Ngo Thuy T M, Liu Bailey, Wang Feng, Basu Aakash, Wu Carl, Ha Taekjip
Department of Physics, Center for Physics in Living Cells University of Illinois Urbana-Champaign, Urbana, United States.
Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, United States.
Elife. 2024 Apr 24;13:RP95514. doi: 10.7554/eLife.95514.
The organization of nucleosomes into chromatin and their accessibility are shaped by local DNA mechanics. Conversely, nucleosome positions shape genetic variations, which may originate from mismatches during replication and chemical modification of DNA. To investigate how DNA mismatches affect the mechanical stability and the exposure of nucleosomal DNA, we used an optical trap combined with single-molecule FRET and a single-molecule FRET cyclization assay. We found that a single base-pair C-C mismatch enhances DNA bendability and nucleosome mechanical stability for the 601-nucleosome positioning sequence. An increase in force required for DNA unwrapping from the histone core is observed for single base-pair C-C mismatches placed at three tested positions: at the inner turn, at the outer turn, or at the junction of the inner and outer turn of the nucleosome. The results support a model where nucleosomal DNA accessibility is reduced by mismatches, potentially explaining the preferred accumulation of single-nucleotide substitutions in the nucleosome core and serving as the source of genetic variation during evolution and cancer progression. Mechanical stability of an intact nucleosome, that is mismatch-free, is also dependent on the species as we find that yeast nucleosomes are mechanically less stable and more symmetrical in the outer turn unwrapping compared to nucleosomes.
核小体组装成染色质及其可及性受局部DNA力学影响。相反，核小体位置塑造遗传变异，这些变异可能源于复制过程中的错配和DNA的化学修饰。为了研究DNA错配如何影响核小体DNA的机械稳定性和暴露情况，我们使用了光镊结合单分子荧光共振能量转移（FRET）以及单分子FRET环化分析。我们发现，对于601 - 核小体定位序列，单个碱基对C - C错配增强了DNA的弯曲性和核小体的机械稳定性。在核小体内侧转角、外侧转角或内外侧转角交界处的三个测试位置放置单个碱基对C - C错配时，观察到从组蛋白核心解开DNA所需的力增加。这些结果支持了一个模型，即错配会降低核小体DNA的可及性，这可能解释了单核苷酸替换在核小体核心中优先积累的现象，并作为进化和癌症进展过程中遗传变异的来源。完整的、无错配的核小体的机械稳定性也取决于物种，因为我们发现与其他核小体相比，酵母核小体在外侧转角解开时机械稳定性较低且更具对称性。
