title: The effect of internucleosomal interaction on folding of the chromatin fiber.
abstract: The folding of the nucleosome chain into a chromatin fiber modulates DNA accessibility and is therefore an important factor for the control of gene expression. The fiber conformation depends crucially on the interaction between individual nucleosomes. However, this parameter has not been accurately determined experimentally, and it is affected by posttranslational histone modifications and binding of chromosomal proteins. Here, the effect of different internucleosomal interaction strengths on the fiber conformation was investigated by Monte Carlo computer simulations. The fiber geometry was modeled to fit that of chicken erythrocyte chromatin, which has been examined in numerous experimental studies. In the Monte Carlo simulation, the nucleosome shape was described as an oblate spherocylinder, and a replica exchange protocol was developed to reach thermal equilibrium for a broad range of internucleosomal interaction energies. The simulations revealed the large impact of the nucleosome geometry and the nucleosome repeat length on the compaction of the chromatin fiber. At high internucleosomal interaction energies, a lateral self-association of distant fiber parts and an interdigitation of nucleosomes were apparent. These results identify key factors for the control of the compaction and higher order folding of the chromatin fiber.
authors.affiliation: University of Applied Sciences Stralsund, System Engineering and Information Management, 18435 Stralsund, Germany.
authors.forename: René
authors.initials: R
authors.lastname: Stehr
authors.forename: Nick
authors.initials: N
authors.lastname: Kepper
authors.forename: Karsten
authors.initials: K
authors.lastname: Rippe
authors.forename: Gero
authors.initials: G
authors.lastname: Wedemann
mesh_terms: D000818:Animals; D002645:Chickens; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry; D004912:Erythrocytes / Q000737:chemistry; D008958:Models, Molecular; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D009707:Nucleosomes / Q000737:chemistry* / Q000378:metabolism*; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D009707:Nucleosomes; D004247:DNA