Spontaneous access to DNA target sites in folded chromatin fibers
Spontaneous access to DNA target sites in folded chromatin fibers
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DOI：
10.1016/j.jmb.2008.04.025
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发表时间：
2008-06-13
影响因子：
5.6
通讯作者：
Widom, Jonathan
中科院分区：
文献类型：
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作者：
Poirier, Michael G.;Bussiek, Malte;Widom, Jonathan
包裹在核小体中的DNA在空间上被许多必须作用于它的蛋白质复合物所阻挡；这些复合物如何进入核小体DNA尚不清楚。对分离核小体的体外研究表明，它们经历自发的部分解包裹构象转变，这使得包裹的核小体DNA暂时可接近。因此，位点暴露可能提供了一种允许蛋白质复合物进入核小体DNA的一般机制。然而，现有的位点暴露定量分析主要集中在单个核小体上，而邻近核小体的存在和伴随的染色质折叠可能会显著影响位点暴露。在这项工作中，我们对核小体DNA在均匀核小体阵列中的可及性进行了定量研究。出现了两个惊人的发现。染色质纤维的组织改变核小体DNA的可接近性只是适度的，可接近性从类似于3倍的减少到类似于8倍的增加。这意味着核小体阵列本质上是动态的，甚至当它们明显浓缩时也是可访问的。相反，染色质折叠使连接DNA的可及性降低了50倍。因此，核小体定位显著影响核小体内靶位点的可及性，而染色质折叠显著调节连接体DNA中靶位点的可及性。(C) 2008 Elsevier Ltd版权所有。
DNA wrapped in nucleosomes is sterically occluded from many protein complexes that must act on it; how such complexes gain access to nucleosomal DNA is not known. In vitro studies on isolated nucleosomes show that they undergo spontaneous partial unwrapping conformational transitions, which make the wrapped nucleosomal DNA transiently accessible. Thus, site exposure might provide a general mechanism allowing access of protein complexes to nucleosomal DNA. However, existing quantitative analyses of site exposure focused on single nucleosomes, while the presence of neighbor nucleosomes and concomitant chromatin folding might significantly influence site exposure. In this work, we carried out quantitative studies on the accessibility of nucleosomal DNA in homogeneous nucleosome arrays. Two striking findings emerged. Organization into chromatin fibers changes the accessibility of nucleosomal DNA only modestly, from similar to 3-fold decreases to similar to 8-fold increases in accessibility. This means that nucleosome arrays are intrinsically dynamic and accessible even when they are visibly condensed. In contrast, chromatin folding decreases the accessibility of linker DNA by as much as similar to 50-fold. Thus, nucleosome positioning dramatically influences the accessibility of target sites located inside nucleosomes, while chromatin folding dramatically regulates access to target sites in linker DNA. (C) 2008 Elsevier Ltd. All rights reserved.