title: Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure.
abstract: Why most of the in vivo experiments do not find the 30-nm chromatin fiber, well studied in vitro, is a puzzle. Two basic physical inputs that are crucial for understanding the structure of the 30-nm fiber are the stiffness of the linker DNA and the relative orientations of the DNA entering/exiting nucleosomes. Based on these inputs we simulate chromatin structure and show that the presence of non-histone proteins, which bind and locally bend linker DNA, destroys any regular higher order structures (e.g., zig-zag). Accounting for the bending geometry of proteins like nhp6 and HMG-B, our theory predicts phase-diagram for the chromatin structure as a function of DNA-bending non-histone protein density and mean linker DNA length. For a wide range of linker lengths, we show that as we vary one parameter, that is, the fraction of bent linker region due to non-histone proteins, the steady-state structure will show a transition from zig-zag to an irregular structure-a structure that is reminiscent of what is observed in experiments recently. Our theory can explain the recent in vivo observation of irregular chromatin having co-existence of finite fraction of the next-neighbor (i + 2) and neighbor (i + 1) nucleosome interactions.
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Bajpai
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
authors.forename: Ishutesh
authors.initials: I
authors.lastname: Jain
authors.affiliation: Department of Civil Engineering, Indian Institute of Technology Bombay, Mumbai, India.
authors.forename: Mandar M
authors.initials: MM
authors.lastname: Inamdar
authors.affiliation: Department of Physics, Indian Institute of Technology Bombay, Mumbai, India.
authors.forename: Dibyendu
authors.initials: D
authors.lastname: Das
authors.affiliation: Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
authors.forename: Ranjith
authors.initials: R
authors.lastname: Padinhateeri
mesh_terms: D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry* / Q000648:ultrastructure*; D002868:Chromosomal Proteins, Non-Histone / Q000737:chemistry* / Q000648:ultrastructure*; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000648:ultrastructure; D055119:Elastic Modulus; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D004268:DNA-Binding Proteins; D004247:DNA