Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
Preferentially quantized linker DNA lengths in Saccharomyces cerevisiae.
复制标题
DOI：
10.1371/journal.pcbi.1000175
复制
发表时间：
2008-09-12
影响因子：
4.3
通讯作者：
Widom J
中科院分区：
文献类型：
--
作者：
Wang JP;Fondufe-Mittendorf Y;Xi L;Tsai GF;Segal E;Widom J
连接相邻核小体的接头DNA的确切长度指定真核染色质纤维的内在三维结构。一些研究表明，接头DNA的长度优先出现在某些量化值，通过DNA螺旋重复的整数倍，10 bp，从另一个不同;然而，在文献中的研究是不一致的。在这里，我们调查接头DNA长度分布在酵母酿酒酵母基因组中，使用两种新的方法：傅立叶分析的基因组二核苷酸周期邻近实验映射的核小体和持续时间隐马尔可夫模型应用于实验定义的dinucleosomes。这两种方法都表明，酵母中的接头DNA长度优先在DNA螺旋重复序列（约10 bp）处是周期性的，服从10 n +5 bp（整数n）的形式。这10 bp的周期性意味着一个有序的超螺旋固有结构的平均染色质纤维在酵母中。真核基因组DNA以染色质形式存在，DNA局部包裹成蛋白质-DNA复合物（“核小体”）的重复阵列，由未包裹的“接头”DNA的短片段分开。核小体阵列进一步压缩成30 nm宽的高阶染色质结构。尽管经过了几十年的研究，但对于30 nm光纤的结构仍然没有达成一致意见，甚至连这种结构是有序的还是随机的都没有。DNA的螺旋对称性将核小体沿着DNA的一维分布与染色质纤维的内在三维结构相结合。随机链接长度分布意味着随机的三维内在纤维结构，而不同的可能的非随机长度分布意味着不同的有序结构。在这里，我们使用两种独立的计算方法，两种独立的实验数据，实验定义的概率分布的连接DNA的长度在酵母。这两种方法都认为，酵母中的接头DNA长度是一组优先量化的长度，彼此相差10 bp，DNA螺旋重复序列，优选的相位偏移为5 bp。长度的优先量化意味着平均染色质纤维的内在三维结构是有序的，而不是随机的。5 bp偏移暗示了该内在结构的特定几何结构。
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, ∼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 (∼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. Eukaryotic genomic DNA exists as chromatin, with the DNA wrapped locally into a repeating array of protein–DNA complexes (“nucleosomes”) separated by short stretches of unwrapped “linker” DNA. Nucleosome arrays further compact into ∼30-nm-wide higher-order chromatin structures. Despite decades of work, there remains no agreement about the structure of the 30 nm fiber, or even if the structure is ordered or random. The helical symmetry of DNA couples the one-dimensional distribution of nucleosomes along the DNA to an intrinsic three-dimensional structure for the chromatin fiber. Random linker length distributions imply random three-dimensional intrinsic fiber structures, whereas different possible nonrandom length distributions imply different ordered structures. Here we use two independent computational methods, with two independent kinds of experimental data, to experimentally define the probability distribution of linker DNA lengths in yeast. Both methods agree that linker DNA lengths in yeast come in a set of preferentially quantized lengths that differ one from another by ∼10 bp, the DNA helical repeat, with a preferred phase offset of 5 bp. The preferential quantization of lengths implies that the intrinsic three-dimensional structure for the average chromatin fiber is ordered, not random. The 5 bp offset implies a particular geometry for this intrinsic structure.
登录
查看更多内容
使用混合模型改善了核小体DNA序列的比对。
影响因子：
14.9
作者：
Wang, JPZ;Widom, J
通讯作者：
Widom, J
影响因子：
2.9
作者：
Bertin, A;Leforestier, A;Livolant, F
通讯作者：
Livolant, F
影响因子：
5.6
作者：
Kato, M;Onishi, Y;Kiyama, R
通讯作者：
Kiyama, R
影响因子：
11.4
作者：
STRAUSS, F;PRUNELL, A
通讯作者：
PRUNELL, A
DOI：
10.1111/j.2517-6161.1977.tb01600.x
发表时间：
1977-01-01
期刊：
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL
影响因子：
--
作者：
DEMPSTER, AP;LAIRD, NM;RUBIN, DB
通讯作者：
RUBIN, DB