Grigoryev Sergei A, Arya Gaurav, Correll Sarah, Woodcock Christopher L, Schlick Tamar
Department of Biochemistry and Molecular Biology, Penn State University College of Medicine, H171, Milton S. Hershey Medical Center, PO Box 850, 500 University Drive, Hershey, PA 17033, USA.
Proc Natl Acad Sci U S A. 2009 Aug 11;106(32):13317-22. doi: 10.1073/pnas.0903280106. Epub 2009 Jul 27.
The architecture of the chromatin fiber, which determines DNA accessibility for transcription and other template-directed biological processes, remains unknown. Here we investigate the internal organization of the 30-nm chromatin fiber, combining Monte Carlo simulations of nucleosome chain folding with EM-assisted nucleosome interaction capture (EMANIC). We show that at physiological concentrations of monovalent ions, linker histones lead to a tight 2-start zigzag dominated by interactions between alternate nucleosomes (i +/- 2) and sealed by histone N-tails. Divalent ions further compact the fiber by promoting bending in some linker DNAs and hence raising sequential nucleosome interactions (i +/- 1). Remarkably, both straight and bent linker DNA conformations are retained in the fully compact chromatin fiber as inferred from both EMANIC and modeling. This conformational variability is energetically favorable as it helps accommodate DNA crossings within the fiber axis. Our results thus show that the 2-start zigzag topology and the type of linker DNA bending that defines solenoid models may be simultaneously present in a structurally heteromorphic chromatin fiber with uniform 30 nm diameter. Our data also suggest that dynamic linker DNA bending by linker histones and divalent cations in vivo may mediate the transition between tight nucleosome packing within discrete 30-nm fibers and self-associated higher-order chromosomal forms.
染色质纤维的结构决定了DNA在转录和其他模板导向的生物过程中的可及性，但其结构仍然未知。在这里，我们结合核小体链折叠的蒙特卡罗模拟与电子显微镜辅助的核小体相互作用捕获（EMANIC）技术，研究了30纳米染色质纤维的内部组织。我们发现，在生理浓度的单价离子条件下，连接组蛋白导致形成紧密的双起始锯齿状结构，这种结构以交替核小体（i +/- 2）之间的相互作用为主导，并由组蛋白N端尾巴封闭。二价离子通过促进一些连接DNA的弯曲，从而增加连续核小体间的相互作用（i +/- 1），进一步压缩了纤维。值得注意的是，从EMANIC和模型推断，直的和弯曲的连接DNA构象都保留在完全压缩的染色质纤维中。这种构象变异性在能量上是有利的，因为它有助于在纤维轴内适应DNA交叉。因此，我们的结果表明，双起始锯齿状拓扑结构和定义螺线管模型的连接DNA弯曲类型可能同时存在于直径为30纳米的结构异质的染色质纤维中。我们的数据还表明，体内连接组蛋白和二价阳离子引起的连接DNA动态弯曲可能介导离散的30纳米纤维内紧密核小体堆积与自我关联的高阶染色体形式之间的转变。
