Institute for Quantitative Biosciences-QB3, University of California, Berkeley, Berkeley, United States.
Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.
Elife. 2019 Jul 31;8:e48281. doi: 10.7554/eLife.48281.
Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.
核小体是 RNA 聚合酶 II（Pol II）在转录过程中必须克服的机械和能量障碍。目前仍然缺乏对障碍地形的高分辨率描述、其被表观遗传修饰的调节以及它们对 Pol II 核小体穿越动力学的影响的描述。在这里，我们以接近碱基对的分辨率和精度获得了规范核小体、H2A.Z 核小体和单泛素化 H2B（uH2B）核小体的地形和转录（Pol II 停留时间）图谱。Pol II 穿越动力学很复杂，在特定位置出现暂停、回溯和缠绕状态之间的核小体跳跃。虽然 H2A.Z 拓宽了障碍，但 uH2B 则使其升高，这两种修饰都大大延长了 Pol II 穿越时间。我们利用 Pol II 在每个核小体位置的停留时间来提取障碍的能量。H2A.Z 和 uH2B 的正交障碍修饰及其对 Pol II 动力学的影响，解释了它们在+1 核小体中的富集，并为选择性控制基因表达提供了一种机制。
