Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.
Nucleic Acids Res. 2010 Jan;38(3):709-19. doi: 10.1093/nar/gkp1043. Epub 2009 Nov 24.
Large-scale and genome-wide studies have concluded that approximately 80% of the yeast (Saccharomyces cerevisiae) genome is occupied by positioned nucleosomes. In vivo this nucleosome organization can result from a variety of mechanisms, including the intrinsic DNA sequence preferences for wrapping the DNA around the histone core. Recently, a genome-wide study was reported using massively parallel sequencing to directly compare in vivo and in vitro nucleosome positions. It was concluded that intrinsic DNA sequence preferences indeed have a dominant role in determining the in vivo nucleosome organization of the genome, consistent with a genomic code for nucleosome positioning. Some other studies disagree with this view. Using the large amount of data now available from several sources, we have attempted to clarify a fundamental question concerning the packaging of genomic DNA: to what extent are nucleosome positions in vivo determined by histone-DNA sequence preferences? We have analyzed data obtained from different laboratories in the same way, and have directly compared these data. We also identify possible problems with some of the experimental designs used and with the data analysis. Our findings suggest that DNA sequence preferences have only small effects on the positioning of individual nucleosomes throughout the genome in vivo.
大规模和全基因组研究已经得出结论，大约 80%的酵母（酿酒酵母）基因组被定位的核小体占据。在体内，这种核小体组织可以通过多种机制产生，包括将 DNA 缠绕在组蛋白核心周围的固有 DNA 序列偏好。最近，一项使用大规模平行测序的全基因组研究报告直接比较了体内和体外核小体位置。研究得出的结论是，固有 DNA 序列偏好确实在决定基因组的体内核小体组织中起主导作用，这与核小体定位的基因组编码一致。其他一些研究不同意这种观点。利用现在从多个来源获得的大量数据，我们试图澄清一个关于基因组 DNA 包装的基本问题：在多大程度上，体内的核小体位置是由组蛋白-DNA 序列偏好决定的？我们以相同的方式分析了来自不同实验室的数据，并直接比较了这些数据。我们还确定了一些实验设计和数据分析中可能存在的问题。我们的研究结果表明，DNA 序列偏好对体内整个基因组中单个核小体的定位只有很小的影响。
