Binding of DNA-bending non-histone proteins destabilizes regular 30-nm chromatin structure

被引:21
作者
Bajpai, Gaurav [1 ]
Jain, Ishutesh [1 ]
Inamdar, Mandar M. [2 ]
Das, Dibyendu [3 ]
Padinhateeri, Ranjith [1 ]
机构
[1] Indian Inst Technol, Dept Biosci & Bioengn, Bombay, Maharashtra, India
[2] Indian Inst Technol, Dept Civil Engn, Bombay, Maharashtra, India
[3] Indian Inst Technol, Dept Phys, Bombay, Maharashtra, India
关键词
MOBILITY-GROUP PROTEINS; HIGHER-ORDER STRUCTURE; SACCHAROMYCES-CEREVISIAE; MITOTIC CHROMOSOMES; IN-SITU; NUCLEOPROTEIN STRUCTURES; CRYOELECTRON MICROSCOPY; MOLECULAR-DYNAMICS; NUCLEOSOME ARRAYS; LINKER DNA;
D O I
10.1371/journal.pcbi.1005365
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
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.
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页数:19
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