Gale J M, Smerdon M J
Biochemistry/Biophysics Program, Washington State University, Pullman 99164-4660.
J Mol Biol. 1988 Dec 20;204(4):949-58. doi: 10.1016/0022-2836(88)90054-x.
Recently, we reported that the distribution of ultraviolet light (u.v.) induced pyrimidine dimers in nucleosome core DNA has a striking 10.3(+/- 0.1) base periodicity and the regions of enhanced quantum yield map to positions where DNA strands are farthest from the core histone surface. Improvement of the mapping procedure has allowed us to analyze this distribution in more detail, and compare the distribution pattern for nucleosome cores from intact chromatin having different higher-order structures (from the 10 nm filament to the 30 nm fiber). At all levels of chromatin compaction, we observed the following. (1) The average periodicity in pyrimidine dimer yield is 10.3 bases. (2) The peak-to-peak spacing in this distribution is significantly different from 10.3 bases in the region covering three helix turns immediately 5' of the dyad axis. (3) There is a suppression of photoproduct formation in the region of the dyad axis, especially at position 84 from the 5' end. (4) The approximately 10 base ensembles have alternating peak intensities throughout core DNA. Furthermore, peak deconvolution analysis of the pyrimidine dimer pattern yielded a striking similarity in photoproduct yield for the different levels of chromatin compaction. Irradiation of isolated core DNA yields a much more random distribution of photoproducts, although a weak modulation pattern is observed (indicating that there is a non-random alignment of adjacent pyrimidines in our core DNA preparations). This pattern includes a depression in photoproduct yield near position 95, suggesting that the sequence in this region plays a role in nucleosome positioning. These results show that the u.v. photofootprint is a sensitive, diagnostic probe of core histone-DNA interactions in intact chromatin, and these interactions are not significantly altered by changes in the structural state of the chromatin fiber.
最近，我们报道了紫外线（UV）诱导的核小体核心DNA中嘧啶二聚体的分布具有显著的10.3（±0.1）碱基周期性，并且量子产率增强的区域映射到DNA链离核心组蛋白表面最远的位置。映射程序的改进使我们能够更详细地分析这种分布，并比较来自具有不同高阶结构（从10nm细丝到30nm纤维）的完整染色质的核小体核心的分布模式。在染色质压缩的所有水平上，我们观察到以下情况。（1）嘧啶二聚体产量的平均周期性为10.3个碱基。（2）在二分体轴5'端紧邻的三个螺旋圈区域内，这种分布的峰峰间距与10.3个碱基有显著差异。（３）在二分体轴区域，尤其是从５'端起的第84位，光产物形成受到抑制。（4）整个核心DNA中约10个碱基的集合具有交替的峰强度。此外，嘧啶二聚体模式的峰去卷积分析表明，不同水平的染色质压缩在光产物产量上具有惊人的相似性。尽管观察到微弱的调制模式（表明在我们的核心DNA制剂中相邻嘧啶存在非随机排列），但分离的核心DNA的照射产生的光产物分布要随机得多。这种模式包括在位置95附近光产物产量的降低，表明该区域的序列在核小体定位中起作用。这些结果表明，紫外线光足迹是完整染色质中核心组蛋白-DNA相互作用的敏感诊断探针，并且这些相互作用不会因染色质纤维结构状态的变化而显著改变。
