Wang Ji-Ping, Fondufe-Mittendorf Yvonne, Xi Liqun, Tsai Guei-Feng, Segal Eran, Widom Jonathan
Department of Statistics, Northwestern University, Evanston, Illinois, United States of America.
PLoS Comput Biol. 2008 Sep 12;4(9):e1000175. doi: 10.1371/journal.pcbi.1000175.
The exact lengths of linker DNAs connecting adjacent nucleosomes specify the intrinsic three-dimensional structures of eukaryotic chromatin fibers. Some studies suggest that linker DNA lengths preferentially occur at certain quantized values, differing one from another by integral multiples of the DNA helical repeat, approximately 10 bp; however, studies in the literature are inconsistent. Here, we investigate linker DNA length distributions in the yeast Saccharomyces cerevisiae genome, using two novel methods: a Fourier analysis of genomic dinucleotide periodicities adjacent to experimentally mapped nucleosomes and a duration hidden Markov model applied to experimentally defined dinucleosomes. Both methods reveal that linker DNA lengths in yeast are preferentially periodic at the DNA helical repeat ( approximately 10 bp), obeying the forms 10n+5 bp (integer n). This 10 bp periodicity implies an ordered superhelical intrinsic structure for the average chromatin fiber in yeast.
连接相邻核小体的连接DNA的确切长度决定了真核染色质纤维的固有三维结构。一些研究表明，连接DNA长度优先出现在某些量化值上，彼此相差约10 bp的DNA螺旋重复整数倍；然而，文献中的研究结果并不一致。在这里，我们使用两种新方法研究了酿酒酵母基因组中的连接DNA长度分布：对实验定位核小体附近的基因组二核苷酸周期性进行傅里叶分析，以及将持续时间隐马尔可夫模型应用于实验定义的双核小体。两种方法都表明，酵母中的连接DNA长度在DNA螺旋重复（约10 bp）处优先呈周期性，符合10n + 5 bp（整数n）的形式。这种10 bp的周期性意味着酵母中平均染色质纤维具有有序的超螺旋固有结构。
