Fitzgerald D J, Dryden G L, Bronson E C, Williams J S, Anderson J N
Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392.
J Biol Chem. 1994 Aug 19;269(33):21303-14.
Intrinsic DNA curvature has previously been implicated in the condensation of satellite DNA in chromatin. In this article, electrophoretic methods and computer programs for predicting DNA structure from nucleotide sequence were used to determine if curvature is a conserved feature of satellite DNA. The results revealed that satellite sequences display wide variation in magnitude of intrinsic bending. Less than half of the satellites examined were strongly bent when compared with control DNA. However, a conserved pattern of bending was seen in all 57 satellite sequences that were studied. The pattern consisted of repeating units of two 50-60-base pair bending elements which were separated by a 20-30-base pair region of low curvature. This pattern resembles qualitatively the bending of DNA in the nucleosome where the helix is folded approximately two turns around the histone octomer with the turns interrupted by a less bent segment in the center of the particle. The distance between successive pairs of bending elements was also similar to the average spacing of nucleosomes in chromatin. Thus, the conserved structures could play some role in the positioning of nucleosomes along satellite chromatin. In order to strengthen the correlation between DNA structure and nucleosome positioning, sequences were examined which have been shown to position nucleosomes at single major sites. This analysis revealed a conserved pattern of DNA structure resembling the two peak units seen in satellites. In addition, the nucleotide sequence patterns responsible for the conserved patterns of bending were similar in both satellite and nucleosome positioning DNA. Likewise, nucleotide sequence patterns that are thought to direct the rotational orientation of DNA in the nucleosome were similar in both sequence sets. These results are considered in terms of a general model for the role of DNA bending and nucleotide sequence in the control of nucleosome positioning and chromatin condensation in eukaryotes.
内在DNA曲率先前已被认为与染色质中卫星DNA的凝聚有关。在本文中，使用电泳方法和从核苷酸序列预测DNA结构的计算机程序来确定曲率是否是卫星DNA的保守特征。结果显示，卫星序列在内在弯曲程度上表现出广泛的差异。与对照DNA相比，所检测的卫星中不到一半有强烈弯曲。然而，在研究的所有57个卫星序列中都观察到了一种保守的弯曲模式。该模式由两个50 - 60碱基对弯曲元件的重复单元组成，这些单元被一个20 - 30碱基对的低曲率区域隔开。这种模式在性质上类似于核小体中DNA的弯曲，其中螺旋围绕组蛋白八聚体折叠大约两圈，中间由颗粒中心一个弯曲程度较小的片段中断。连续的弯曲元件对之间的距离也类似于染色质中核小体的平均间距。因此，这些保守结构可能在核小体沿卫星染色质的定位中发挥某种作用。为了加强DNA结构与核小体定位之间的相关性，研究了已被证明能在单个主要位点定位核小体的序列。该分析揭示了一种类似于卫星中所见的两个峰单元的DNA结构保守模式。此外，负责弯曲保守模式的核苷酸序列模式在卫星和核小体定位DNA中相似。同样，在两个序列组中，被认为指导DNA在核小体中旋转方向的核苷酸序列模式也相似。根据DNA弯曲和核苷酸序列在真核生物中核小体定位和染色质凝聚控制中的作用的一般模型来考虑这些结果。
