IMA Complex Systems Seminar

1:30, Thursday, March 25, 2004           



Spatial patterns of transcriptional activity in the chromosome of Escherichia coli



Arkady Khodursky

244A Gortner Laboratory

Biochemistry, Molecular Biology and Biophysics

University of Minnesota

Minneapolis, MN 


We used a combination of genomic and signal processing techniques to investigate the properties of transcription in the genome of Escherichia coli as a function of the position of genes on the chromosome. Transcriptional activity of the bacterial chromosome was represented as a signal in a spatial domain. Analysis of the signal revealed the existence of a structure (patterns) in the spatial series of transcriptional activity. The statistically significant patterns could be classified on the basis of spatial ranges of correlations into three categories: i) short-range, over18-20 kbp; ii) medium-range, over 100-125 kbp; iii) long-range, over 600-800 kbp. Localization of structural components, initially defined in the overall signal, revealed an asymmetry in the distribution of spatial patterns of transcription along the bacterial chromosome. We demonstrated that transcriptional patterns could be modulated pharmacologically and genetically, likely through interference with the DNA gyrase function. We observed that the distribution of DNA gyrase along the bacterial chromosome might play a critical role in the spatial pattern formation. All these observations taken together offer for the first time a strong evidence of physiologically determined higher-order organization of transcription in the bacterial chromosome.