Dipartimento di Chimica, Università di Roma La Sapienza, P.le A. Moro, 5 I-00185, Roma, Italy.
Biophys Chem. 2011 May;155(2-3):53-64. doi: 10.1016/j.bpc.2011.03.006. Epub 2011 Apr 9.
In eukaryotic genomes, nucleosomes are responsible for packaging DNA and controlling gene expression. For this reason, an increasing interest is arising on computational methods capable of predicting the nucleosome positioning along genomes. In this review we describe and compare bioinformatic and physical approaches adopted to predict nucleosome occupancy along genomes. Computational analyses attempt at decoding the experimental nucleosome maps of genomes in terms of certain dinucleotide step periodicity observed along DNA. Such investigations show that highly significant information about the occurrence of a nucleosome along DNA is intrinsic in certain features of the sequence suggesting that DNA of eukaryotic genomes encodes nucleosome organization. Besides the bioinformatic approaches, physical models were proposed based on the sequence dependent conformational features of the DNA chain, which govern the free energy needed to transform recurrent DNA tracts along the genome into the nucleosomal shape.
在真核生物基因组中，核小体负责包装 DNA 并控制基因表达。因此，人们对能够预测基因组中核小体定位的计算方法越来越感兴趣。在这篇综述中，我们描述并比较了用于预测基因组中核小体占有率的生物信息学和物理方法。计算分析试图根据 DNA 上观察到的特定二核苷酸步周期性，对基因组的实验核小体图谱进行解码。这些研究表明，在 DNA 上发生核小体的特定序列特征中固有地包含了有关核小体在 DNA 上出现的高度显著信息，这表明真核生物基因组的 DNA 编码核小体组织。除了生物信息学方法之外，还基于 DNA 链的序列依赖性构象特征提出了物理模型，这些模型控制了将基因组中反复出现的 DNA 片段转化为核小体形状所需的自由能。
