Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes
Long-range correlations between DNA bending sites: Relation to the structure and dynamics of nucleosomes
复制标题
DOI：
10.1006/jmbi.2001.5363
复制
发表时间：
2002-03-01
影响因子：
5.6
通讯作者：
Thermes, C
中科院分区：
文献类型：
--
作者：
Audit, B;Vaillant, C;Thermes, C
核小体在基因组DNA上的精确定位已经被证实，至少对于其中的一小部分来说，可以通过依赖于序列的过程来实现。然而，DNA序列在核小体主要部分的定位中发挥多大作用仍存在争议。本研究的目的是检验长程相关(LRC)与核小体的存在在多大程度上相关。利用小波变换技术，我们对DNA文本和基于核小体定位数据的曲率表生成的相应弯曲轮廓进行了比较分析。通过所谓的“小波变换显微镜”对一些真核生物和细菌基因组的探索揭示了一个100200个碱基的特征尺度，该尺度分隔了两个不同的LRC区域。在这里，我们专注于LRC在小规模区域(10-200bp)的存在，这实际上是在真核基因组中观察到的，与它们在真细菌基因组中的缺失形成对比。对病毒DNA基因组的分析表明，与宿主的基因组一样，真核病毒存在LRC，但真细菌病毒不存在。痘病毒的基因组有一个例外，它们不在细胞核内复制，也不表现出LRC。除了逆转录病毒外，在所有被检查的RNA病毒的基因组中都没有检测到小规模的LRC。这些结果再加上已知参与核小体形成的特定序列基序之间的LRC的观察，强烈表明10-200bP的LRC是核小体定位依赖于序列的标志。最后，我们讨论了从物理机制的角度对这些LRC的可能解释，这些物理机制可能通过合作过程控制核小体沿DNA链的定位和动力学。(C)2002年爱思唯尔科学有限公司。
It has been established that the precise positioning of nucleosomes on genomic DNA can be achieved, at least for a minority of them, through sequence-dependent processes. However, to what extent DNA sequences play a role in the positioning of the major part of nucleosomes is still debated. The aim of the present study is to examine to what extent long,, range correlations (LRC) are related to the presence of nucleosomes. Using the wavelet transform technique, we perform a comparative analysis of the DNA text and of the corresponding bending profiles generated with curvature tables based on nucleosome positioning data. The exploration of a number of eukaryotic and bacterial genomes through the optics of the socalled ''wavelet transform microscope'' reveals a characteristic scale of 100200 bp that separates two regimes of different LRC. Here, we focus on the existence of LRC in the small-scale regime (10-200 bp) which are actually observed in eukaryotic genomes, in contrast to their absence in eubacterial genomes. Analysis of viral DNA genomes shows that, like their host's genomes, eukaryotic viruses present LRC but eubacterial viruses do not. There is one exception for genomes of poxviruses (Vaccinia and Melamoplus san-guinipes) which do not replicate in the cell nucleus and do not exhibit LRC. No small-scale LRC are detected in the genomes of all examined RNA viruses, with the exception of retroviruses. These results together with the observation of LRC between particular sequence motifs known to participate in the formation of nucleosomes (e.g. AA dinucleotides) strongly suggest that the 10-200 bp LRC are a signature of the sequence-dependence of nucleosome positioning. Finally, we discuss possible interpretations of these LRC in terms of the physical mechanisms that might govern the positioning and the dynamics of the nucleosomes along the DNA chain through cooperative processes. (C) 2002 Elsevier Science Ltd.