Jeong Kyeong Soo, Ahn Jaeyong, Khodursky Arkady B
Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA.
Genome Biol. 2004;5(11):R86. doi: 10.1186/gb-2004-5-11-r86. Epub 2004 Oct 27.
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.
尽管染色体上的基因按固定顺序排列，但转录中的空间相关性尚未得到系统评估。我们结合基因组和信号处理技术，研究了大肠杆菌K12基因组中转录特性与染色体上基因位置的关系。
转录序列的频谱分析揭示了转录活性空间序列中存在具有统计学意义的模式。这些模式可分为三类：短程，长达16千碱基（kb）；中程，超过100 - 125 kb；长程，超过600 - 800 kb。我们表明，基因活性的显著相似性超出了操纵子的长度，并且共表达的局部模式依赖于DNA超螺旋。与短程模式不同，中程和长程转录模式的形成并不严格依赖于DNA超螺旋水平。长程模式似乎与细菌染色体上DNA促旋酶的分布模式相关。
转录信号中结构成分的定位揭示了转录模式沿细菌染色体分布的不对称性。转录空间模式可通过药理学和遗传学方法进行调节，以及对转录模式分子相关性的鉴定，首次为细菌染色体中转录的生理决定的高阶组织提供了有力证据。
