Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.
Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.
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DOI：
10.1186/gb-2004-5-11-r86
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发表时间：
2004
期刊：
影响因子：
12.3
通讯作者：
Khodursky AB
中科院分区：
文献类型：
--
作者：
Jeong KS;Ahn J;Khodursky AB
对大肠杆菌K12的转录活性分析表明，其转录模式沿细菌染色体的分布不对称，表明转录的空间模式可以通过药理学和遗传学进行调节。虽然染色体上的基因以固定的顺序组织，但转录的空间相关性尚未得到系统的评估。我们使用基因组学和信号处理技术的组合来研究大肠杆菌K12基因组中的转录特性作为基因在染色体上位置的函数。转录序列的谱分析表明，在转录活性的空间序列中存在统计学上显著的模式。这些模式可以分为三类：近距离，最多16千碱基（kb）；中程，超过100-125 kb；远距离的，超过600-800 kb。我们表明，基因活动的显著相似性超出了操纵子的长度，并且局部共表达模式依赖于DNA超卷曲。与短程模式不同，中长期转录模式的形成并不严格依赖于DNA超卷曲的水平。长程模式似乎与细菌染色体上DNA旋切酶的分布模式有关。转录信号中结构成分的定位揭示了沿细菌染色体转录模式分布的不对称性。转录的空间模式可以被药理学和遗传学调节的证明，以及转录模式的分子相关性的鉴定，首次为生理决定的细菌染色体高阶转录组织提供了强有力的证据。
Analysis of the transcriptional activity in Escherichia coli K12 revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome and showed that spatial patterns of transcription could be modulated pharmacologically and genetically. Although genes on the chromosome are organized in a fixed order, the spatial correlations in transcription have not been systematically evaluated. We used a combination of genomic and signal processing techniques to investigate the properties of transcription in the genome of Escherichia coli K12 as a function of the position of genes on the chromosome. Spectral analysis of transcriptional series revealed the existence of statistically significant patterns in the spatial series of transcriptional activity. These patterns could be classified into three categories: short-range, of up to 16 kilobases (kb); medium-range, over 100-125 kb; and long-range, over 600-800 kb. We show that the significant similarities in gene activities extend beyond the length of an operon and that local patterns of coexpression are dependent on DNA supercoiling. Unlike short-range patterns, the formation of medium and long-range transcriptional patterns does not strictly depend on the level of DNA supercoiling. The long-range patterns appear to correlate with the patterns of distribution of DNA gyrase on the bacterial chromosome. Localization of structural components in the transcriptional signal revealed an asymmetry in the distribution of transcriptional patterns along the bacterial chromosome. The demonstration that spatial patterns of transcription could be modulated pharmacologically and genetically, along with the identification of molecular correlates of transcriptional patterns, offer for the first time strong evidence of physiologically determined higher-order organization of transcription in the bacterial chromosome.
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DOI：
10.1073/pnas.97.17.9419
发表时间：
2000-08-15
影响因子：
11.1
作者：
Khodursky, AB;Peter, BJ;Cozzarelli, NR
通讯作者：
Cozzarelli, NR
DOI：
10.1073/pnas.1131966100
发表时间：
2003-05-27
影响因子：
11.1
作者：
Nagy, PL;Cleary, ML;Lieb, JD
通讯作者：
Lieb, JD
影响因子：
4.4
作者：
Kluger Y;Yu H;Qian J;Gerstein M
通讯作者：
Gerstein M
影响因子：
7
作者：
Gutiérrez-Ríos, RM;Rosenblueth, DA;Collado-Vides, J
通讯作者：
Collado-Vides, J
影响因子：
56.9
作者：
Lemon, KP;Grossman, AD
通讯作者：
Grossman, AD