调控核小体中DNA的旋转定位由碱基序列决定。一种用于模拟首选超螺旋的算法。
DNA rotational positioning in a regulatory nucleosome is determined by base sequence. An algorithm to model the preferred superhelix.
作者信息
Piña B, Truss M, Ohlenbusch H, Postma J, Beato M
机构信息
Institut für Molekularbiologie und Tumorforschung, Marburg, FRG.
出版信息
Nucleic Acids Res. 1990 Dec 11;18(23):6981-7. doi: 10.1093/nar/18.23.6981.
Abstract
MMTV-LTR sequences -190/-45 position a histone octamer both in vivo and in vitro. Experimental evidence suggested that nucleosome rotational positioning is determined by the DNA sequence itself. We developed an algorithm that is able to predict the most favorable path of a given DNA sequence over a histone octamer, based on rotational preferences of different dinucleotides. Our analysis shows that these preferences are sufficient for explaining the observed rotational positioning of the MMTV-LTR nucleosome, at one base pair accuracy level. Computer-generated 3-D models of the experimentally calculated and predicted MMTV-LTR nucleosome show that the predicted orientation is fully compatible with the currently available data in terms of accessibility of relevant sequences to regulatory proteins.
摘要
MMTV-LTR序列在-190/-45位置在体内和体外定位一个组蛋白八聚体。实验证据表明核小体的旋转定位由DNA序列本身决定。我们开发了一种算法，该算法能够根据不同二核苷酸的旋转偏好预测给定DNA序列在组蛋白八聚体上最有利的路径。我们的分析表明，这些偏好足以在一个碱基对的精度水平上解释观察到的MMTV-LTR核小体的旋转定位。实验计算和预测的MMTV-LTR核小体的计算机生成三维模型表明，就相关序列对调节蛋白的可及性而言，预测的方向与目前可用的数据完全兼容。
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