Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.
Features of genomic organization in a nucleotide-resolution molecular model of the Escherichia coli chromosome.
复制标题
基因组组织在大肠杆菌染色体的核苷酸分辨率分子模型中的特征。
DOI：
10.1093/nar/gkx541
复制
发表时间：
2017-07-27
影响因子：
14.9
通讯作者：
Elcock AH
中科院分区：
文献类型：
--
作者：
Hacker WC;Li S;Elcock AH
我们描述了大肠杆菌染色体的结构模型，其中每条 DNA 链的所有 460 万个核苷酸的位置均已解析。已经构建了与两种基本染色体方向一致的模型，其复制起点的定位不同。在这两种类型的模型中，染色体都被划分为皮线体丰富和无皮线体区域，皮线体长度和分支模式与实验分布相匹配，并且高度转录的染色体区域的空间分布与最近对RNA聚合酶分布的实验测量相匹配。模型的物理分析表明，DNA 的有效持久长度以及扭曲和扭动对染色体负超螺旋的相对贡献与实验估计非常一致。这些模型表现出类似于“分形球”的特征，甚至染色体上基因组最远的部分也可以通过线性扩散和节段间转移相结合的路径进行物理连接，平均长度仅为~10 000 bp。最后，分析了共表达基因的宏结构域结构和空间分布：后者被证明强烈依赖于染色体的整体方向。我们预计这些模型将有助于探索细菌染色体的其他静态和动态特征。
We describe structural models of the Escherichia coli chromosome in which the positions of all 4.6 million nucleotides of each DNA strand are resolved. Models consistent with two basic chromosomal orientations, differing in their positioning of the origin of replication, have been constructed. In both types of model, the chromosome is partitioned into plectoneme-abundant and plectoneme-free regions, with plectoneme lengths and branching patterns matching experimental distributions, and with spatial distributions of highly-transcribed chromosomal regions matching recent experimental measurements of the distribution of RNA polymerases. Physical analysis of the models indicates that the effective persistence length of the DNA and relative contributions of twist and writhe to the chromosome's negative supercoiling are in good correspondence with experimental estimates. The models exhibit characteristics similar to those of ‘fractal globules,’ and even the most genomically-distant parts of the chromosome can be physically connected, through paths combining linear diffusion and inter-segmental transfer, by an average of only ∼10 000 bp. Finally, macrodomain structures and the spatial distributions of co-expressed genes are analyzed: the latter are shown to depend strongly on the overall orientation of the chromosome. We anticipate that the models will prove useful in exploring other static and dynamic features of the bacterial chromosome.
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影响因子：
--
作者：
Black, Lindsay W.;Thomas, Julie A.
通讯作者：
Thomas, Julie A.
影响因子：
14.9
作者：
Faith JJ;Driscoll ME;Fusaro VA;Cosgrove EJ;Hayete B;Juhn FS;Schneider SJ;Gardner TS
通讯作者：
Gardner TS
影响因子：
5.5
作者：
Clauvelin, Nicolas;Olson, Wilma K.;Tobias, Irwin
通讯作者：
Tobias, Irwin
大肠杆菌中空间中遥远的染色体基因座的共定位：细菌核仁。
影响因子：
10.5
作者：
Gaal T;Bratton BP;Sanchez-Vazquez P;Sliwicki A;Sliwicki K;Vegel A;Pannu R;Gourse RL
通讯作者：
Gourse RL
影响因子：
14.9
作者：
Fritsche M;Li S;Heermann DW;Wiggins PA
通讯作者：
Wiggins PA