Nikitina Tatiana, Guiblet Wilfried M, Cui Feng, Zhurkin Victor B
National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.
Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, New York, USA.
J Biol Chem. 2025 Feb;301(2):108138. doi: 10.1016/j.jbc.2024.108138. Epub 2024 Dec 26.
Spatial organization of chromatin is essential for cellular functioning. However, the precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, considering the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover additional factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (∼100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. We found that removal of the histone N-tails promoted displacement of the predominant positions of nucleosomes, accompanied by redistribution of the AT-rich and GC-rich motifs in nucleosome sequences. Importantly, most of these sequence changes occurred at superhelical locations (SHLs) ±4, ±1, and ± 2, where the H2A and H4 N-tails interact with the DNA minor grooves. Furthermore, a substantial number of H4-tailless nucleosomes exhibit rotational settings opposite to that of the wild-type nucleosomes, the effect known to change the topological properties of chromatin fiber. Thus, the histone N-tails are operative in the selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.
染色质的空间组织对于细胞功能至关重要。然而，控制核小体在DNA上序列依赖性定位的精确机制仍不清楚。现有的算法考虑到DNA的序列依赖性可变形性及其与组蛋白球状结构域的相互作用，仅预测了体内映射的65%的人类核小体的旋转设置。为了揭示负责核小体定位的其他因素，我们分析了组蛋白N端尾巴在这一过程中的潜在作用。为此，我们在人类BRCA1 DNA（约100 kb）上重建了无H2A/H4 N端尾巴的核小体，并将它们的位置和序列与野生型核小体进行了比较。我们发现，去除组蛋白N端尾巴促进了核小体主要位置的位移，同时伴随着核小体序列中富含AT和富含GC基序的重新分布。重要的是，这些序列变化大多发生在超螺旋位置（SHLs）±4、±1和±2处，H2A和H4 N端尾巴在这些位置与DNA小沟相互作用。此外，大量无H4尾巴的核小体表现出与野生型核小体相反的旋转设置，这种效应已知会改变染色质纤维的拓扑性质。因此，组蛋白N端尾巴在核小体位置的选择中起作用，这可能对染色质状态的表观遗传调控具有广泛影响。
