in Nucleosome Repositioning

Abstract

We investigate the mechanisms of histone sliding and detachment with a stochastic model that couples thermally-induced, passive histone sliding with active motor-driven histone unwrapping. Analysis of a passive loop or twist defect-mediated histone sliding mechanism shows that diffusional sliding is enhanced as larger portions of the DNA is peeled off the histone. The mean times to histone detachment and the mean distance traveled by the motor complex prior to histone detachment are computed as functions of the intrinsic speed of the motor. Fast motors preferentially induce detachment over sliding. However, for a fixed motor speed, increasing the histone-DNA affinity (and thereby decreasing the passive sliding rate) increases the mean distance traveled by the motor.

5 pp, 4 figs

References in corpus (5)

• Polymer reptation and nucleosome repositioning
• Chromatin dynamics: Nucleosomes go mobile through twist defects
• Kinetic Accessibility of Buried DNA Sites in Nucleosomes
• Mean first-passage and residence times of random walks on asymmetric disordered chains
• A length-dynamic Tonks gas theory of histone isotherms

Cited by in corpus (9)

• Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective
• Master equations and the theory of stochastic path integrals
• Statistical-mechanical lattice models for protein-DNA binding in chromatin
• Unwinding and rewinding the nucleosome inner turn: Force dependence of the kinetic rate constants
• Stochastic model for nucleosome sliding in the presence of DNA ligands
• Stochastic dynamics and ribosome-RNAP interactions in Transcription-Translation Coupling
• Footprint traversal by ATP-dependent chromatin remodeler motor
• A molecule that detects the length of DNA by using chain fluctuations
• Stochastic nucleosome disassembly mediated by remodelers and histone fragmentation