Meng He, Andresen Kurt, van Noort John
Biological and Soft Matter Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, Leiden, The Netherlands.
Department of Physics, Gettysburg College, Gettysburg, PA 17325, USA.
Nucleic Acids Res. 2015 Apr 20;43(7):3578-90. doi: 10.1093/nar/gkv215. Epub 2015 Mar 16.
Single-molecule techniques allow for picoNewton manipulation and nanometer accuracy measurements of single chromatin fibers. However, the complexity of the data, the heterogeneity of the composition of individual fibers and the relatively large fluctuations in extension of the fibers complicate a structural interpretation of such force-extension curves. Here we introduce a statistical mechanics model that quantitatively describes the extension of individual fibers in response to force on a per nucleosome basis. Four nucleosome conformations can be distinguished when pulling a chromatin fiber apart. A novel, transient conformation is introduced that coexists with single wrapped nucleosomes between 3 and 7 pN. Comparison of force-extension curves between single nucleosomes and chromatin fibers shows that embedding nucleosomes in a fiber stabilizes the nucleosome by 10 kBT. Chromatin fibers with 20- and 50-bp linker DNA follow a different unfolding pathway. These results have implications for accessibility of DNA in fully folded and partially unwrapped chromatin fibers and are vital for understanding force unfolding experiments on nucleosome arrays.
单分子技术可实现对单个染色质纤维的皮牛顿级操控和纳米级精度测量。然而，数据的复杂性、单个纤维组成的异质性以及纤维伸长过程中相对较大的波动，使得对此类力-伸长曲线进行结构解释变得复杂。在此，我们引入一种统计力学模型，该模型基于每个核小体定量描述单个纤维在受力时的伸长情况。拉开染色质纤维时可区分出四种核小体构象。引入了一种新的瞬时构象，它在3至7皮牛顿之间与单个包裹的核小体共存。单个核小体与染色质纤维之间的力-伸长曲线比较表明，将核小体嵌入纤维中可使核小体稳定10kBT。具有20和50碱基对连接DNA的染色质纤维遵循不同的解折叠途径。这些结果对完全折叠和部分解包裹的染色质纤维中DNA的可及性具有启示意义，对于理解核小体阵列的力解折叠实验至关重要。
