Genome Diversity Center, Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Phys Life Rev. 2011 Mar;8(1):39-50. doi: 10.1016/j.plrev.2011.01.004. Epub 2011 Jan 19.
Various aspects of packaging DNA in eukaryotic cells are outlined in physical rather than biological terms. The informational and physical nature of packaging instructions encoded in DNA sequences is discussed with the emphasis on signal processing difficulties--very low signal-to-noise ratio and high degeneracy of the nucleosome positioning signal. As the author has been contributing to the field from its very onset in 1980, the review is mostly focused at the works of the author and his colleagues. The leading concept of the overview is the role of deformational properties of DNA in the nucleosome positioning. The target of the studies is to derive the DNA bendability matrix describing where along the DNA various dinucleotide elements should be positioned, to facilitate its bending in the nucleosome. Three different approaches are described leading to derivation of the DNA deformability sequence pattern, which is a simplified linear presentation of the bendability matrix. All three approaches converge to the same unique sequence motif CGRAAATTTYCG or, in binary form, YRRRRRYYYYYR, both representing the chromatin code.
本文以物理而非生物学术语概述了真核细胞中 DNA 的包装的各个方面。讨论了 DNA 序列中编码的包装指令的信息和物理性质，重点讨论了信号处理的困难——核小体定位信号的信噪比非常低，简并性很高。由于作者从 1980 年该领域的开始就一直在做出贡献，因此该综述主要集中在作者及其同事的工作上。该综述的主要概念是 DNA 的变形特性在核小体定位中的作用。研究的目标是推导出描述各种二核苷酸元件应在 DNA 上的何处定位的 DNA 柔韧性矩阵，以促进其在核小体中的弯曲。描述了三种不同的方法，这些方法导致了 DNA 可变形序列模式的推导，这是柔韧性矩阵的简化线性表示。所有三种方法都收敛到相同的独特序列基序 CGRAAATTTYCG 或二进制形式 YRRRRRYYYYYR，两者都代表染色质代码。
