Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions.

在整个基因组中，核小体通常形成规则阵列，其核小体重复长度 (NRL)、接头组蛋白 H1 的占据和转录活性不同。在这里，我们报告了具有四个生理相关 NRL 的人类含 H1 的四核小体阵列的冷冻电镜结构。这些结构显示核小体呈锯齿形排列，核小体 1 和 3 形成堆叠。H1 与堆叠核小体的结合取决于 NRL，而 H1 总是与非堆叠核小体 2 和 4 结合。短 NRL 导致接头 DNA 的轨迹改变，这些改变的轨迹在空间上损害 H1 与我们结构中堆叠核小体的结合。随着 NRL 的增加，接头 DNA 轨迹放松，使 H1 接触和结合成为可能。