Modeling a self-avoiding chromatin loop: Relation to the packing problem, action-at-a-distance, and nuclear context

被引:20
作者
Bon, M
Marenduzzo, D
Cook, PR
机构
[1] Univ Oxford, Sir William Dunn Sch Pathol, Oxford OX1 3RE, England
[2] Univ Warwick, Math Inst, Coventry CV4 7AL, W Midlands, England
[3] Univ Oxford, Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England
基金
英国工程与自然科学研究理事会;
关键词
D O I
10.1016/j.str.2005.10.016
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
There is now convincing evidence that genomes are organized into loops, and that looping brings distant genes together so that they can bind to local concentrations of polymerases in "factories" or "hubs." As there remains no systematic analysis of how looping affects the probability that a gene can access binding sites in such factories/hubs, we used an algorithm that we devised and Monte Carlo methods to model a DNA or chromatin loop as a semiflexible (self-avoiding) tube attached to a sphere; we examine how loop thickness, rigidity, and contour length affect where particular segments of the loop lie relative to binding sites on the sphere. Results are compared with those obtained with the traditional model of an (infinitely thin) freely jointed chain. They provide insights into the packing problem (how long genomes are packed into small nuclei), and action-at-a-distance (how firing of one origin or gene can prevent firing of an adjacent one).
引用
收藏
页码:197 / 204
页数:8
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