Pitman Mary, Dalal Yamini, Papoian Garegin A
Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland; Department of Chemistry and Biochemistry, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland.
Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
Biophys J. 2020 May 5;118(9):2309-2318. doi: 10.1016/j.bpj.2020.01.042. Epub 2020 Feb 12.
Histone variants regulate replication, transcription, DNA damage repair, and chromosome segregation. Though widely accepted as a paradigm, it has not been rigorously demonstrated that histone variants encode unique mechanical properties. Here, we present a new theoretical approach called minimal cylinder analysis that uses strain fluctuations to determine the Young's modulus of nucleosomes from all-atom molecular dynamics simulations. Recently, we validated this computational tool against in vitro single-molecule nanoindentation of histone variant nucleosomes. In this report, we further extend minimal cylinder analysis to study the biophysical properties of hybrid nucleosomes that are known to exist in human cancer cells and contain H3 histone variants CENP-A and H3.3. Here, we report that the heterotypic nucleosome has an intermediate elasticity (8.5 ± 0.5 MPa) compared to CENP-A (6.2 ± 0.4 MPa) and H3 (9.8 ± 0.7 MPa) and that the dynamics of both canonical and CENP-A nucleosomes are preserved and partitioned across the nucleosome pseudodyad. Furthermore, we investigate the mechanism by which the elasticity of these heterotypic nucleosomes augments cryptic binding surfaces. From these analyses, we predict that the heterotypic nucleosome is permissive to the binding of one copy of the kinetochore protein CENP-C while still retaining a closed DNA end configuration required for linker histone H1 to bind. We discuss that the ectopic deposition of CENP-A in cancer by H3.3 chaperones HIRA and DAXX may fortuitously result in hybrid nucleosome formation. Using these results, we propose biological outcomes that might arise when such heterotypic nucleosomes occupy large regions of the genome.
组蛋白变体调控复制、转录、DNA损伤修复和染色体分离。尽管作为一种范例已被广泛接受，但尚未得到严格证明的是，组蛋白变体编码独特的机械特性。在此，我们提出一种名为最小圆柱体分析的新理论方法，该方法利用应变波动，通过全原子分子动力学模拟来确定核小体的杨氏模量。最近，我们针对组蛋白变体核小体的体外单分子纳米压痕实验验证了这一计算工具。在本报告中，我们进一步扩展最小圆柱体分析，以研究已知存在于人类癌细胞中且包含H3组蛋白变体CENP - A和H3.3的杂合核小体的生物物理特性。在此，我们报告称，与CENP - A（6.2±0.4 MPa）和H3（9.8±0.7 MPa）相比，异型核小体具有中等弹性（8.5±0.5 MPa），并且经典核小体和CENP - A核小体的动力学均得以保留，并在核小体假二分体上分布。此外，我们研究了这些异型核小体弹性增强隐蔽结合表面的机制。通过这些分析，我们预测异型核小体允许一个动粒蛋白CENP - C拷贝的结合，同时仍保留连接组蛋白H1结合所需的封闭DNA末端构型。我们讨论了H3.3伴侣蛋白HIRA和DAXX在癌症中CENP - A的异位沉积可能偶然导致杂合核小体形成。利用这些结果，我们提出了当此类异型核小体占据基因组大片区域时可能出现的生物学结果。
