Basak Rajib, Rosencrans William, Yadav Indresh, Yan Peiyan, Berezhnoy Nikolay V, Chen Qinming, van Kan Jeroen A, Nordenskiöld Lars, Zinchenko Anatoly, van der Maarel Johan R C
Department of Physics, National University of Singapore, Singapore, Republic of Singapore.
Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland.
Biophys J. 2020 Dec 1;119(11):2326-2334. doi: 10.1016/j.bpj.2020.10.018. Epub 2020 Oct 27.
Chromatin compaction and internal motion are fundamental aspects of gene expression regulation. Here, we have investigated chromatin fibers comprising recombinant histone octamers reconstituted with double-stranded bacteriophage T4-DNA. The size of the fibers approaches the typical size of genomic topologically associated domains. Atomic force and fluorescence (correlation) microscopy have been used to assess the structural organization, histone-induced compaction, and internal motion. In particular, the fibers are stretched on arrays of nanochannels, each channel with a diameter of 60 or 125 nm. Major intrafiber segregation and fast internal fluctuations are observed. Full compaction was only achieved by triggering an attractive nucleosome interaction through the addition of magnesium cations. Besides compaction, histone complexation results in a dramatic decrease in the fiber's relaxation time. The relaxation times are similar to those of naked DNA with a comparable stretch, which indicates that internal motion is governed by the dynamics of uncompressed linker strands. Furthermore, the main reorganization process is association-dissociation of individually compacted regions. We surmise that the modulation of chromatin's internal motion by histone complexation might have implications for transcriptional bursting.
染色质压缩和内部运动是基因表达调控的基本方面。在此，我们研究了由用双链噬菌体T4-DNA重构的重组组蛋白八聚体组成的染色质纤维。这些纤维的大小接近基因组拓扑相关结构域的典型大小。原子力显微镜和荧光（相关）显微镜已被用于评估其结构组织、组蛋白诱导的压缩和内部运动。特别是，这些纤维被拉伸在纳米通道阵列上，每个通道的直径为60或125纳米。观察到主要的纤维内部分离和快速的内部波动。只有通过添加镁离子触发有吸引力的核小体相互作用才能实现完全压缩。除了压缩外，组蛋白复合还导致纤维弛豫时间显著缩短。弛豫时间与具有可比拉伸的裸DNA相似，这表明内部运动受未压缩连接链的动力学控制。此外，主要的重组过程是单个压缩区域的缔合-解离。我们推测组蛋白复合对染色质内部运动的调节可能对转录爆发有影响。
